From d2b184b86a7dd0f295e3d2db6f8b45fa25f7f854 Mon Sep 17 00:00:00 2001 From: Senthilkumar Panneerselvam Date: Tue, 16 Jan 2024 13:34:40 +0100 Subject: [PATCH 1/5] Covidmapp DH --- content/english/highlights/covimapp.md | 49 ++++++++++++++++++++ static/highlights/banners/covimapp_logo.png | Bin 0 -> 27301 bytes 2 files changed, 49 insertions(+) create mode 100644 content/english/highlights/covimapp.md create mode 100644 static/highlights/banners/covimapp_logo.png diff --git a/content/english/highlights/covimapp.md b/content/english/highlights/covimapp.md new file mode 100644 index 000000000..5e9511a07 --- /dev/null +++ b/content/english/highlights/covimapp.md @@ -0,0 +1,49 @@ +--- +title: CoViMAPP – new resources for the analysis of the soluble blood proteome alterations in COVID-19 +date: 2024-01-16 +summary: Babačić and colleagues expanded the coverage of the soluble blood proteome using mass spectrometry. In order to support further research in this area, their results have been added to an open-access app. +banner: /highlights/banners/covimapp_logo.png +banner_large: /highlights/banners/covimapp_logo.png +banner_caption: CoViMAPP logo. +highlights_topics: [COVID-19] +tags: [COVID-19, Covimapp, Meta-analysis, R shiny, App, proteome, SciLifeLab Serve] +authors: [Katarina Öjefors Stark] +announcement: "This data highlight was also published on the SciLifeLab Data Platform, as the work described in this highlight constitutes data-driven life science. The Platform is a hub for data-driven life science in Sweden, containing multiple relevant resources, tools, and services. It includes information on multiple subjects, including infectious diseases, please check out the Data Platform for more." +images: [/highlights/banners/covimapp_logo.png"] +--- + +Over the last few years, the COVID-19 pandemic has greatly impacted both society and healthcare. Although the effects of COVID-19 have now been mitigated using vaccines and non-pharmaceutical measures, COVID-19 can still cause severe disease and even death in some individuals. Continued research is essential in increasing our understanding of COVID-19, and therefore in protecting the elderly and other individuals with a relatively increased risk of developing severe disease. + +Research has shown that cytokine storms (elevated release of cytokines in the blood) cause systemic hyperinflammation in patients with COVID-19. Systemic hyperinflammation is considered to be one of the most important pathophysiological mechanisms behind severe COVID-19, and can lead to multi-organ damage and death. The inflammation is caused by systemic immunological perturbations in the human body that are mediated by the blood. Therefore, plasma (the liquid component of blood) is often used for studies into the systemic biological processes involved in COVID-19 pathogenesis. + +Multiple types of circulating molecules (e.g., lipids, metabolites, mRNAs, and proteins) have been studied in COVID-19 patients, but proteins remain most commonly used in clinical practice. Using global mass spectrometry (MS) methods, studies have identified a few hundred protein biomarkers in plasma or serum. However, the soluble blood proteome is known to contain more than 4,500 proteins, meaning that much of the proteome remains unexplored. Continued research in this area is crucial in order to allow us to prevent the onset of severe COVID-19. +In a recent article by Haris Babačić et al. in Nature Communications, researchers from Karolinska Institutet, Karolinska University Hospital, The Laboratory for Molecular Infection Medicine Sweden (MIMS) at Umeå University, Linköping University, and Science for Life Laboratory (SciLifeLab), led by Jonas Klingström and Maria Pernemalm, performed systematic analyses of circulating, soluble proteins using mass spectrometry proteomics to expand the soluble blood proteome coverage. + +Babačić and colleagues used serum samples from twenty hospitalised COVID-19 patients (ancestral SARS-CoV-2), and seven PCR-negative and seronegative controls. More information about the cohort used is available in Varnaitė _et al._ (2020). The samples were analysed using high-resolution isoelectric focusing (HiRIEF) coupled with liquid chromatography tandem mass spectrometry (LC-MS/MS). In addition, the researchers performed _in vitro_ SARS-CoV-2 infection experiments in human lung adenocarcinoma (Calu-3) cells to compare to proteome and phosphoproteome changes evident in the blood of COVID-19 patients. The results showed that a large part of the soluble blood proteome was altered in COVID-19 patients compared to healthy controls. COVID-19 patients were, for example, found to have elevated serum levels of NF-kB-, interferon-, purine metabolism-, heat shock-, and proteasomal- proteins. Furthermore, many of these proteins were also found to be changed in _in vitro_ SARS-CoV-2 infection experiments. Additionally, changes were identified in phosphorylated peptides in the serum of both COVID-19 patients and SARS-CoV-2-infected cells. + +In order to provide estimates of the alterations that occurred due to COVID-19, Babačić and colleagues performed a meta-analysis of global MS proteomics datasets, as well as their own dataset (1709 individuals, including 1039 patients), and identified >1500 proteins that were identified in at least two cohorts. In order to aid further research and clinical use of these state-of the art- MS results, the researchers developed an open-access app called CoViD-19 Meta-Analysis of Plasma Proteins (CoViMAPP). CoViMAPP includes information about the effect sizes of alterations and the diagnostic potential of soluble blood proteins in COVID-19. The app also includes summary estimates obtained from published studies of plasma proteome profiling in COVID-19 using unbiased mass-spectrometry proteomics. + +In summary, this study is a comprehensive analysis of the soluble blood proteome alterations that occur in COVID-19. The results validate multiple previous findings and pinpoint new alterations. Furthermore, this study provides the current MS-based state-of-the-art concluding estimates for soluble blood proteome alterations in COVID-19. The researchers aim for CoViMAPP to be used as a dynamic tool for future dynamic meta-analysis, and additional curated studies may therefore be included to update the summary estimates. + +#### Data and code availability + +* All results described in the manuscript are presented in main or supplementary figures or datasets. All results from the meta-analysis are available as a R Shiny app. +* Raw and processed MS data are deposited via ProteomeXchange to the PRIDE database, with accession codes PXD037486, PXD037451, and PXD040982. +* Source data are provided with this paper. +* The custom code for the Nextflow proteomics workflow is deposited in this GitHub repository. +* The R code used for the analyses is deposited in this GitHub repository. +* The R shiny app COViMAPP is available on SciLifeLab Serve. + +#### Article + +DOI: 10.1038/s41467-023-41159-z + +Babačić, H., Christ, W., Araújo, J. E., Mermelekas , G., Sharma, N., Tynell , J., García, M., Varnaite, R., Asgeirsson, H., Glans, H., Lehtiö, J., Gredmark-Russ, S., Klingström, J., & Pernemalm, M. (2023) Comprehensive proteomics and meta-analysis of COVID-19 host response. In: Nature communications (Vol. 14, Issue 1, 5921). + +#### Funding + +This study was supported grants from the Knut and Alice Wallenberg foundation (KAW), within the SciLifeLab KAW COVID-19 national research program, the Swedish Research Marianne and Marcus Wallenberg Foundation (SGR), Region Stockholm (clinical research appointment), and by Centre for Innovative Medicine. + +#### Infrastructure + +The Clinical Proteomics Facility and the Data Centre at Science for Life Laboratory was used for parts of this study. diff --git a/static/highlights/banners/covimapp_logo.png b/static/highlights/banners/covimapp_logo.png new file mode 100644 index 0000000000000000000000000000000000000000..61dd27630eae5087202c4db492526f8c6aeeeccb GIT binary patch literal 27301 zcmb@uWmH_v5;lr!a1tcQ;O@cQ2|;Am3 znBBAK?p>$b{1#LO!oh$(RZ8n+Ko@X(d2u1I ziV3_U(3b#1)$c~q(qPn}G8`B*I64^QM-|X77&tB%^gm@VFiG&Q|0~ObQ~p~A0t_tJ z6b$O$I=?{Ik0R~I$N#R7IpF`N#~g_N)&{@Lf&6b74EWJ5X{Eygbb+^#P_qXEqbK?J z19vIpcLH^#W~!*_peilJrEhIXuWMkfXGrg2Y4gzvjK_rwRJ1g7&;__yT3Fe0x$qMI zQ-cds{0!P(iF-kF8o+Rm7PiIbC)fsvVknVAk$gU;U7%0btK&dQ$TKb`!y9}z=)eLGVd z2UBY+z(>Ejde)8(yu`#G5BlHFf9P~DHTpkKva|R@_gLo zlC?861U>nqe?BIje`@}}?*0259)^#H|6j!XXQcn!1r3!CfrsILY~w?~(b|Fq0}}xI zE+VMt0)FZVouRRJch6G6eUfHTv(yv}@ZJ1b*YufkUWn>W{;5&By-=vVP_an9fbLf} zuM31PX+YDN(VDZ-;F;IKD&y!_%lPS#>rMJtqDuC|d4{`2{!d>_K><`$C@65yWyl1o z4u{u0wG9A(gM;w%0bPpV-~^Ll1^-tA0xBTKxSMEH?wA@C+ZC7|p&>%Nb`Y&X?jSGYr0Dd%)hi);o}kf`(ax1{%>)Q)$ibGU1%93h%AWM(Foe~}R_e!Ii92T6k_6J>xax!>LNVw(5(?8*S_myuus?ju~`5+7Hh4;1`>*rLx zE(moi%7(Z+3Tw!Ukf1tI5)Pl-(_ScsBrG>F3)-9s7uW# zj9-~9*c*5FNCrlVa$``z0)|1%*c?^8x zVmS|yjiD(QN}~IQgspC?eHpobaU+Y~c99Cq7rG>XcNJLL_XlO= zBxtzXwg$n^iQ;8Oidt^n0V)Zdb~p~TC9_zN53StftI^*uL1f;Fg2)7(M~+FM`dDjc zmYlQEl?57#?FFDstI;vW%i%rOL4U8L|A*TsAKY&IQ75%aA32{L=^<$kx z))XZxW39(H7so~Tn4b?$dp?L6k;8TIn-9tJ*MH32ZW#_cdK_|ac$q;s1U%k z&#~ot6~uzbFJOldn)>VRZQ#Ti<-<2Ar~!n)E?0g`KOqkY>MTUV)h6tLfkZ&&cN6lI zAOS6L32)E>{_{>S{K+009EnV>nn4XbayURo<*QoB^FU;f@donl9(N8+Hn@6upA8|q z&kRT{pnfd+A+h0a_E_N0Fa4J%NQ^Vu=2f+p8Ug{lR!}RU!t81>-jBabkOpk)lSe?} z9>WP*iIW-aajE;15WlyXQ;g@(lQU7g)pweHUb3Hw6X5hh)3I@Usl-!JFQx@4o76xb z)Z4LThEz*>;x4_1z)`U63gNZP-Dm;=3GkKU9RxtD}lD712R+JthL0 zYoqh@F|I+>s)= zOcFuevT-+8&2`De$U?Qd-zJKaU`G5#VNBC0*Muk^=5hO4OavkdClW+d#5!N92R)Ha zaTcsMX;?@jiloDCgz5B8u%tY_M@KR2;TFxX4>{roO+>ACv|*r{pHFTP6gc@53~zH~ zBp!@1+2b#KDZ>P(#EwFcq7=9%0ZsDrgQ{{08JvkjfiOe4-?R~#ZHsZAQnmZ9A;O$K z`X`e4`1B7p@_w)}t34rc7YrgOkNGhpfitr2oaA%lxTeNtsESN%?%M4tYQ6aQ+#m=9>2NtpM|t42x8j#X?@wZuc&}*2mgFj zw{|0m>eils^&Lfpa^~cJ)}!qL|3sA0oy>PGbjIvj zn3g#==k=$i>B~GpiFOy9E)8)K!W`5vnZr#gp8nJ}hV=ga=7X?_V_~ z)wsk{^T^&mXrMcBywesQ6Njon5)nZNzBM%%omw|U1O;YwXn z(SjMJG@9GEqDbmjAii-Q%Fy!;R6q1O#c|Yug`*V8U#)E_yH#y zvYVS_)QXJ>Z`)#1c{ESZx;vqW>JPJ!9--ZACv*pL5}p<3-dacQ zPhOH+ZdLG++Ut%(aDimp?@R^1s7NhvLADKr}u!ti&{$ z_;S^uhjytuqn^Ec;?a3GW9c?xX?nMPeJWMSi#mE^^@iF3j0prL;YVfOU57V`z(7RUXk^sNyPuYP z_1M$;yYLoT@D+0bNbLp+m>Fo}K!-{xgN(SZ2T(T}Q&pE{#Q!9-aif!IQ(`Y=-0cvN z%Gy=5-=|f8@n2Ju|D3k)J;&MGPuijjT z|D00Eaf>9MbN@764fo<5HsLqq)SkMW!!%jSd-+9AwLz%ln5za`2#bnx-m!49&L01p z-xB{b@@;MDAq*-&se7W7-*^6GwR9u;I#FjWixS_pRW8Pi`!aUr+`<9n{G z6FbwQ|3#J~KIc;{l1X6BO)U-KAZ-rd=ETOU_jT$vL9U%S0A_e zBy^puUVKI2J&PE$^!@ljC!1eI z317-Vaz+MKf(%06eOZB%1c$~P&4dh+Dyrd2xw&G0CGPg3&Mfimxe-UU2b46T+3@ls zbwbv)FB-f^3Ai1tI`qPIZ_b64zw?6fE(5GiyUk|H4I&EE4s7n+#IkL92POW-$xq{zMnSG#@KVWx9!EsxKq>5A>C1}mQnK8 z!s1vM3K-k^ch0Tm#VcW2p&C}*zSgyS7PX!s)4t9{huF)ux2`o&Fd*3xfTJ}ZypY6r zfGxtAZcKXnLuNm72{|H_Jp2rCm{}%C7IJ<>4;aNSa3>G9H0J(w{>X~F`ovGlecybuQA{|Nk8%@|k;{oU#XE5jB? z-(PLON-VlJL{nK1Vu6pjo#5YXC#ORTu;ngf#UElNY~iner||`gD5x|(-4377BNNI# zOegU6rjA~co)iesNY~~lSYNL-{_3{C3lkq$b{-m@?fG}SZgRMm?lP{4H(Cp?CxK?Y z!{(_VdF1VOTIg#Xsp-Q!yHpGR5y*Fe25EE!U%RNN?&h8c&j*T4LT}^|<^zfiLHPbV zf(mTJa7x@2X-b}F^chig%7_x!a+D2WE1C7Jw1QhMW6oLzt;n2V1R6BQn4-*ZF=LhMOGO3FBHupA?DwdkdrhH&zumR(}wCPEU60=_S;TziF0T(Lm0B!S2mYkaA`3u z#1(!2PxYV5Gehw40GI;g}?~lpmm#E~+8A-^h zQ6!f1waDSUWkI*))+PSo#~8W|*#Lpbpi!*HT|sbY!1L^Tc1HoZdMoTQ!r3|*n7MWt!|88}00D$*<({_N*vQF`u#u|)FX}jN zDfX3eLxYm{0r_m0J{ji1F8BC8&NQMh`GHuOjtECTDd=J5AZ$!iTi^yLlvx% zeNsFU(GdT|+TlT*8{Nvg7aY;-i%)!3V3lG(@EB8y75T6#c!kiJ92^LD3dZY=eh z^GC3sK+T8qKx<&%q>Z)L%_cv~%uFS8WJ)263olGmNR}yw_~Sbc+N~Jn)>OfBh660A z9ZEcra#be89%>_Qp~LSjEy>IgLG7BhfR>f-b(OM+rr(QkX z0;7=55Vt)=WWztZ)ehp(4*E!csCB&7w0#o;?E`VGWq!+yJ74}ZS%8C%t)3mriZe_p zHR`n{waV-p$-pGVmrT&2t*fv?_>5a{WRhzbl?mt0mRz(EZX(P5Lbuy45FneI!)2yR z(rrrlVz)(c0rBcC=ta&9t=;Q2vf_pE%|K(Ybcp+jcC78RS09uzT0rVJ@F;RA)z#dzB<(58zIUA8?`HRYs{ZOdrX`L-Bdfj!+dr85p#bWb|1ztT)1c`;ebLxiRqNv8N-ZzR9aqt#$tUaW`l zNq*8FVhF0#Wq`08FJW-=L)5MzXUx$aSQ8>LQCppu@w>vDh+24<4-dgx1ji6v4WD^S z)O6wvi{dopS(DHd1eBvNqy z0ucbpb0jArN)K+gQUj*9rQ4DRGdr{=U$`oygXAU+{P% zzcwSrAo+vg?)|8_t#R_l;`bOD3@gmym>6-+3UVZiVS98wNlnST>M5L~b8(~vVp7k- z7_rL%2iI^!iDo5_tf2ZWC5H#yqUHGAg!&YwQe5fcqvL`?^|p>UVyO2oD$TR)SkLwE zq=ZDh{SqsJ2;(P$eJ8%jH8V@fc#wm~J5+C8M~YJ7Kvbw12$1lYRwFI3ht|}}3NJ|$ zDq+-$;3DfyK6C_CsA%Q1ZB>6Vj90Jq?JHZaf^o8D;Bjw|si^&4$Hoyh%y<$*lu=ld zW(V@IO@5$&p0PkzJ5er}e{JKbTIKUSh(Oi~;_szkn`0m)C zZEx|1Gm(>a=bS6+#$4l9E_4-zjvII&qdk|xN(~7rv1XC;tG&&|5??Alkc=AXZ@3c--2;vSS&+2H4pZFhQOZ|QGnlkxKUP3lt4}iwHIgD*u+e4NaXLQg{N3hZ& z^l%V=13*^J6oPLdXf9UCZ8-E#-eVKS7H<`nCwD{FhT@+AA$EBiRHWwI=6g$j^3IT# zuu)w~djBlH6*&pX;=iHv+IzwE1-FQ(AcH{w z%5>;pZ1wtE1jXU{t0SX|Vhqvhv#Gf|yCw1Y%VR9kbXMN*I(+vIs-O_o3~hnBAi(oOI6K_q6Im4ccMHPnr-RE2{WZ_vTAaOOF{UnhMKU%gpxyIc$kos{|=&V&6~n+LMtK5 zVfm-hpWC!~i@eoc!(9~o+`7%+w+sa3N|DK+$dW}*=Bxfc4tYDLw35}2p3-!b{0C!i zNg2#@8?(M)_OSMYuZeLEsE3CFy=%^S_kYDYh>eFyWGBa7uKYAobZDwf;$V~V&Yj5=+o!pzxrrax>5(*F z&tK^3(kQ7b+hU3D3!SXs<6|)db<)tLVk#Mz03d5Og8`0=*IPZ)TY!b+&_J}fEP=;c z_>;^}U$Y9q)c~)MB^_3pPpa>|E89z!0Up7O|Bh+|gYTO$f6*2ceSn*00YR1A$T;{_ z=aX!B|D~GzYU@LB>fZGiI*Fq&-1n!LG{_DMfqlLt?Ag~Vwq<>OqqR%5L%P2h)%1lr zLppw4a3BRh2#(jBm<1O=sa)w7CV(l-rWN z?>|x*A>Q_tTFEP88An{~s0d!(gLSt?ono_D_zvOTwA27XC}aAmm>fC8{Foo24ew&PT5lbAp7 zdMfzB+7|qBNg>WAdBWEtt##J1Iz{?kJQ@5Gwu$`VAxwintL)nfYU;!z8eCmN&R(uN z+BJ~zgoM3Yk=X&Ws^hFx@jT9P9XB&T2b+JU*s>dVl^fzn_|)IXbIEAdDWK<6qY^_5 zf);{7z8}4;&^%!3Y5T^+`yNM8(~c8CxdP8l)1qj=$|lYB_X=JOOLK}Hl#mQo+WQ@9 z37-R#Xo-D+hX>A2R0-n`80Y4EXmudcC)+NLed7TTYKoQb;Da{T#2pV~8VGg(e(2@M zdm4__qxdUM**<<44&vy;6?RyJPVG$~nYx=PHLFVQ(T~EFx8UA`lnnkZ?$d0aR8^&$ z^%2O&jsVr|P8mw16$C6U1%^z@a<6&yhJ1~E}VzEfq6%H%d$xLx!0L^c`h_&5cXzU38b*l zQ)sB?>K|8@t9LN8{oc=<1>l|Jt|HT!o`cMptumRnRzHx}^K;J;Wr91{sr$qDL$7;L zs1E_l_ zE8&I4H5z5R4CRw6$II38+%6w{;;sm)gu;j19Ss-oHjkZcXysUQr1!49Vk== zHgv&_m!T_aJ?ScDIL8)nj3*(<_Bx8J(%*Kxefs9v4(Gx%q;8LJikO7N{ny{S`RjP& zi(ivN&Z&8}@Ob0`lDdi&NJs;G9&`WvwK7=JNHD>4_qtSonlBd*8FFm`ptO*vKp+}J zh)g-c8@au9Q0pI~0E(E?rZvZbzO8Tqvru8P+JHS>laO0ZI z6$v-uFl2gqtY6`x;$Nh~cE5AtX7V^j$v_&wF4W(Bfh+9oXjc z)p%K3DRDYvu8E0doQ{D~7ygUv8t#4~xy?V+=#+bv`-a-6;4-`AKc8E>{L^umm6Gd3 zkMawR6c|mO;7gkZp{uXd(DO z)N}jpg&DYoed$A&W77a2FE` zaHT%0bbjmE<^wv;Ph-{MzfN=;)zHkW{cRIqyCXm2U)RetvAs{r*C<+%a zMAOr5P6H9?z6Ho{qzs)C=3=>RfVd-z3qEp=Cxs|yJ=U2O(fKJfCGHOw&^GnNI~DX| zFrV8cJo!t)+Q)PlL2=cESyGli5?CWMZBh7D5WosDp0Y?2oa|x6HF&tKiG4YI4t)2Y zKrvaA7AAulX3S&~TUOwYye7_89ca&1r=F+%Q8>2q;M^wcdor3_ifp?d zw$O`k^xMZlVx|7{ovNNVyXMnAC~`HUA!3dp`+vjp>QU3Sai(0`s!)j#5q zb*SmjyorX?QVh3n!hN8Uh8N3!+=Rxb*gs=+f|m+~FD8sh~Yf2|N(-zF>R@K~)? z$qRA$PHOfo7F)~VWM_cE|0@(#yXi&HosE@8rq;cOO_?hAUJdr0ito55~Cw%aMv_YIP5x>U} zgwJRf561mn_ocRj!iIqy*?gEb1A0Wr>ymB`+@9Cy4hJQN33SQ%UXS-@K?4$2R%D50 zE2bJ*pE9MODEIjXl`qzsLhn8JBNEAm_&q-NGZhsY@BHk+-0#RtXYXosM~qQpNl9I3y{kK%48=DY7 z%rD&ngczaRk^P2X;XL6ZRKbO3p7@lx-RBZ=+Jq3}cRz=8CjL&t;5QSi4RtQ^)CSRR z_q))W6X5=mSUe-wuSa$>t&M-@;KhIpb6;?B;C;0Qpo^>@*H~&gRa)_3wx{mOddG~dc(W@wL-Z+R)(nCM z3<9^ENw#lF27iS|-d=lN&R_TjN94WSJ)OtJGn zqCA>hAV%?`i4JB9O-kpbFDIZ-<0C-e_uc9D`-}PBh=$vA>)zpaYlW1^LHJ};rgna6IvgW+W`%`=k8w^zLZ z_XWw|b45{xFY?UDzHrS+cWqA%B|jJd`5aUr&xDZ&q zfOAA~!W;g{7PXSn!%H4mVLLAtT_p%BlwpD&K<(98&HMo=2pIivDGa}+g^ym%FXZkF z4{n-U2tRQi~o zAD*UPR|serglGiKsiANI86XedT{l&(FwC6A7K!;_RRDndDF)3LKd^31Pz(1N&BT;q z!;OwCuvlbkT0C#_kc3hqO5|`N@{jIyDW)Hv>!(6kkavg*H4q5as@}rZDY#{!tpMLl zgdMbfN3#99%!VF#`-pak*kgN&I|l5W1bFw?*xoTD+GBu7ZEn7(F#|PEfr09=qR>cZ z%ZV16Kc-~&MF${fetP%A)D|>vP_TeO>RFRzc;lUZ?0@)~IH6#J5|{Xk;1Ar^J*by}ZIrGP6#19}+{Jymz~+)PKLDrV=U8-v z?iCx<@%JV|OYc^~Mfo(n8DMB zKS~NkStOTJNRT`4UlmX2nLP-pDOWg>Xm8YA{Y6Ij)a{U|9(by~<~M>kfn%;voUH#L zXVplP{d@Ou{m)VO+&{IoQ7RV@dDW06(^wJ1zt9PZiuNZ6^}NFRcfavPVjd2d;lB>L zH#zB|&slAB;3Ee^va+(izFvcG*ele;scvyC+lussix3~4oP@ImXZE#3j7yM7ij3^p zktyQ*X!W(1KHO}Nuh#jjlUX~-u6Xli{zbCioH-RZ`De$61Q$mAM0eU86+uo0A|462 zjle2;>2k2cz39_8*@5?Krv43e(i>a?5rPI1?` zbsx?D#!)OUJW{`)RXUL#l3@4#`ap4e(}T!x+qiYb_q;SIzxZq-l({7n(nU@9yf}!y z-1!DP=~cSue4F%sW64E|c7Hx=eApm7-%M1|!kMKHk~?)@Z*v_fOx7xSdER*ceR;M; z)CxS&e&;gd|B*y1SJC7C!SXQ{t&Jqoh%99uJc$=XpKBS@3P4w*6w-q9S30hqP$M@Ac^cSo|`xD4&L^4{sW z$XRa3R31;G+5`^fMQ__Q)yvyY2ieh`1q9YhHPF^=R|7dGS6E^v+#U3U8_pY^k9`z; zxh0>sFCrVWvtM>8n(pS+cUmPzY;$Un&ZR56(8&|ShY>8*SnJqe3!&$whFvVyta9tB zU)Xj$Tp@cfdA^4M7*RpG1`;jyCPHkpqV>F|vGesz(7fp|FI+%_TY@yo{h}Rgwt*h4A<&q=zWHx2QY@sH}=xCm#GAean-X+*mKnHv6f@B@ADsGQ>zs z%CI_t$EDL#Q>Yt;?^o;X?zZEs3snXc@5`zv1TLH4m!p$E_Xyt~2Y)69w<{|v|E@TR zV3`2(4!IH6)zur|AwQnvdp@o5yo`LhIiR?;-wvffu7P|!ckT>dYjuuZoD{JZd*N$Z z_xhZ5Hz^?e<+Qs80o!OcE^38mnm*WK5Z(+ymLtewZTM$a-f;5+K6Xu(#+WTsjqD+S zW<&`pB!o%?Ge!Q++h{VY990e*9euu9+ol`ZOf!9)&5%ol*+yY#v%(vhhwuw0ic*#r z@F>8o?42yXGPeY|<$gC_mb@-f`{C$McEu&nHX=?J)gZp}YL#V3ZFFUpjnsfMLc7jw zBiXR89wRnzQte`6dOCKB{4Idv`K^U#GTQrP=c;jTr=^8!Z&5#5y2yFWae-`B-_!Gj z%lmm{gM9S>qahUAg#GF!``zPb`>+OFvs+>oyOuoe#Y^Ih-J~_H$O20$y}0Gd zRnL!+(gI=cOujpB;B(Pkq0l)I0FUdHYuAlv&qP_^5;U<$yu7@x=0uteBeB_T$HlJ; z+bF65;~GzY`0l8x7So$sa}mN5I^SO}c0gK0v3Z!Lq6wm4RH=MFxMWg!o|Y||0fp~T z=f(8>O5prugr+iJ$s?qdM4vOJLOqeAYStId#k+MH`A}3)iKOp%S~i{9h+?O1vC!7D z^W}PUvC&%F`|E&Dh~2xZu`z{e0{?u^4UX#J9^%I106RLp^-6=Kh-uHy*D|ekTmt|{ zQFZ|04i6Cx@1w-=^wo<3$K`YOPFH1T^!nY2PO)0ZHj0*STcWtIInG+TZbmP;BD;zb zkx&L#f2!aC%L)29Xb02<7jc?TjBQ8;ah};aeM23X?cogTrRTeyux(t*3v*4YU)yK7{>>Wg`+X zHP3uw#~oebl=pRfHXbR0F&clkn?BS5|N9e)*QGxpX-MMm;g8S7gD}RnK+qB<nS_a}TTPWU#*4^i(iHV85Vf)WC z9nM{5VUIm#zT4Z|P^YSE-2q-a74}!2*G#rR_~fA(?S7kYO2R@UTvQAUvQ2%j5zSMh zVtwM(vqxn8wZ{BBt@nVbWeMOVYQ*QlDh5@El@~-^`fNc#E%^h2K{cq{1)FU!7N{24}DfHB!?%^24j4xnf50aa!;f8*S5;9 zXv}GfJyzOn5U$}WJ*qOPqrZo`C~(3J2<_RH!#<dl>a>|>jW(DXcssKQ z7?Ah%%^(Y%ufO_8&D^vCU| zM`e0wbOwc)B}3(hE>^7av5zVK-e?QStzGBf1ZR7fjTQr=Ze#IbL{tC95wCSf#??!G zu2`ClM!mII9!HzsUT%PFwF08&A&p~-p1C*;U13j3uJsJ%)4bW z#Z-O4tTT8PtF!RLm``)90`0|<)a-{hDI7J1;eJRq^$%DuS*2LhYPLAY3+ktA_G3Vk zQ;#{SsHo`Q?2iKoFW;_~guKSnSUJw>{sJqRy7jJHBXVw#*r>xP4m}98`9NYsp;|w< z@pY8RK3Ds(2dm2K73d|*&DQd~jn$blm7%SuT4K|S#7?R~c)siX{+x{)L*bOIgtGhV zPZsl^iDNi=DG9auuDI}NgriYGC+OF?N9eFQr~-_O&H-2pT6X!R7Dsa-{uevZHy}I% zVAYGGel(}!h-^ed>$exoTKYcXZVL=a=t{l;u8PzB(O;ggIDB+yIfQ~#YEc3?rRqyI z$4>@QwUVqQOK!c!iCK~9370VED6I+9e-=j*=(u=SsNeEz(EskCS0HTb-2n z(XT&jFP8IS9Ib!l4hSkAqLjV&`u-ySwV0gY*{%O-yNQ7uflhOZ=yj0kOx-8=ut228 zM~RK_^~hErMV0>)Yh!u2#Od$qY8mRons;>MbqGcjQmz+wri|f01kS5t$8};Q=_;WK z=0obFhgkdM4TVf+r>2F+8{cVFFYvXM|2j6BbQWiXGRl7i&+~Q~{%*S(fZy2T^-|3g zqOY>(W2J**f{9hiKf^A1r65rgJ2fYe-xRw%c#iM=a;4AqO$wVfQpQgv`FbA*i>5MG zaJ4j8p(-zG;#*p#6qzO}DstxAac%pzpMJ2Xgb%e*CX@7KFIrpx-w3tKxXn<4^_y!#)_U^1@`yh5hozc z4ydzPEP~Bj4^CPcRcd@sOWX>l^NmrBaJeoU3SX7*N|6 zjy2yndn_vLuZFq|rpX+qi*A?QkcZzxO{A^$fIO=#DBd>{NXzBA?|YB>cdF1`ZookT zcd7P1T`RSWacXFKS})^XZYR-nDcu#A`C(bMZ`RV%NasyEQC`Bm!(&t(bgiYLo?0Vm z`{LiQb5zKfX$w2?k-i(%xk1*!U=#|omd?;3Wy=1B`mWvae8MkaLQ$wlcHZ_l60S>2 zl_ixt!}bFWdtZh3hf2EtC_*c6>g`g$ogCKAb8? z6wA+2da9nidvz|PVohC#lGeZ4?u(S6(s6hf>Kf@QI)*%QA9^^;#M`_@rp)SI(;%PC zrhxa?FZJ0XEoZqSYQ~v?*n-Bk>=^YfeiN3960~AdPZ|B)kd;@Ch7@YSM?#B9y>0B%ww zd-ArQ+KI6Wd!gMz_uo1z7X9iyk;?Bh0jjS|-Sv!`yxpw9U6jJM(+hOEaT=}JjEf|b zoYj16fz>*?Jq@M_EX~NAVUQ&0UjPoby)0Wo{0%?|X5_r+)K$lxwKGO_+)e9}d?w_a z(W3%F8rTStMb6IJ+&a907oo$r(}~`bEder2cKju9ZY9{mR#Yo??N3PCKj0bD8vjxify-c9=R6^UxyK4&p_PIcK+^-$g0lxfK zz~}0Se&FF_a%^?o7S}1nV?N=liAX5q4;0EMFQMd&-9Ssi0X;=5^C1STs|G}m%<_w+ zR^5pV&T6wApfa(X+wb(P;?h6K3r^d8kW;9>Y)T2GPeXT4uD4R^Ae@>NJCrlJ2z-m< z!1bF19=GkeZX*VaWIFEgS<)8to#ubVN~f*@7PQ#6WMKs;(*;#-|BYgw*j}uG?X4tItAQxbUgap6iRj^M}i*q zb=WMSs6CnJUutU7sE!0L>_7B*UxM8uDGpDm2Vm4KeEIO?j3FECCpg6&FZ5KteW6;I zpTFPf6G`viLHt5{*!hJ!BsB9WgKlaG$wFrfwZg*ltyKF}vb|r-?383&OsBf%L9Hbw z;<~=lQ~I;|;B!Q@Bc9h0K=WO-^kHF#l@EBB5ASvS%D%y^TCE2y5zK#i-8A_`WycmTA4^PPf-7g zXmt1SS;4l9$TPRPK~mtIeJ>wb==-byd#21cjhI35M3w8ZWz;hP^eR%=@3vUJOoUOLd;2 z=}{Nr9p2iO{Sww9#XM=R#ebV8-|icxFD!=!w~I$K*UT|!3ONp0nPl&(VkCsdMCq~Z zqc&?4YPue_5JIm1?3cBdUJk67!DZcTE15P`X!wOJkzac`D9M0c%(S_sLv?!Jr)T68 z9`@O(a2w@--*}qmYd&a?bRdFp6Pg#AV@dg z4wP1F4|3$(88R$YE|*_hL&u#S-U=qH@Pg6GKDTcW4Dn{t^R`Z+y#xkRkJ-LoCwHE* zlNWrlqn2soqq-pJ@AyS7h^qr2rTh7o77z(hkoTL{#kqN(a21%pYae zcL8r-FEsSeV1jJ$T?k4kKnEh|i5YJhl<0|L3(cKq)g%1t*lJ1xlNIQ*95hChamgV1 z-dZeJ$A;-JnHjlv^UZUH9K;S)qq9h-iBGz`ufny9IP29CI;_^Xs<2Z-Kil_>4ckA? z*iZ60t1ht3^Vin1i7V?va*S*j0vlM^M=aH#_?0(okz+>~;I59;mIl)>`aY>}d`CQa z)E9Xz%8!yP8VPda2l-3{I#p*wY;JjQR z!aww1EpdLfc+uDyjEv+@vQEnBd%%bOS1E5GWB6($pCcduhE&3 z>L1wre@_kXqnhiE-sfQ~oL=_ zie44` zI@~~F%|JJ<(3r-ezE$0+yumYG%)g%VJaeL!1^0HcALM}0cvn!kQK1G}-%2Y}V@yLqClWHU!?$`RAt-G1l2qQDH7yHYa%p#>wBarHQq3s7dgGQsd)V&#+<(Yj) zm_4kEa}bt8(H_@-?@@y*sp$P3&-KFQw1hR@c6;;&1`@3Q32sCA4udd0&ueTWDU<|A z{8oO!=}9h1T`1^uc&rp1?fMXoGn}bqD$^ecJ@vpPui3bQ;CkEQ5P^U%I_cV0?-CY%SV?AA6Xhy zFy9nf>@8ifcq=;v-?kkwZ~I}($0a(p3aiFSf-EOARE;Kra&s6Jl1Oeo@)HCB2On1I zCfWz=-*f&kNN^Ig4;G7}YX1Lp>nAYrfpH!Xf`kA2asa^B4>$s;mD2p5IRqW_bOk9O z&>0ud$@c%uh5;l9>!{VmGDP~9HqMXij|^`pD6oHdY9Rp1PGCFDEBp6#0{=G|1}Gr- zKI9t3fdm)MXfn@$%&!X@Eym+eA4;+WG~J++>p9aVl>OEWE!tj4zESk5Mv6ThF5qJ< zRNCNsWT2E90~QE$D*AM1m3eZwT}Fs?f22cKLtY?TXQ0XK4>gDbfb|lB>cNzibyEmV$eBzpyK~i)Kvz>*>p>sU3_tu z#VvSnw;;jY2@oJaa0u=m2oT(Y27(25hv4oK+})kPeR%7ux>fsgwsxe?nKLupy;O|< zUMVYj&};@(K&>6-Je7WSvK(5pimuLB087{PIZGGb%o@+d4H@!fkgsS;JkP@zhX@@J z%kh?KegVbUO!(>Q{OvUL_@WFp%%I-eN^X{G>Gd2@0s_Q$TVw%$IbB%J;?jQxJa-xLLu-oROd)xpIRp z;*)UqL^wyp-w8w}SVcv7=zbIWVz_haC$T%psmXv&s?5O>UpI|gn~>Y2PYMXkg$ z*+8m|*`l}y49{7pL5FE-4M>t!x~rJGJftgcZY&ZvsC zwCtLioof71YDiXSdE+y!N(Z*V{U-JK zrL@ksVC;mE@M%5c|5GR34Jq17boz%hf-m z?V4x;r`-03MJ5{QUyp9wA4g^6z+=|&CeJn6%wMwyVgtW+JKC&>B4$zhILUrdgNouw zT3b!9uvy#+>0_R$Cw!cRaXC{qEjd>nd{pvo-!R1WJJfGAQO3Fe9ik`uKm?d>JUW~$ ziH3^E3n+faZ*oG-?a2&t(YuzN`NYxvX}k;jqHB5zDHA(z)ELAHaor-o=`6J0>xWDA z)#>&Pj_B7Pv=mcs4wm|vIKE4J(5Kr%eC{~|Lv5Ozj+WJBeqSh>J;hTBifXD^_RF< zR>SmKMs;4p%5qFl{nJ-psytBKyQ;guYE_p5$DZgh|CNvGx>O-xcE=U@@gSHeKE~YS zPOE?wMbegt(il8Wmkr~EB64|g#3N}^s^WditnKPmS!F3BT}1`I{kCXO2`IOF`LVm6+Hvpu!VhEBBD7Nd89U8buiq(kPxViQBFWYrjR>|NXka zYrtjeM_N2py=fOLsK3U*Dw`tVa8R-n%R!>w_{syugvH<@IlpIsBl9r9MbXak6-?0Q z!Vb*Rf6Tm?soFl(w=_a}?~Yl+!&UhZ=NJFYV-rL40AO2`+nxvoOA7-$h0o;y+*1UC(;Fy6>5GVy)L@EQ}* zVfc`-!l85Yqb8sLV8{U@`=64GMUqsaV|6kz$xj$zx5OU0mn+3|`7!rwK2OEF3tXWw zCeNhU78Jeb`wxAvtuC}TEpECp{}Pu<%n<|dLP~(E{knldq|RN0Mh(hm1CTQ1ZeQj0 z5rtN7-JChYOaQOoID&qCrS^5}&TukSxBbGX8w3+}f2{jLCok%NEv!s>C>BW>+x$uz zSZ*DANPJ97A9onbWKYsCnVp$asY2_HwTZcd$L&(@>cIdjAsM)|UcNEVuQT15p&0aE z7{o;k*rK9L5+CT+^30+`;9Jt$t^SsGQb&=uw^v(qzjrN(eJQ3d=(+j@RTa9YHc0`S zbR^Z%CXVB(LP-!U_bs&fg?}&00ANah0f!4`>-uW%GL(G{;pY0B$J7@p>`1kuQJVpn z&*A+pQiO|HUy?XmJXG9vkbA^F=Z+z+kEGb}St~K2oSp`F&Pa9&2u|!s`t5X79x{uiSW3$-kb2X! zfx;KVmsOe-R`=o5+k-6aw4GvR&Kn^_mOPbPV_x{p-`yOQYAt1@Yw4m!&LcI805ic{CGqPsQef%M=j7EnIb zDXe`D&pb(zXZ=IJ+9^#y`N+V z3}UfVt8pgZ#-FcH&0TbY1811kn@H{diId(PpR&J{yvRNpC9v21ZiGcXy(2=25sHDs zGX&X1wlHGTQPBr>a040Dhgd9`DojQ!LJI4Mt~_0$11bCx1BdFHT31rn#s~R^k6~=Z zltnxpDaHssz8o&NmzkFu-+Hc*ngk~v#zd))P)%n0L}U>d@4?(cUN<=BpC!-F`>xog z?`J>qc!cqUZ0tXG7Vc3>o!=QQx#!$9{9{PB#c$3V`8S!U-{Fq4`i2{Mf)j3ZI_KVtv2zV@IEZ{!< z#>iPQB1DOQslxrHGXSPn+iE8(dKo%p-~Bm8Pq?dFVx!`AAMGIW56kn1FP2B&53u_A zICjRJ$hHnvzd3@Mc~;s0*1+HIA!4g1nMLiJ+Vi(l_MO!yj)WOx?1bnb$SqlFHSUes znAEx4F4bv8E#QZw5Zvf6-1AqV*HKvcFS6N;t%l)wWdg*xcW`bT#QAa(R%ZXG!~lEY zT8NvTY80u=hd+WTqIiH=--KH>0djW5YkJ!vz^ah$I^zneqTH!puU|Vzp`i+phym9ltSgp<_D7x@-(BW2`$d>)rJ(E?jO7bz zRkw3l6^{wme8ApJhV%0jVIRfWpE(WWRgy7DQM0#$W9@-mfidmh2G)ou;qu&D*fx&8 z?0C!*uw^JFTTdl9`|eUyVxzw_6#6NJ*vw|%j%arY_yrjs zgDJu9;+{Q0vuoNDX2p(Vz%cHJ9k3PA4S((7-)R>kwbiWFdB@A$@!M%LcD3GW(0=FT zSQE%u(xwMdx67YwoqJC;K=*VE>=;*!vZ4fWBWkD$5Q$}6r^0V-`|7xS7v z+KtPu)<-hFB(_wbhck6grPbs0Hq84|^~IM?EP67i=xA~(>Ku+XBSN_3?o0wdXa-;# z*)doigpiNIeuSIsqs?ETJb3{Etp*B|g40Cc6pQnEh_>dP@@CEY=Q@9%nhp_hfPq}R z)RhZEF58??<(2r;`4$Hbjk|r6q|$FBIP~M%cW^g`)!8<77+fd(ksoeBo~xr|`Aii> zV5v!OuU;YHI_aXOGc|7EGk2+{tv6P+RDSnNe5;;zi&BdP^gqC?a-N>NzbTx^NN?si z-H9Z&ou@5FN~tLxT2Cp*YbaDb_v3+%{qJ>;Bf!}2}iC6A#o0XKplXdDI4Kk~qGYi_) z=sl{+n~H+ZsCUrhR94LnP=B~2O8s_`jp2ZI8Pq!i_` zvW`g@yVeA^G}pgsezzB=q<+20h+9hX_l333wj9OWv=sB-|$d*KBb*HZb3BK zc-QEgl>TfbeUYfY-9Op#^!gVh->4<*W`>7Ih&wz1>};JD?#s8f2}CyGo2rRFu^@lI-NEefowydctobjDUY;~G*K&dEz2GQvvZo2+pHO)+ELsMt>VH}-V% za6WrWcW@7NrSxQvR6*?!!MOB5G2&NCH*{WFlEUfp9xjs$GAh4|gOc*pNm`jF+{BTO zfug0cR$e;^H^M8UT|TYs__*=X&57Ro`ljRGdrWqY&fUI4t}pS+f=zo_8s5f*G%Lvl zxL`M1#KC5J}W@RftdtkvZ?u8;a#t}a5_q3JJOe=G9G;(Ca90ed~; z8)DC2?B6Znqb9mP&!x!DEs$0W8-sn0IT2iBQp6sv(Z_O*+i&Cjd~Q=7<0AhPNFew$ zxluEKD7+Vw;}gC{J|i<;a7pOYsaz)JH{;N&Hot}vVNo$;utK$GW`se*Oo*?kS$vY-(Ba$&OBZe=n5_wV_?VDmQ+d)JAiQAlsi$J)%af@iV2v9p`@lf90OFx~-u>pHT7k z6Bed`teX6|npiBkjSzG%<-?}6G>!qarZ~{G@3cQBg+KIi@FdFvi}R`kZ;Bl&aJ)yp z=$|==ltjkJbsx&{r}-YxQSDALymh*~dqkaiJ-)9-KlLKDbWrjM6XLjm!OB&fGe#0C z;hIZU=qR`|>6*b3hBnzS?$&OsR;Ezcc~3hi6Cdwzde?Jus{Ak>=kxp_!O$sFewqi@ zcx~;}SI*Q26Qh)FH&ATx_3&m_2W_TTb2lslV%$?sh0yEt0GqSmhC( zUPh28ej}CCqeiTni2ah;Ai%R|D9%`ugu8dWV0YR&e*hn_Eynwc!E+-rFCd4O4QD5T zp3m`y=eEhI8$#SG%yR`5?QW3gUcpYXAv;(QDh$tR7hz*wcLVT6TZrvR{k8$E=Dl4)Z*%;H7mLk z(N#aP`9!2!euh|dJD;3{p|yNzQ#u%J^C$GP zSEs2gmHqL6IW{E3Z&Svll~XvvDjp@xB@6Gh{*Sa%e37m&)!Eieo|NJl_kb^Y+05L` za;d0C6=oAcVQr-G=*JtaJnDD6jVncxFP0v1L|umg95+5gi-P$3!~`QU9~o^8@@Pnz zOyiNHtTEOlIVSJ7S*I5;;0;kvmX!7#>kG`^92t)mV~~Wy)T{0^GcqLZ8UYOf!B7HR{#jv|^VXHl=QO`DRJHtwTUd!v*ZxPvHtQ2(+yhqF{$?W;% z1Kbc46H9szlhIT{^=o8>!k)6s+Alw;U^^A6mo0zib1OZpn3B#>c>GX!z&l1YKPqmt zk+=xf{COp{J?^Cs$u06R;KmKrPBw=7)`u(%xnCO{+4DSil=>$bwNvQC**htZASZPq zEXJq~4jaH%mt(XYde+bKZ{K*x69^Nl8eZ<9`NmGM7C*h?cXa(BP({mmmx=(+(%^J z+>iuI`{0U9Pi1oY+0y;&EYIqpo!AP@H0)7S%F3p76S^V_YeHP$36_h;X4V^YvrKKq zg+-|(K5v37w8OJvu7bm;@$YygPMp_aCnlgq8%c7-9hJ-KYVVH7t*BQI?<5d} zrxTmrS*ps%;v5`g695dEIBwYy=TZ@T;tLp1{JBxSFDCKnGd$4+tvv2Vp~!;S=t|$o z*PkjdfYw~GPOw&(o>0v@;W9HC|J?&6AWY*$*!rbdPc{&6Km2&GYbvzkaHAD!zlm?# zy5Y&a`ojKHR@U>!1G0BOBk|01^R%~Q_0;_vi%!^K{8;+gnjmn>{HH=h{12`^jyW|A zZVDpP{iD<7B940EeOqcWC*}z62oO!9Llv$lNiRAB6((c^SJy(8u_ES2xJT@b{aPB2 zfG~<&)d!slY*Xycu-hZ4Wn(|(=ZCG1tl%y;MAFDvS%W6a$B!tUTpkhr-{VoGg8=;k zstFU5VpnN_g1CtjC_k)yY-^UXj0+7`nAS@7BAvo)7Z5zXL>)pt+e-h_w(ktUMn+4d z%`c?cAUv0}hrWCaB3F%+c)OX$o3qz{wLVOAQ9ftvA0sh#0}*F4a6{v;bA+rjjK4Rw zL46vI!=@L&yI+xA{OFT~ej?nAQ-Y=X_;Q@-<)AS`*4O^HGIFvbP6-Cb`uqE1>Q(w{ zu-4|ye9HVJ>)1QN=+~jBUt6|V=~~KqTw|7L9VOtZx1=;vsg7L8RV&{oi%2VN1UESK zu3r-55r6dP;a=ZfjrXpfj%DGf>f0%incJ!GZN}<-235P)=)Lep1p9}LrX-SE{%{FV z#`AHD(JfGi3CaDgbcl9YQ9_xF z+}%0}X|SqRe@^+Rqpo7_`=Dhy%R5WE-%%3D_0$|fW6^9)k=x|BA>{jq3R%g8#L0TU zc*BkBKjM1$h?BkyUFLngR}>ssX_8A({;xP>w8-fcd+Ge{QSPX=UN6n2? zP=xVuhiohg3UM2mE)>YFi_N|o;BLRcCyiHWL2B($OFnX+sby^Dkwa=aIJB3!eJIRv zb?Lb7T* zOuwI=JZd`!X=0h-H1-;yBfh;fCMCavj$`ainx1ea&V8K-+k~4UBhH6uFx+;1~`s3~+-Cdr8pp z6yqoF1Q*v++y_#YwchAPx_v`(rcCmVQ}2ymU`VpAEz+sOZmTzz{IaWc#XFK%cKbW4 zx+J)T@Vf2B-bJL6{2b?BpepiE?U2I+CI#Pab*UH}K_pE5Up8Ei8~q9dq__WMyZn)` z&cak0w~9IXOk;-)*Qt~_pX=#L?rrgd8W0X>nDlLR?ldh3KgL(PjvS7DoGV;F~M`~9gB+DSLFp$p*{p6kn% zIM1Uo3Eiq}yqU_P$U!=*%$Od#1yO3V>7`KzcX^H@KH*ZdZp*PG$I8zr$73SV{zuTF zh9jmsWvL@Fq?M&WNlcNzZ(3zQZUsC&VcWi1FW%0YtaB;LZSCJ3tEaS|6tZhR8$*~x?{jY5a~}UBLl(U#8!t5D;7fWw z2`&BM_k$&-c;Z;}J9l0%JYU;d<;{NF_Ulk%yFb`=5!%0)^HNLr0<|6>Pd0?#9mGrV zc+p!3xi_f$WA;eH&WKPnPLD`U!iWdQL?>)sKtO^dimguKP{NW8%zq0YhEl??aP*Pn$TS1>+3EuEHBWU?e#2BvgH8=SEQmV!k(+B;!D0vIP z7y55&;}IfzB0}L`9yuZkeHHiREq)}kIP#zVZaKC|p(V$t3*G-=I5NVv8+fmCb)@ca zJRhC2V+WX0fJrz;OHxsGX;D=hy}_hvVIc@8aWHtERHMWeZ6*lQk!9;EnpR77`f3di z=jUmsc@OFJ*(Y`SYq7YMG5{r2$>+3}cWt%C@Iwo|O63&_$4@77&7FMM3`s;m)#6J< zjscWqsAYepKSiU;Ua{rSm7c*vS2f>xJvyQHqj1FBD)T0r@uk0*5R;ScBl!rjFXhmX7F1tv^9+43`Jeuf9S=u^To4BW()Hf4V;S2ll%}{ zf9kWhYlvavGqr!n|47NktH(~MKPMAGYB{1?e-w@&9|!C{1$>93&L0ta)@(*4Z)xkT znzOvfpO+s^<3MjBVm3iT-#jJp={b88k%qmW)=Qb4c~Tm5J}v!$IXTj7$Qcgs-#UML z@4Oi$f>L^9W$xwvLE}e@7#yv2q=iELw))JvT4G9*~BwA zQR6+Q>OD!p(WvYpG)S;r5#>L5NQx2t-0uk#oRcnKnt}V=Gc)S%TGRD5X-Lc40Z~vCNEvni013Irrc(AwU?^A5S5Y{c%Vs!WWIX; zOc0EV3Cnb~k*W}rF9o)W|GsQsMAd7F_Y2%V8j!N2K*P_Ky-k<+>67@EM1*&g=|Ct~ z%O%@=7fS-u)D-nZoyzJ=1`(H<(POB7HuIEI$-Srf!-NWs6;s8|mS7vS-p-Z}5i_r# zz=&8U=S|7}&UIB8Da9`>v?l%cG^ycYqO$m00B8-11GHWn$lEJ;FP0e=rtCt8lf&S5 zc^;|sv}LxA#qt)l3x0W1b6XgjG60TNEW{`qN48Rql5S~tae(}b;b%uplFcV?LOMJb znM;qHYf?#;l;x+R?xt;7;0vUXY>6?5m765o_xF_J9tapg=4f1Lv{Q?XTuHw)y%`8Y z4GCn|_SOgR!;a%%zy>D3rb_SyZeAFy80N0q zRw19Jc^hE3FVgEtBL;^k2EYx5E&>|gv4GG*aY|4?n#{s(!Jep{<>Pg98qd2dkOzjy z&0Nl*9~mJ_#A%}>0pe(TEa=f6_Q?ai zPBD7A*DpT@VaCFMwS>RAYAwZ8IxQQ zPMR{n1uXUFRA`b-ewo03KsW2ejPX$S(*fiHA(rrha(d+MgpukT3dY5PHG>_HSCz}& z0!y`u(EO#c;y4#4$ZJrHoY{ej@m(k&6MS4c<&1b%i6%cnauOV3H8vqVvFwlCxM}-CZopgtRYK)X3awdJ`cp<%- zrrcxN&Na0NCA07Q4^t_M)}nop06OmFD655=pGa{EpaHqGCgrIpmsiA;NgXPeH(z^+ ztPcGd)BNc?X3BUb>0Sd){56F3_VdmPWIFa7vb`7Lw<>(}>$+>*SA!vFE$0~KW#7Iu z!dp07DmRdcyn~~Or2sH-X-3X~2+n_R@=&})BcFi_elzuu=XzG}p8xOYS0sFT`ntzq z>(*Q(-jGSzHp)L-l4rUAiPr!u;*xDtND|v7DDSATFAJ2@nu|-yoA;a3BlWX}2aJ4n z&2uk`Zd;llWujluz+kmJBA1lLovcfxGpErQod94$b`e~_jQppGWbrUyb16!EQ114G z>)G?=`<_@VA@@=>9Q-Ah2{(=9m(RnxEc>Z0MGd~8|TlYjZXU^Bc0ApPfU9;vb%&NvP2r-nib z`GK&Aj)2eABs&03#2M+8ZqWu> Date: Thu, 18 Jan 2024 13:07:09 +0100 Subject: [PATCH 2/5] final edits --- content/english/highlights/covimapp.md | 47 ++++++++++++++++---------- 1 file changed, 30 insertions(+), 17 deletions(-) diff --git a/content/english/highlights/covimapp.md b/content/english/highlights/covimapp.md index 5e9511a07..91163c703 100644 --- a/content/english/highlights/covimapp.md +++ b/content/english/highlights/covimapp.md @@ -1,12 +1,25 @@ --- -title: CoViMAPP – new resources for the analysis of the soluble blood proteome alterations in COVID-19 -date: 2024-01-16 +title: CoViMAPP – analysing changes in soluble blood proteome alterations due to COVID-19 +date: 2024-01-19 summary: Babačić and colleagues expanded the coverage of the soluble blood proteome using mass spectrometry. In order to support further research in this area, their results have been added to an open-access app. banner: /highlights/banners/covimapp_logo.png banner_large: /highlights/banners/covimapp_logo.png banner_caption: CoViMAPP logo. highlights_topics: [COVID-19] -tags: [COVID-19, Covimapp, Meta-analysis, R shiny, App, proteome, SciLifeLab Serve] +tags: + [ + COVID-19, + Covimapp, + Meta-analysis, + R shiny, + App, + Proteome, + SciLifeLab, + Serve, + Blood, + Proteins, + SARS-CoV-2, + ] authors: [Katarina Öjefors Stark] announcement: "This data highlight was also published on the SciLifeLab Data Platform, as the work described in this highlight constitutes data-driven life science. The Platform is a hub for data-driven life science in Sweden, containing multiple relevant resources, tools, and services. It includes information on multiple subjects, including infectious diseases, please check out the Data Platform for more." images: [/highlights/banners/covimapp_logo.png"] @@ -16,34 +29,34 @@ Over the last few years, the COVID-19 pandemic has greatly impacted both society Research has shown that cytokine storms (elevated release of cytokines in the blood) cause systemic hyperinflammation in patients with COVID-19. Systemic hyperinflammation is considered to be one of the most important pathophysiological mechanisms behind severe COVID-19, and can lead to multi-organ damage and death. The inflammation is caused by systemic immunological perturbations in the human body that are mediated by the blood. Therefore, plasma (the liquid component of blood) is often used for studies into the systemic biological processes involved in COVID-19 pathogenesis. -Multiple types of circulating molecules (e.g., lipids, metabolites, mRNAs, and proteins) have been studied in COVID-19 patients, but proteins remain most commonly used in clinical practice. Using global mass spectrometry (MS) methods, studies have identified a few hundred protein biomarkers in plasma or serum. However, the soluble blood proteome is known to contain more than 4,500 proteins, meaning that much of the proteome remains unexplored. Continued research in this area is crucial in order to allow us to prevent the onset of severe COVID-19. -In a recent article by Haris Babačić et al. in Nature Communications, researchers from Karolinska Institutet, Karolinska University Hospital, The Laboratory for Molecular Infection Medicine Sweden (MIMS) at Umeå University, Linköping University, and Science for Life Laboratory (SciLifeLab), led by Jonas Klingström and Maria Pernemalm, performed systematic analyses of circulating, soluble proteins using mass spectrometry proteomics to expand the soluble blood proteome coverage. +Multiple types of circulating molecules (e.g. lipids, metabolites, mRNAs, and proteins) have been studied in COVID-19 patients, but proteins remain the most commonly used in clinical practice. Using global mass spectrometry (MS) methods, studies have identified a few hundred protein biomarkers in plasma or serum. However, the soluble blood proteome is known to contain more than 4,500 proteins, meaning that much of the proteome remains unexplored. Continued research in this area is crucial in order to allow us to prevent the onset of severe COVID-19. -Babačić and colleagues used serum samples from twenty hospitalised COVID-19 patients (ancestral SARS-CoV-2), and seven PCR-negative and seronegative controls. More information about the cohort used is available in Varnaitė _et al._ (2020). The samples were analysed using high-resolution isoelectric focusing (HiRIEF) coupled with liquid chromatography tandem mass spectrometry (LC-MS/MS). In addition, the researchers performed _in vitro_ SARS-CoV-2 infection experiments in human lung adenocarcinoma (Calu-3) cells to compare to proteome and phosphoproteome changes evident in the blood of COVID-19 patients. The results showed that a large part of the soluble blood proteome was altered in COVID-19 patients compared to healthy controls. COVID-19 patients were, for example, found to have elevated serum levels of NF-kB-, interferon-, purine metabolism-, heat shock-, and proteasomal- proteins. Furthermore, many of these proteins were also found to be changed in _in vitro_ SARS-CoV-2 infection experiments. Additionally, changes were identified in phosphorylated peptides in the serum of both COVID-19 patients and SARS-CoV-2-infected cells. +In a recent Nature Communications article by [Babačić _et al._ (2023)](https://doi.org/10.1038/s41467-023-41159-z), researchers from Karolinska Institutet, Karolinska University Hospital, The Laboratory for Molecular Infection Medicine Sweden (MIMS) at Umeå University, Linköping University, and Science for Life Laboratory (SciLifeLab), led by Jonas Klingström and Maria Pernemalm, expanded the coverage of the soluble bood proteome using systematic analyses of circulating soluble proteins and mass spectrometry. -In order to provide estimates of the alterations that occurred due to COVID-19, Babačić and colleagues performed a meta-analysis of global MS proteomics datasets, as well as their own dataset (1709 individuals, including 1039 patients), and identified >1500 proteins that were identified in at least two cohorts. In order to aid further research and clinical use of these state-of the art- MS results, the researchers developed an open-access app called CoViD-19 Meta-Analysis of Plasma Proteins (CoViMAPP). CoViMAPP includes information about the effect sizes of alterations and the diagnostic potential of soluble blood proteins in COVID-19. The app also includes summary estimates obtained from published studies of plasma proteome profiling in COVID-19 using unbiased mass-spectrometry proteomics. +Babačić and colleagues used serum samples from twenty hospitalised COVID-19 patients (ancestral SARS-CoV-2), and seven PCR-negative and seronegative controls. More information about the cohort used is available in [Varnaitė _et al._ (2020)](https://doi.org/10.4049/jimmunol.2000717). The samples were analysed using high-resolution isoelectric focusing (HiRIEF) coupled with liquid chromatography tandem mass spectrometry (LC-MS/MS). In addition, the researchers performed _in vitro_ SARS-CoV-2 infection experiments in human lung adenocarcinoma (Calu-3) cells to compare to proteome and phosphoproteome changes evident in the blood of COVID-19 patients. The results showed that a large part of the soluble blood proteome was altered in COVID-19 patients compared to healthy controls. COVID-19 patients were, for example, found to have elevated serum levels of NF-kB-, interferon-, purine metabolism-, heat shock-, and proteasomal- proteins. Furthermore, many of these proteins were also found to be changed in _in vitro_ SARS-CoV-2 infection experiments. Additionally, changes were identified in phosphorylated peptides in the serum of both COVID-19 patients and SARS-CoV-2-infected cells. -In summary, this study is a comprehensive analysis of the soluble blood proteome alterations that occur in COVID-19. The results validate multiple previous findings and pinpoint new alterations. Furthermore, this study provides the current MS-based state-of-the-art concluding estimates for soluble blood proteome alterations in COVID-19. The researchers aim for CoViMAPP to be used as a dynamic tool for future dynamic meta-analysis, and additional curated studies may therefore be included to update the summary estimates. +In order to provide estimates of the alterations that occurred due to COVID-19, Babačić and colleagues performed a meta-analysis of global MS proteomics datasets, as well as their own dataset (1709 individuals, including 1039 patients), and identified over 1500 proteins that were present in at least two cohorts. In order to aid further research and clinical use of these state-of-the-art MS results, the researchers developed an open-access app called [CoViD-19 Meta-Analysis of Plasma Proteins (CoViMAPP)](https://covimapp.serve.scilifelab.se). CoViMAPP includes information about the effect sizes of alterations and the diagnostic potential of soluble blood proteins in COVID-19. The app also includes summary estimates obtained from published studies of plasma proteome profiling in COVID-19 using unbiased mass-spectrometry proteomics. + +In summary, this study is a comprehensive analysis of the soluble blood proteome alterations that occur in COVID-19. The results validate multiple previous findings and pinpoint new alterations. Furthermore, this study provides the current MS-based state-of-the-art concluding estimates for soluble blood proteome alterations in COVID-19. The researchers aim for CoViMAPP to be used as a dynamic tool for future meta-analyses. Additional curated studies can and will be included to update the summary estimates. #### Data and code availability -* All results described in the manuscript are presented in main or supplementary figures or datasets. All results from the meta-analysis are available as a R Shiny app. -* Raw and processed MS data are deposited via ProteomeXchange to the PRIDE database, with accession codes PXD037486, PXD037451, and PXD040982. -* Source data are provided with this paper. -* The custom code for the Nextflow proteomics workflow is deposited in this GitHub repository. -* The R code used for the analyses is deposited in this GitHub repository. -* The R shiny app COViMAPP is available on SciLifeLab Serve. +- All results described in the manuscript are presented in main or supplementary figures or datasets. All results from the meta-analysis are available as an R Shiny app, [CoViMAPP](https://covimapp.serve.scilifelab.se), which is available on [SciLifeLab Serve](https://serve.scilifelab.se/apps/). To understand more about CoViMAPP, please see the associated entry in the [SciLifeLab Data Repository](https://doi.org/10.17044/scilifelab.22293148). +- Raw and processed MS data are deposited via ProteomeXchange to the PRIDE database, with accession numbers [PXD037486](https://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD037486), [PXD037451](https://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD037451), and [PXD040982](https://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD040982). +- [Source data](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10516886/bin/41467_2023_41159_MOESM20_ESM.zip) are provided with the publication. +- The custom code for the Nextflow proteomics workflow is deposited in [this GitHub repository](https://github.com/lehtiolab/ddamsproteomics). +- The R code used for the analyses is deposited in [this GitHub repository](https://github.com/harbab/covid19proteomics) #### Article -DOI: 10.1038/s41467-023-41159-z +DOI: [10.1038/s41467-023-41159-z](https://doi.org/10.1038/s41467-023-41159-z) Babačić, H., Christ, W., Araújo, J. E., Mermelekas , G., Sharma, N., Tynell , J., García, M., Varnaite, R., Asgeirsson, H., Glans, H., Lehtiö, J., Gredmark-Russ, S., Klingström, J., & Pernemalm, M. (2023) Comprehensive proteomics and meta-analysis of COVID-19 host response. In: Nature communications (Vol. 14, Issue 1, 5921). #### Funding -This study was supported grants from the Knut and Alice Wallenberg foundation (KAW), within the SciLifeLab KAW COVID-19 national research program, the Swedish Research Marianne and Marcus Wallenberg Foundation (SGR), Region Stockholm (clinical research appointment), and by Centre for Innovative Medicine. +This study was supported grants from the Knut and Alice Wallenberg foundation (KAW), within the SciLifeLab KAW COVID-19 national research program, the Swedish Research Marianne and Marcus Wallenberg Foundation (SGR), Region Stockholm (clinical research appointment), and by Centre for Innovative Medicine. #### Infrastructure -The Clinical Proteomics Facility and the Data Centre at Science for Life Laboratory was used for parts of this study. +The Clinical Proteomics Facility and the Data Centre at Science for Life Laboratory (SciLifeLab) were used for parts of this study. From 6924bddcf6a7ff8ea30eb8f696709ec0478cd9e7 Mon Sep 17 00:00:00 2001 From: Kazi Jahurul Islam Date: Thu, 18 Jan 2024 13:07:32 +0100 Subject: [PATCH 3/5] Update available data December 2023 Chores: - added available data December 2023 to json file. --- data/available_datasets.json | 19211 +++++++++++++++------------------ 1 file changed, 8963 insertions(+), 10248 deletions(-) diff --git a/data/available_datasets.json b/data/available_datasets.json index 78f504c86..76902757e 100644 --- a/data/available_datasets.json +++ b/data/available_datasets.json @@ -1,10250 +1,8965 @@ { - "last_updated": "2023-12-15", - "datasets": [ - { - "doi": "10.1136/bmjopen-2022-064240", - "available_items": [ - { - "type": "data", - "repo_name": "Zenodo", - "accession_number": "", - "description": "A collection of serology data created by WHO Unity Studies Global SARS-CoV2 Seroepidemiological Investigations. Includes both data published in studies and other data not used in publications.", - "data_type": [ - "Serology data" - ], - "data_url": "https://zenodo.org/communities/unity-sero-2021?q=&l=list&p=1&s=20&sort=newest" - } - ], - "title": "Systematic review of seroprevalence of SARS-CoV-2 antibodies and appraisal of evidence, prior to the widespread introduction of vaccine programmes in the WHO European Region, January–December 2020", - "issue": "11", - "volume": "13", - "publisher": "BMJ", - "published": "2023-11-06", - "author": [ - "Vaughan A.", - "Duffell E.", - "Freidl G. S.", - "Lemos D. S.", - "Nardone A." - ] - }, - { - "doi": "10.1186/s13613-023-01201-1", - "available_items": [ - { - "type": "code", - "repo_name": "Zenodo", - "accession_number": "", - "description": "Data curation pipeline for patient data extracted for medical records up to 60th day of ICU stay (written in R, Version v3.0.1 used).", - "data_type": [ - "Other data", - "Public health data" - ], - "data_url": "https://zenodo.org/records/6063905" - }, - { - "type": "data", - "repo_name": "Zenodo", - "accession_number": "", - "description": "Data dictionaries associated with data curation pipeline used.", - "data_type": [ - "Other data", - "Public health data" - ], - "data_url": "https://zenodo.org/records/6063905" - } - ], - "title": "Early mobilisation in critically ill COVID-19 patients: a subanalysis of the ESICM-initiated UNITE-COVID observational study", - "issue": "1", - "volume": "13", - "publisher": "Springer Science and Business Media LLC", - "published": "2023-11-14", - "author": [ - "Kloss P.", - "Lindholz M.", - "Milnik A.", - "Azoulay E.", - "Cecconi M." - ] - }, - { - "doi": "10.1016/j.xcrm.2023.101267", - "available_items": [ - { - "type": "data", - "repo_name": "Sequence Read Archive", - "accession_number": "PRJNA1014462", - "description": "Raw sequence reads related to SARS-CoV-2 antibodies from children exhibiting broad neutralisation.", - "data_type": [ - "Biochemistry data", - "Health data", - "Serology data" - ], - "data_url": "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1014462/" - }, - { - "type": "data", - "repo_name": "Electron Microscopy Databank", - "accession_number": "EMD-41075", - "description": "SARS-CoV-2 spike in complex with Fab 71281-33.", - "data_type": [ - "Biochemistry data", - "Health data", - "Serology data" - ], - "data_url": "https://www.ebi.ac.uk/emdb/EMD-41075" - }, - { - "type": "data", - "repo_name": "Electron Microscopy Databank", - "accession_number": "EMD-41076", - "description": "SARS-CoV-2 spike in complex with Fab 71281-33 (2).", - "data_type": [ - "Biochemistry data", - "Health data", - "Serology data" - ], - "data_url": "https://www.ebi.ac.uk/emdb/EMD-41075" - } - ], - "title": "SARS-CoV-2 antibodies from children exhibit broad neutralization and belong to adult public clonotypes", - "issue": "11", - "volume": "4", - "publisher": "Elsevier BV", - "published": "2023-12-02", - "author": [ - "Wall S. C.", - "Suryadevara N.", - "Kim C.", - "Shiakolas A. R.", - "Holt C. M." - ] - }, - { - "doi": "10.2807/1560-7917.es.2023.28.46.2300595", - "available_items": [ - { - "type": "data", - "repo_name": "GISAID", - "accession_number": "", - "description": "Whole genome sequence data from individuals for all Swedish BA.2.86 cases is available on GISAID. The accession numbers are avilable in the supplementary materials (linked here).", - "data_type": [ - "Other data", - "Genomics & transcriptomics data" - ], - "data_url": "https://www.eurosurveillance.org/docserver/fulltext/eurosurveillance/28/46/23-00595_MOVERT_Supplement.pdf?expires=1702970040&id=id&accname=guest&checksum=39802568B41757067FA9C2CC9B13E7F2" - }, - { - "type": "data", - "repo_name": "GISAID", - "accession_number": "", - "description": "The findings of the BA.2.86 marker specificity assessment are based on metadata associated with 13,513 sequences available on GISAID from 1 July to 19 October 2023.", - "data_type": [ - "Other data", - "Genomics & transcriptomics data" - ], - "data_url": "https://www.epicov.org/epi3/epi_set/EPI_SET_231113ve?main=true" - }, - { - "type": "data", - "repo_name": "ENA", - "accession_number": "PRJEB67638", - "description": "Wastewater raw reads from Uppsala, Örebro, Umeå, and Kalmar.", - "data_type": [ - "Other data", - "Genomics & transcriptomics data" - ], - "data_url": "https://www.ebi.ac.uk/ena/browser/view/PRJEB67638" - } - ], - "title": "Early detection of the emerging SARS-CoV-2 BA.2.86 lineage through integrated genomic surveillance of wastewater and COVID-19 cases in Sweden, weeks 31 to 38 2023", - "issue": "46", - "volume": "28", - "publisher": "European Centre for Disease Control and Prevention (ECDC)", - "published": "2023-11-16", - "author": [ - "Espinosa-Gongora C.", - "Berg C.", - "Rehn M.", - "Varg J. E.", - "Dillner L." - ] - }, - { - "doi": "10.1038/s41586-023-06717-x", - "available_items": [ - { - "type": "data", - "repo_name": "NCBI database", - "accession_number": "PRJNA989123", - "description": "Raw RNA sequence reads produced when patient whole blood samples were analysed by RNA sequencing in order to monitor global changes in transcript abundance levels post-interferon treatment.", - "data_type": [ - "Biochemistry data", - "Genomics & transcriptomics data", - "Health data" - ], - "data_url": "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA989123" - } - ], - "title": "Autoantibodies against type I IFNs in humans with alternative NF-κB pathway deficiency", - "issue": "7988", - "volume": "623", - "publisher": "Springer Science and Business Media LLC", - "published": "2023-11-08", - "author": [ - "Le Voyer T.", - "Parent A. V.", - "Liu X.", - "Cederholm A.", - "Gervais A." - ] - }, - { - "doi": "10.1186/s13059-023-03080-y", - "available_items": [ - { - "type": "data", - "repo_name": "European Genome-Phenome Archive (EGA)", - "accession_number": "EGAS00001006186", - "description": "Raw sequence data are available under contrlled ccess due to the sensitive nature of the data.", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://ega-archive.org/studies/EGAS00001006186" - }, - { - "type": "data", - "repo_name": "European Genome-Phenome Archive (EGA)", - "accession_number": "EGAC00001002635", - "description": "Raw sequence data are available under contrlled ccess due to the sensitive nature of the data.", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://ega-archive.org/dacs/EGAC00001002635" - }, - { - "type": "data", - "repo_name": "Mendeley Dataset", - "accession_number": "", - "description": "Processed gene count matrices, related metadata, corresponding ST tissue microscopy images, and RNAScope images used in the Validation analysis.", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://data.mendeley.com/datasets/xb2w7xvs2b/1" - }, - { - "type": "data", - "repo_name": "Mendeley Dataset", - "accession_number": "", - "description": "ISS images for SARS-CoV-2 S and E genes.", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://data.mendeley.com/datasets/gwjk2cxsf4/1" - }, - { - "type": "data", - "repo_name": "FigShare", - "accession_number": "", - "description": "RNAscope images for the SARS-CoV-2 S gene for sample 1C.", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://figshare.com/articles/figure/RNAscope_images_for_SARS-CoV-2_S_gene_from_Sample_1/19333442" - }, - { - "type": "data", - "repo_name": "FigShare", - "accession_number": "", - "description": "RNAscope images for the SARS-CoV-2 S gene for sample 2C.", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://figshare.com/articles/figure/RNAscope_image_for_SARS-CoV-2_S_gene_from_Sample_2/19351781" - }, - { - "type": "data", - "repo_name": "FigShare", - "accession_number": "", - "description": "RNAscope images for the SARS-CoV-2 S gene for sample 3C.", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://figshare.com/articles/figure/RNAscope_image_for_SARS-CoV-2_S_gene_from_Sample_3/19351784" - }, - { - "type": "data", - "repo_name": "FigShare", - "accession_number": "", - "description": "RNAscope images for the SARS-CoV-2 S gene for sample 4nC.", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://figshare.com/articles/figure/RNAscope_image_for_SARS-CoV-2_S_gene_from_Sample_4/19351787" - }, - { - "type": "data", - "repo_name": "FigShare", - "accession_number": "", - "description": "RNAscope images for the SARS-CoV-2 S gene for sample 5nC.", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://figshare.com/articles/figure/RNAscope_image_for_SARS-CoV-2_S_gene_from_Sample_5/19351796" - }, - { - "type": "data", - "repo_name": "FigShare", - "accession_number": "", - "description": "Deconvolution results as an R object", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://figshare.com/articles/dataset/Analysed_R_object_with_deconvolution_results/22436074" - }, - { - "type": "data", - "repo_name": "Zenodo", - "accession_number": "", - "description": "All RNAScope images for the SARS-CoV-2 S gene probe, positive control probe, and negative control probe.", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://zenodo.org/records/8039011" - }, - { - "type": "code", - "repo_name": "Github", - "accession_number": "", - "description": "Scripts to generate the count matrices and all related R scripts used in the clustering, differential expression, colocalization analysis, and the program for the computational validation.", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://github.com/giacomellolab/DualST_Study" - }, - { - "type": "code", - "repo_name": "Zenodo", - "accession_number": "", - "description": "Scripts to generate the count matrices and all related R scripts used in the clustering, differential expression, colocalization analysis, and the program for the computational validation.", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://zenodo.org/records/8314652" - } - ], - "title": "Dual spatially resolved transcriptomics for human host–pathogen colocalization studies in FFPE tissue sections", - "issue": "1", - "volume": "24", - "publisher": "Springer Science and Business Media LLC", - "published": "2023-10-19", - "author": [ - "Sounart H.", - "Lázár E.", - "Masarapu Y.", - "Wu J.", - "Várkonyi T." - ] - }, - { - "doi": "10.1038/s41467-023-42200-x", - "available_items": [ - { - "type": "data", - "repo_name": "Electron Microscopy Data Bank", - "accession_number": "EMD-15475", - "description": "Structure of the Ancestral Scaffold Antigen-5 of Coronavirus Spike protein (map).", - "data_type": [ - "Biochemistry data", - "Protein data" - ], - "data_url": "https://www.ebi.ac.uk/emdb/EMD-15475" - }, - { - "type": "data", - "repo_name": "Electron Microscopy Data Bank", - "accession_number": "EMD-15482", - "description": "Structure of the Ancestral Scaffold Antigen-6 of Coronavirus Spike protein (map).", - "data_type": [ - "Biochemistry data", - "Protein data" - ], - "data_url": "https://www.ebi.ac.uk/emdb/EMD-15482" - }, - { - "type": "data", - "repo_name": "Protein Data Bank", - "accession_number": "8AJA", - "description": "Structure of the Ancestral Scaffold Antigen-5 of Coronavirus Spike protein (atomic coordinates).", - "data_type": [ - "Biochemistry data", - "Protein data" - ], - "data_url": "https://www.rcsb.org/structure/8AJA" - }, - { - "type": "data", - "repo_name": "Protein Data Bank", - "accession_number": "8AJL", - "description": "Structure of the Ancestral Scaffold Antigen-6 of Coronavirus Spike protein (atomic coordinates).", - "data_type": [ - "Biochemistry data", - "Protein data" - ], - "data_url": "https://www.rcsb.org/structure/8AJL" - } - ], - "title": "Design, structure and plasma binding of ancestral β-CoV scaffold antigens", - "issue": "1", - "volume": "14", - "publisher": "Springer Science and Business Media LLC", - "published": "2023-10-16", - "author": [ - "Hueting D.", - "Schriever K.", - "Sun R.", - "Vlachiotis S.", - "Zuo F." - ] - }, - { - "doi": "10.1093/biomethods/bpad021", - "available_items": [ - { - "type": "data", - "repo_name": "Protein Model Database", - "accession_number": "PM0084589", - "description": "The designed vaccine structure for Vacdeltm.", - "data_type": [ - "Protein data" - ], - "data_url": "http://srv00.recas.ba.infn.it/PMDB/zip_model.php?target=9367" - }, - { - "type": "data", - "repo_name": "Protein Model Database", - "accession_number": "PM0084590", - "description": "The designed vaccine structure for VacFL.", - "data_type": [ - "Protein data" - ], - "data_url": "http://srv00.recas.ba.infn.it/PMDB/zip_model.php?target=9368" - } - ], - "title": "De novo design of anti-variant COVID-19 vaccine", - "issue": "1", - "volume": "8", - "publisher": "Oxford University Press (OUP)", - "published": "2023-09-23", - "author": [ - "Goswami A.", - "Kumar M.", - "Ullah S.", - "Gore M. M." - ] - }, - { - "doi": "10.1101/2023.07.05.23292245", - "available_items": [ - { - "type": "data", - "repo_name": "GitHub", - "accession_number": "", - "description": "Data used in modelling, including location and population size.", - "data_type": [ - "Biochemistry data", - "Serology data", - "Health data" - ], - "data_url": "https://github.com/covid19-forecast-hub-europe/aggregation-info-loss/tree/main/data" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Data processing code in R is available on Github", - "data_type": [ - "Biochemistry data", - "Serology data", - "Health data" - ], - "data_url": "https://github.com/covid19-forecast-hub-europe/aggregation-info-loss/tree/main/code" - } - ], - "title": "Characterising information loss due to aggregating epidemic model outputs", - "issue": "", - "volume": "", - "publisher": "Cold Spring Harbor Laboratory", - "published": "2023-07-07", - "author": [ - "Sherratt K.", - "Srivastava A.", - "Ainslie K.", - "Singh D. E.", - "Cublier A." - ] - }, - { - "doi": "10.1016/j.lanepe.2023.100646", - "available_items": [ - { - "type": "data", - "repo_name": "GitHub", - "accession_number": "", - "description": "Data processing code in R is available on Github", - "data_type": [ - "Health data", - "Serology data", - "Public health data", - "Biochemistry data" - ], - "data_url": "https://github.com/johanssonresearch/Correlate-of-vaccine-protection-against-fatal-COVID-19" - } - ], - "title": "Vaccine-induced correlate of protection against fatal COVID-19 in older and frail adults during waves of neutralization-resistant variants of concern: an observational study", - "issue": "", - "volume": "30", - "publisher": "Elsevier BV", - "published": "2023-07-03", - "author": [ - "Vikström L.", - "Fjällström P.", - "Gwon Y.", - "Sheward D. J.", - "Wigren-Byström J." - ] - }, - { - "doi": "10.1101/2023.06.14.23290814", - "available_items": [ - { - "type": "data", - "repo_name": "Figshare", - "accession_number": "", - "description": "Clinical data and biobanks samples from 250 critically ill COVID-19 patients. Appropriate permits are required for access.", - "data_type": [ - "Genomics & transcriptomics data", - "Biochemistry data", - "Serology data", - "Health data" - ], - "data_url": "https://doi.org/10.17044/scilifelab.14229410.v1" - }, - { - "type": "data", - "repo_name": "BQC-19", - "accession_number": "", - "description": "Data from the BQC-19 repository is available after appropriate permissions and data access agreements", - "data_type": [ - "Genomics & transcriptomics data", - "Biochemistry data", - "Serology data", - "Health data" - ], - "data_url": "https://en.quebeccovidbiobank.ca/" - } - ], - "title": "Sustained IFN signaling is associated with delayed development of SARS-CoV-2-specific immunity", - "issue": "", - "volume": "", - "publisher": "Cold Spring Harbor Laboratory", - "published": "2023-06-20", - "author": [ - "Brunet-Ratnasingham E.", - "Morin S.", - "Randolph H. E.", - "Labrecque M.", - "Bélair J." - ] - }, - { - "doi": "10.3389/fpsyg.2023.1124627", - "available_items": [ - { - "type": "data", - "repo_name": "OSF", - "accession_number": "d99ed5ce0ed641ca80965e54c11afc81", - "description": "Data used in analysis assessing personality traits", - "data_type": [ - "Health data", - "Public health data", - "Social science and humanities data" - ], - "data_url": "https://osf.io/f7ucb/?view_only=d99ed5ce0ed641ca80965e54c11afc81" - }, - { - "type": "code", - "repo_name": "OSF", - "accession_number": "d99ed5ce0ed641ca80965e54c11afc81", - "description": "Script for data re-analysis of traits", - "data_type": [ - "Health data", - "Public health data", - "Social science and humanities data" - ], - "data_url": "https://osf.io/f7ucb/?view_only=d99ed5ce0ed641ca80965e54c11afc81" - } - ], - "title": "Regional differences in personalities account for substantial heterogeneity of loneliness change from before to during the COVID-19", - "issue": "", - "volume": "14", - "publisher": "Frontiers Media SA", - "published": "2023-05-05", - "author": [ - "Xiao S.", - "Dang J." - ] - }, - { - "doi": "10.1007/s41669-023-00418-x", - "available_items": [ - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "POETIC-COVID CEA PROJECT - R code that supports the findings of the study", - "data_type": [ - "Other data", - "Public health data" - ], - "data_url": "https://github.com/EECCnetwork/POETIC_CEA" - } - ], - "title": "Cost Effectiveness of Strategies for Caring for Critically Ill Patients with COVID-19 in Tanzania", - "issue": "", - "volume": "", - "publisher": "Springer Science and Business Media LLC", - "published": "2023-05-13", - "author": [ - "Shah H. A.", - "Baker T.", - "Schell C. O.", - "Kuwawenaruwa A.", - "Awadh K." - ] - }, - { - "doi": "10.1038/s41467-023-38020-8", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Data cannot be shared publicly, but applications can be made for access.", - "data_type": [ - "Serology data", - "Health data" - ], - "data_url": "mailto:\"geldmacher@lrz.uni-muenchen.de\"" - } - ], - "title": "Nucleocapsid-specific T cell responses associate with control of SARS-CoV-2 in the upper airways before seroconversion", - "issue": "1", - "volume": "14", - "publisher": "Springer Science and Business Media LLC", - "published": "2023-05-24", - "author": [ - "Eser T. M.", - "Baranov O.", - "Huth M.", - "Ahmed M. I. M.", - "Deák F." - ] - }, - { - "doi": "10.1016/j.lanepe.2023.100646", - "available_items": [ - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Data processing code is available on GitHub", - "data_type": [ - "Serology data", - "Health data" - ], - "data_url": "https://github.com/johanssonresearch/Correlate-of-vaccine-protection-against-fatal-COVID-19" - } - ], - "title": "Vaccine-induced correlate of protection against fatal COVID-19 in older and frail adults during waves of neutralization-resistant variants of concern: an observational study", - "issue": "", - "volume": "", - "publisher": "Elsevier BV", - "published": "2023-05-15", - "author": [ - "Vikström L.", - "Fjällström P.", - "Gwon Y.", - "Sheward D. J.", - "Wigren-Byström J." - ] - }, - { - "doi": "10.1128/jvi.01992-22", - "available_items": [ - { - "type": "data", - "repo_name": "zenodo", - "accession_number": "7826331", - "description": "Movies and data to accompany the study", - "data_type": [ - "Imaging data", - "Biochemistry data", - "Genomics & transcriptomics data", - "Health data" - ], - "data_url": "https://zenodo.org/record/7826331" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Image and time series analysis code written in MATLAB is available on GitHub", - "data_type": [ - "Imaging data", - "Biochemistry data", - "Genomics & transcriptomics data", - "Health data" - ], - "data_url": "https://github.com/kassonlab/micrograph-spot-analysis" - } - ], - "title": "Single-Virus Fusion Measurements Reveal Multiple Mechanistically Equivalent Pathways for SARS-CoV-2 Entry", - "issue": "5", - "volume": "97", - "publisher": "American Society for Microbiology", - "published": "2023-05-31", - "author": [ - "Sengar A.", - "Cervantes M.", - "Bondalapati S. T.", - "Hess T.", - "Kasson P. M." - ] - }, - { - "doi": "10.1038/s41598-023-33168-1", - "available_items": [ - { - "type": "data", - "repo_name": "GenBank", - "accession_number": "", - "description": "Nucleotide sequence are available as assembled FASTA consensus sequences at GenBank. Accession-ID: OP585690-OP585783", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://www.ncbi.nlm.nih.gov/nuccore/?term=OP585690:OP585783[pacc]" - } - ], - "title": "Comparison of SARS-CoV-2 whole genome sequencing using tiled amplicon enrichment and bait hybridization", - "issue": "1", - "volume": "13", - "publisher": "Springer Science and Business Media LLC", - "published": "2023-04-20", - "author": [ - "Koskela von Sydow A.", - "Lindqvist C. M.", - "Asghar N.", - "Johansson M.", - "Sundqvist M." - ] - }, - { - "doi": "10.3389/fviro.2023.1128253", - "available_items": [ - { - "type": "data", - "repo_name": "GenBank", - "accession_number": "ON086926", - "description": "The HC sequences of CAB-F52 anti-SARS-CoV-2 immunoglobulin heavy chain variable region mRNA", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://www.ncbi.nlm.nih.gov/nuccore/ON086926" - }, - { - "type": "data", - "repo_name": "GenBank", - "accession_number": "ON086941", - "description": "The LC sequences of CAB-F52 anti-SARS-CoV-2 immunoglobulin heavy chain variable region mRNA", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://www.ncbi.nlm.nih.gov/nuccore/ON086941.1/" - }, - { - "type": "data", - "repo_name": "ProteomeXchange", - "accession_number": "PXD031945", - "description": "The hydrogen–deuterium exchange mass spectrometry data", - "data_type": [ - "Protein data" - ], - "data_url": "https://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD031945" - } - ], - "title": "Frequent use of IGHV3-30-3 in SARS-CoV-2 neutralizing antibody responses", - "issue": "", - "volume": "3", - "publisher": "Frontiers Media SA", - "published": "2023-03-01", - "author": [ - "Pushparaj P.", - "Nicoletto A.", - "Castro Dopico X.", - "Sheward D. J.", - "Kim S." - ] - }, - { - "doi": "10.1038/s41380-023-02062-7", - "available_items": [ - { - "type": "data", - "repo_name": "OSF", - "accession_number": "", - "description": "Anonymised databases with the individual participant data and the metadata for Bayesian analyses, along with a data dictionary", - "data_type": [ - "Other data" - ], - "data_url": "https://osf.io/m5cvj/" - }, - { - "type": "protocol", - "repo_name": "OSF", - "accession_number": "", - "description": "The Study Protocol and Bayesian Statistical Analysis Plan", - "data_type": [ - "Other data" - ], - "data_url": "https://osf.io/2xn5m/" - } - ], - "title": "Treating intrusive memories after trauma in healthcare workers: a Bayesian adaptive randomised trial developing an imagery-competing task intervention", - "issue": "", - "volume": "", - "publisher": "Springer Science and Business Media LLC", - "published": "2023-04-26", - "author": [ - "Ramineni V.", - "Millroth P.", - "Iyadurai L.", - "Jaki T.", - "Kingslake J." - ] - }, - { - "doi": "10.1016/j.tbench.2023.100088", - "available_items": [ - { - "type": "data", - "repo_name": "Mendeley Data", - "accession_number": "", - "description": "COVID19, Pneumonia, and Normal Chest X-ray Posteroanterior Dataset", - "data_type": [ - "Health data" - ], - "data_url": "https://data.mendeley.com/datasets/mxc6vb7svm" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Scripts used in this project to analyse the datasets", - "data_type": [ - "Health data" - ], - "data_url": "https://github.com/Asraf047/COVID19-CNN-RNN" - } - ], - "title": "Diagnosis of COVID-19 from X-rays using combined CNN-RNN architecture with transfer learning", - "issue": "4", - "volume": "2", - "publisher": "Elsevier BV", - "published": "2023-03-27", - "author": [ - "Islam M. M.", - "Islam M. Z.", - "Asraf A.", - "Al-Rakhami M. S.", - "Ding W." - ] - }, - { - "doi": "10.1371/journal.pgph.0001110", - "available_items": [ - { - "type": "data", - "repo_name": "FigShare", - "accession_number": "", - "description": "Fully anonymised data from two cross-sectional surveys", - "data_type": [ - "Public health data", - "Other data" - ], - "data_url": "https://figshare.com/articles/dataset/Community_survey_data_from_the_DClare_Project_Faridpur_District_Bangladesh/19337831/1" - } - ], - "title": "Changes in non-communicable diseases, diet and exercise in a rural Bangladesh setting before and after the first wave of COVID-19", - "issue": "9", - "volume": "2", - "publisher": "Public Library of Science (PLoS)", - "published": "2022-09-30", - "author": [ - "King C.", - "Shaha S. K.", - "Morrison J.", - "Ahmed N.", - "Kuddus A." - ] - }, - { - "doi": "10.1371/journal.pgph.0001204", - "available_items": [ - { - "type": "data", - "repo_name": "Zenodo", - "accession_number": "", - "description": "Municipal-level vaccination data compiled from several publicly available data sources", - "data_type": [ - "Public health data" - ], - "data_url": "https://zenodo.org/record/6983689#YvVPOHZBw2z" - } - ], - "title": "Variations in vaccination uptake: COVID-19 vaccination rates in Swedish municipalities", - "issue": "10", - "volume": "2", - "publisher": "Public Library of Science (PLoS)", - "published": "2022-10-20", - "author": [ - "Larsson E. C.", - "Wittberg E.", - "Lundåsen S. W." - ] - }, - { - "doi": "10.3390/ijerph20043642", - "available_items": [ - { - "type": "data", - "repo_name": "Figshare", - "accession_number": "", - "description": "Questionaire data on levels of physical activity and sedentary behaviour", - "data_type": [ - "Social science and humanities data", - "Health data" - ], - "data_url": "https://doi.org/10.6084/m9.figshare.21802941.v1" - } - ], - "title": "How Have Physical Activity and Sedentary Behavior, Changed during the COVID-19 Pandemic? A Swedish Repeated Cross-Sectional Design Study", - "issue": "4", - "volume": "20", - "publisher": "MDPI AG", - "published": "2023-02-18", - "author": [ - "Lindberg D.", - "Elvén M.", - "Nilsson K. W.", - "Von Heideken Wågert P.", - "Stier J." - ] - }, - { - "doi": "10.3390/ijerph20043559", - "available_items": [ - { - "type": "code", - "repo_name": "Figshare", - "accession_number": "", - "description": "Codes for analysis", - "data_type": [ - "Social science and humanities data" - ], - "data_url": "https://figshare.com/articles/software/Nature_visits_and_covid19/22056869/1" - } - ], - "title": "Visiting Urban Green Space and Orientation to Nature Is Associated with Better Wellbeing during COVID-19", - "issue": "4", - "volume": "20", - "publisher": "MDPI AG", - "published": "2023-02-17", - "author": [ - "Lin B. B.", - "Chang C.", - "Andersson E.", - "Astell-Burt T.", - "Gardner J." - ] - }, - { - "doi": "10.12688/wellcomeopenres.17403.3", - "available_items": [ - { - "type": "data", - "repo_name": "Zenodo", - "accession_number": "", - "description": "Characteristics and outcomes of COVID-19 patients with COPD", - "data_type": [ - "Health data" - ], - "data_url": "https://doi.org/10.5281/zenodo.5729423" - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Aggregate data from COVID-19 patients with COPD", - "data_type": [ - "Health data" - ], - "data_url": "https://data.ohdsi.org/Covid19CharacterizationCharybdis/" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Code used for analysis", - "data_type": [ - "Health data" - ], - "data_url": "https://github.com/ohdsi-studies/Covid19CharacterizationCharybdis" - }, - { - "type": "code", - "repo_name": "Zenodo", - "accession_number": "", - "description": "Archived code used for analysis", - "data_type": [ - "Health data" - ], - "data_url": "https://doi.org/10.5281/zenodo.5779264" - } - ], - "title": "Characteristics and outcomes of COVID-19 patients with COPD from the United States, South Korea, and Europe", - "issue": "", - "volume": "7", - "publisher": "F1000 Research Ltd", - "published": "2023-02-24", - "author": [ - "Moreno-Martos D.", - "Verhamme K.", - "Ostropolets A.", - "Kostka K.", - "Duarte-Sales T." - ] - }, - { - "doi": "10.1038/s42255-023-00742-w", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Summary statistics related to body mass index (BMI)", - "data_type": [ - "Health data", - "Genomics & transcriptomics data", - "Protein data" - ], - "data_url": "https://portals.broadinstitute.org/collaboration/giant/" - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Summary statistics on plasma proteome from the deCODE study", - "data_type": [ - "Health data", - "Genomics & transcriptomics data", - "Protein data" - ], - "data_url": "https://www.decode.com/summarydata/" - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Summary statistics related to COVID-19 outcomes", - "data_type": [ - "Health data", - "Genomics & transcriptomics data", - "Protein data" - ], - "data_url": "https://www.covid19hg.org/results/r7/" - }, - { - "type": "data", - "repo_name": "GTEx", - "accession_number": "phs000424.v9", - "description": "Long Read RNASeq data", - "data_type": [ - "Health data", - "Genomics & transcriptomics data", - "Protein data" - ], - "data_url": "https://gtexportal.org/home/datasets/" - }, - { - "type": "data", - "repo_name": "OpenGWAS", - "accession_number": "ukb-b-8909", - "description": "Body fat percentage data", - "data_type": [ - "Health data", - "Genomics & transcriptomics data", - "Protein data" - ], - "data_url": "https://gwas.mrcieu.ac.uk/datasets/ukb-b-8909/" - }, - { - "type": "data", - "repo_name": "OpenGWAS", - "accession_number": "ukb-b-19393", - "description": "Whole body fat mass data", - "data_type": [ - "Health data", - "Genomics & transcriptomics data", - "Protein data" - ], - "data_url": "https://gwas.mrcieu.ac.uk/datasets/ukb-b-19393/" - }, - { - "type": "data", - "repo_name": "OpenGWAS", - "accession_number": "ukb-b-13354", - "description": "Whole body fat-free mass data", - "data_type": [ - "Health data", - "Genomics & transcriptomics data", - "Protein data" - ], - "data_url": "https://gwas.mrcieu.ac.uk/datasets/ukb-b-13354/" - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "scRNA-seq data of COVID-19 lung autopsy samples", - "data_type": [ - "Health data", - "Genomics & transcriptomics data", - "Protein data" - ], - "data_url": "https://singlecell.broadinstitute.org/single_cell/study/SCP1052/covid-19-lung-autopsy-samples" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Custom analysis codes", - "data_type": [ - "Health data", - "Genomics & transcriptomics data", - "Protein data" - ], - "data_url": "https://github.com/satoshi-yoshiji/TwostepMR_obesity_COVID/" - } - ], - "title": "Proteome-wide Mendelian randomization implicates nephronectin as an actionable mediator of the effect of obesity on COVID-19 severity", - "issue": "2", - "volume": "5", - "publisher": "Springer Science and Business Media LLC", - "published": "2023-02-20", - "author": [ - "Yoshiji S.", - "Butler-Laporte G.", - "Lu T.", - "Willett J. D. S.", - "Su C." - ] - }, - { - "doi": "10.3389/fphar.2023.1090717", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Supplementary material including information on proteomics, mutations, T-cell epitope prediction, and much more, including accession numbers for other open data sources", - "data_type": [ - "Genomics & transcriptomics data", - "Protein data" - ], - "data_url": "https://www.frontiersin.org/articles/10.3389/fphar.2023.1090717/full#supplementary-material" - } - ], - "title": "Variant-specific deleterious mutations in the SARS-CoV-2 genome reveal immune responses and potentials for prophylactic vaccine development", - "issue": "", - "volume": "14", - "publisher": "Frontiers Media SA", - "published": "2023-02-07", - "author": [ - "Islam M. A.", - "Shahi S.", - "Marzan A. A.", - "Amin M. R.", - "Hasan M. N." - ] - }, - { - "doi": "10.3390/ijerph20043040", - "available_items": [ - { - "type": "data", - "repo_name": "GitHub", - "accession_number": "", - "description": "Data related to development of a statistical methodology for predicting true daily quantities and their uncertainty, estimated using historical reporting delays", - "data_type": [ - "Other data" - ], - "data_url": "https://github.com/adamaltmejd/covid_reporting_delay_prediction" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "R code related to development of a statistical methodology for predicting true daily quantities and their uncertainty, estimated using historical reporting delays", - "data_type": [ - "Other data" - ], - "data_url": "https://github.com/adamaltmejd/covid_reporting_delay_prediction" - } - ], - "title": "Nowcasting COVID-19 Statistics Reported with Delay: A Case-Study of Sweden and the UK", - "issue": "4", - "volume": "20", - "publisher": "MDPI AG", - "published": "2023-02-09", - "author": [ - "Altmejd A.", - "Rocklöv J.", - "Wallin J." - ] - }, - { - "doi": "10.3389/fpubh.2023.1052946", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Information on open data sources used e.g. for socioeconomic factors, environment, biodiveristy, health, among others.", - "data_type": [ - "Other data", - "Health data", - "Public health data" - ], - "data_url": "https://www.frontiersin.org/articles/10.3389/fpubh.2023.1052946/full#h12" - } - ], - "title": "Monkeypox outbreaks in the context of the COVID-19 pandemic: Network and clustering analyses of global risks and modified SEIR prediction of epidemic trends", - "issue": "", - "volume": "11", - "publisher": "Frontiers Media SA", - "published": "2023-01-24", - "author": [ - "Gao J.", - "Zhou C.", - "Liang H.", - "Jiao R.", - "Wheelock Å. M." - ] - }, - { - "doi": "10.1016/j.xgen.2021.100065", - "available_items": [ - { - "type": "data", - "repo_name": "Gene Expression Omnibus", - "accession_number": "GSE185715", - "description": "Genome-wide Spatial Expression Profiling in Formalin-fixed Tissues", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE185715" - }, - { - "type": "data", - "repo_name": "Mendeley", - "accession_number": "", - "description": "Processed genome-wide spatial expression profiling data", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://data.mendeley.com/datasets/xjtv62ncwr/1" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "FFPE mouse brain spatial transcriptomics data explorer app", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://github.com/ludvigla/FFPE_mouse_brain_explorer" - }, - { - "type": "code", - "repo_name": "Mendeley", - "accession_number": "", - "description": "Original analysis code", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://data.mendeley.com/datasets/xjtv62ncwr/1" - } - ], - "title": "Genome-wide spatial expression profiling in formalin-fixed tissues", - "issue": "3", - "volume": "1", - "publisher": "Elsevier BV", - "published": "2022-08-05", - "author": [ - "Gracia Villacampa E.", - "Larsson L.", - "Mirzazadeh R.", - "Kvastad L.", - "Andersson A." - ] - }, - { - "doi": "10.1371/journal.pdig.0000007", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Protein quantities table along with the associated metadata", - "data_type": [ - "Protein data" - ], - "data_url": "https://europepmc.org/article/MED/36812516#sec011" - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Input proteomics data for training machine learning models", - "data_type": [ - "Protein data" - ], - "data_url": "https://europepmc.org/articles/PMC9931303/bin/pdig.0000007.s005.zip" - }, - { - "type": "code", - "repo_name": "", - "accession_number": "", - "description": "Scripts training machine learning models", - "data_type": [ - "Protein data" - ], - "data_url": "https://europepmc.org/articles/PMC9931303/bin/pdig.0000007.s005.zip" - }, - { - "type": "data", - "repo_name": "ProteomeXchange Consortium", - "accession_number": "PXD029009", - "description": "Mass spectrometry proteomics data used for survival analysis", - "data_type": [ - "Protein data" - ], - "data_url": "http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD029009" - } - ], - "title": "A proteomic survival predictor for COVID-19 patients in intensive care", - "issue": "1", - "volume": "1", - "publisher": "Public Library of Science (PLoS)", - "published": "2022-01-18", - "author": [ - "Demichev V.", - "Tober-Lau P.", - "Nazarenko T.", - "Lemke O.", - "Kaur Aulakh S." - ] - }, - { - "doi": "10.1038/s41597-022-01811-7", - "available_items": [ - { - "type": "data", - "repo_name": "Open Science Framework", - "accession_number": "", - "description": "Data used in the Shiny app for The Psychological Science Accelerator's COVID-19 Rapid-Response Project", - "data_type": [ - "Social science and humanities data" - ], - "data_url": "https://osf.io/gvw56/" - }, - { - "type": "code", - "repo_name": "Open Science Framework", - "accession_number": "", - "description": "Code for the Shiny app for The Psychological Science Accelerator's COVID-19 Rapid-Response Project", - "data_type": [ - "Social science and humanities data" - ], - "data_url": "https://osf.io/gvw56/" - } - ], - "title": "The Psychological Science Accelerator’s COVID-19 rapid-response dataset", - "issue": "1", - "volume": "10", - "publisher": "Springer Science and Business Media LLC", - "published": "2023-02-11", - "author": [ - "Buchanan E. M.", - "Lewis S. C.", - "Paris B.", - "Forscher P. S.", - "Pavlacic J. M." - ] - }, - { - "doi": "10.1016/j.concog.2023.103464", - "available_items": [ - { - "type": "data", - "repo_name": "OSF", - "accession_number": "", - "description": "Students survey data on COVID-19 status", - "data_type": [ - "Social science and humanities data" - ], - "data_url": "https://osf.io/9stbm/" - } - ], - "title": "COVID-19 infection does not seem to affect cognition in college students", - "issue": "", - "volume": "108", - "publisher": "Elsevier BV", - "published": "2023-01-30", - "author": [ - "Francis G.", - "Thunell E." - ] - }, - { - "doi": "10.1038/s41597-022-01880-8", - "available_items": [ - { - "type": "data", - "repo_name": "OSF", - "accession_number": "", - "description": "Familydemic survey data related to the work and family nexus", - "data_type": [ - "Social science and humanities data" - ], - "data_url": "https://osf.io/mjfz3/" - } - ], - "title": "Familydemic Cross Country and Gender Dataset on work and family outcomes during COVID-19 pandemic", - "issue": "1", - "volume": "10", - "publisher": "Springer Science and Business Media LLC", - "published": "2023-01-03", - "author": [ - "Kurowska A.", - "Barardehi I. H.", - "Fuller S.", - "Petts R. J.", - "Kaufman G." - ] - }, - { - "doi": "10.1038/s41586-022-05512-4", - "available_items": [ - { - "type": "data", - "repo_name": "Zenodo", - "accession_number": "", - "description": "Randomised controlled trial data from Sweden and United States for COVID-19 first dose vaccination", - "data_type": [ - "Social science and humanities data", - "Other data" - ], - "data_url": "https://zenodo.org/record/7214856#.Y9obkezMKX0" - }, - { - "type": "code", - "repo_name": "Zenodo", - "accession_number": "", - "description": "Analyses were conducted using STATA 16, the code to replicate the analysis is in the article", - "data_type": [ - "Social science and humanities data", - "Other data" - ], - "data_url": "https://zenodo.org/record/7214856#.Y9obkezMKX0" - } - ], - "title": "Financial incentives for vaccination do not have negative unintended consequences", - "issue": "7944", - "volume": "613", - "publisher": "Springer Science and Business Media LLC", - "published": "2023-01-11", - "author": [ - "Schneider F. H.", - "Campos-Mercade P.", - "Meier S.", - "Pope D.", - "Wengström E." - ] - }, - { - "doi": "10.1371/journal.pone.0280355", - "available_items": [ - { - "type": "data", - "repo_name": "Github", - "accession_number": "", - "description": "Aggregated data of COVID-19 mortality and long-term air pollution concentrations", - "data_type": [ - "Public health data", - "Other data" - ], - "data_url": "https://github.com/LopezFeldman/Airpollution_Covid19" - }, - { - "type": "code", - "repo_name": "Github", - "accession_number": "", - "description": "Stata scripts used to compile the statitics", - "data_type": [ - "Public health data", - "Other data" - ], - "data_url": "https://github.com/LopezFeldman/Airpollution_Covid19" - } - ], - "title": "Association between long-term air pollution exposure and COVID-19 mortality in Latin America", - "issue": "1", - "volume": "18", - "publisher": "Public Library of Science (PLoS)", - "published": "2023-01-17", - "author": [ - "Bonilla J. A.", - "Lopez-Feldman A.", - "Pereda P. C.", - "Rivera N. M.", - "Ruiz-Tagle J. C." - ] - }, - { - "doi": "10.3389/fimmu.2022.1079995", - "available_items": [ - { - "type": "data", - "repo_name": "NCBI", - "accession_number": "PRJNA900274", - "description": "All genomic datasets from this project are available as part of an NCBI BioProject", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://www.ncbi.nlm.nih.gov/biosample?LinkName=bioproject_biosample_all&from_uid=900274" - } - ], - "title": "Persistence of salivary antibody responses after COVID-19 vaccination is associated with oral microbiome variation in both healthy and people living with HIV", - "issue": "", - "volume": "13", - "publisher": "Frontiers Media SA", - "published": "2023-01-10", - "author": [ - "Ghorbani M.", - "Al-Manei K.", - "Naud S.", - "Healy K.", - "Gabarrini G." - ] - }, - { - "doi": "10.1007/s44155-022-00027-9", - "available_items": [ - { - "type": "data", - "repo_name": "FigShare", - "accession_number": "", - "description": "Results of a Qualatrics questionnaire related to perceived risk of viral infection with different social distances.", - "data_type": [ - "Social science and humanities data" - ], - "data_url": "https://su.figshare.com/articles/dataset/On_Interpersonal_Distance_Time_of_a_Conversation_and_Perceived_Virus_Exposure/20472165/1" - } - ], - "title": "Perceived Corona virus exposure as a function of interpersonal distance and time of a conversation", - "issue": "1", - "volume": "2", - "publisher": "Springer Science and Business Media LLC", - "published": "2022-12-05", - "author": [ - "Svenson O." - ] - }, - { - "doi": "10.1101/2022.11.25.22282676", - "available_items": [ - { - "type": "data", - "repo_name": "Zenodo", - "accession_number": "", - "description": "Results of a multi-country longitudinal social contact survey exploring the influence of COVID-19 vaccination status and risk perceptions related to SARS-CoV-2 on social contact.", - "data_type": [ - "Social science and humanities data" - ], - "data_url": "http://www.socialcontactdata.org/data/" - } - ], - "title": "The influence of COVID-19 risk perception and vaccination status on the number of social contacts across Europe: insights from the CoMix study", - "issue": "", - "volume": "", - "publisher": "Cold Spring Harbor Laboratory", - "published": "2022-11-29", - "author": [ - "Wambua J.", - "Loedy N.", - "Jarvis C. I.", - "Wong K. L.", - "Faes C." - ] - }, - { - "doi": "10.1038/s41467-022-35641-3", - "available_items": [ - { - "type": "data", - "repo_name": "Zenodo", - "accession_number": "", - "description": "Models of SARS-CoV-2 virus spike protein bound to 1-3 of ACE2 receptors embedded in lipid nanodisks.", - "data_type": [ - "Protein data" - ], - "data_url": "https://zenodo.org/record/7401939#.Y8AFIy8w2u4" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Code for simulation of high speed AFM imaging.", - "data_type": [ - "Protein data" - ], - "data_url": "https://github.com/matsikora/AFM_emulator" - } - ], - "title": "Force-tuned avidity of spike variant-ACE2 interactions viewed on the single-molecule level", - "issue": "1", - "volume": "13", - "publisher": "Springer Science and Business Media LLC", - "published": "2022-12-24", - "author": [ - "Zhu R.", - "Canena D.", - "Sikora M.", - "Klausberger M.", - "Seferovic H." - ] - }, - { - "doi": "10.1186/s12982-022-00119-6", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Sensitivity analysis and mortality rate data available in the paper.", - "data_type": [ - "Public health data", - "Health data" - ], - "data_url": "https://europepmc.org/article/MED/36550573#id605303" - }, - { - "type": "data", - "repo_name": "Zenodo", - "accession_number": "", - "description": "Mortality rate data.", - "data_type": [ - "Public health data", - "Health data" - ], - "data_url": "http://doi.org/10.5281/zenodo.5136641" - }, - { - "type": "code", - "repo_name": "Zenodo", - "accession_number": "", - "description": "Analysis code", - "data_type": [ - "Public health data", - "Health data" - ], - "data_url": "http://doi.org/10.5281/zenodo.5136641" - } - ], - "title": "Dynamics of COVID-19 progression and the long-term influences of measures on pandemic outcomes", - "issue": "1", - "volume": "19", - "publisher": "Springer Science and Business Media LLC", - "published": "2022-12-22", - "author": [ - "Lan Y.", - "Yin L.", - "Wang X." - ] - }, - { - "doi": "10.1186/s13148-022-01398-1", - "available_items": [ - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Analysis and visualisation scripts", - "data_type": [ - "Health data", - "Genomics & transcriptomics data", - "Other data" - ], - "data_url": "https://github.com/Lerm-Lab/PACS" - } - ], - "title": "Defining post-acute COVID-19 syndrome (PACS) by an epigenetic biosignature in peripheral blood mononuclear cells", - "issue": "1", - "volume": "14", - "publisher": "Springer Science and Business Media LLC", - "published": "2022-12-14", - "author": [ - "Nikesjö F.", - "Sayyab S.", - "Karlsson L.", - "Apostolou E.", - "Rosén A." - ] - }, - { - "doi": "10.1371/journal.pcbi.1010767", - "available_items": [ - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Analysis scripts R", - "data_type": [ - "Public health data" - ], - "data_url": "https://github.com/fannybergstrom/nowcasting_covid19" - }, - { - "type": "data", - "repo_name": "GitHub", - "accession_number": "", - "description": "COVID-19 surveillance data", - "data_type": [ - "Public health data" - ], - "data_url": "https://github.com/fannybergstrom/nowcasting_covid19" - } - ], - "title": "Bayesian nowcasting with leading indicators applied to COVID-19 fatalities in Sweden", - "issue": "12", - "volume": "18", - "publisher": "Public Library of Science (PLoS)", - "published": "2022-12-07", - "author": [ - "Bergström F.", - "Günther F.", - "Höhle M.", - "Britton T." - ] - }, - { - "doi": "10.1371/journal.pcbi.1010078", - "available_items": [ - { - "type": "data", - "repo_name": "GitHub", - "accession_number": "", - "description": "Incidence data on which the model is based.", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://github.com/yunPKU/infer_heterogeneity_from_incidence" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Code for instant-individual heterogeneity model to estimate real-time transmission heterogeneity from incidence data.", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://github.com/yunPKU/infer_heterogeneity_from_incidence" - } - ], - "title": "Monitoring real-time transmission heterogeneity from incidence data", - "issue": "12", - "volume": "18", - "publisher": "Public Library of Science (PLoS)", - "published": "2022-12-01", - "author": [ - "Zhang Y.", - "Britton T.", - "Zhou X." - ] - }, - { - "doi": "10.1016/j.immuni.2022.12.005", - "available_items": [ - { - "type": "data", - "repo_name": "Figshare", - "accession_number": "", - "description": "Individualised IGHV Genotype Sequences of 14 SARS-CoV-2 Convalescent Donors", - "data_type": [ - "Genomics & transcriptomics data", - "Protein data" - ], - "data_url": "http://doi.org/10.17044/scilifelab.19317512" - }, - { - "type": "data", - "repo_name": "ProteomeXchange", - "accession_number": "", - "description": "Mass spectrometry raw files and HDX analysis", - "data_type": [ - "Genomics & transcriptomics data", - "Protein data" - ], - "data_url": "http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD031945" - }, - { - "type": "data", - "repo_name": "PDB", - "accession_number": "8A99", - "description": "SARS Cov2 Spike in 1-up conformation complex with Fab47", - "data_type": [ - "Genomics & transcriptomics data", - "Protein data" - ], - "data_url": "https://www.rcsb.org/structure/unreleased/8A99" - }, - { - "type": "data", - "repo_name": "PDB", - "accession_number": "8A94", - "description": "SARS CoV2 Spike in the 2-up state in complex with Fab47", - "data_type": [ - "Genomics & transcriptomics data", - "Protein data" - ], - "data_url": "https://www.rcsb.org/structure/unreleased/8A94" - }, - { - "type": "data", - "repo_name": "PDB", - "accession_number": "8A96", - "description": "SARS Cov2 Spike RBD in complex with Fab47", - "data_type": [ - "Genomics & transcriptomics data", - "Protein data" - ], - "data_url": "https://www.rcsb.org/structure/unreleased/8A96" - }, - { - "type": "data", - "repo_name": "Electron Microscopy Data Bank", - "accession_number": "EMD-15273", - "description": "SARS Cov2 Spike in 1-up conformation complex with Fab47", - "data_type": [ - "Genomics & transcriptomics data", - "Protein data" - ], - "data_url": "https://www.ebi.ac.uk/emdb/search/EMD-15273" - }, - { - "type": "data", - "repo_name": "Electron Microscopy Data Bank", - "accession_number": "EMD-15269", - "description": "SARS CoV2 Spike in the 2-up state in complex with Fab47", - "data_type": [ - "Genomics & transcriptomics data", - "Protein data" - ], - "data_url": "https://www.ebi.ac.uk/emdb/search/EMD-15269" - }, - { - "type": "data", - "repo_name": "Electron Microscopy Data Bank", - "accession_number": "EMD-15271", - "description": "SARS Cov2 Spike RBD in complex with Fab47", - "data_type": [ - "Genomics & transcriptomics data", - "Protein data" - ], - "data_url": "https://www.ebi.ac.uk/emdb/search/EMD-15271" - }, - { - "type": "data", - "repo_name": "Mendeley", - "accession_number": "", - "description": "Supplemental data, including Cryo-EM models", - "data_type": [ - "Genomics & transcriptomics data", - "Protein data" - ], - "data_url": "https://data.mendeley.com/datasets/mg7p5msrfs/1" - } - ], - "title": "Immunoglobulin germline gene polymorphisms influence the function of SARS-CoV-2 neutralizing antibodies", - "issue": "1", - "volume": "56", - "publisher": "Elsevier BV", - "published": "2023-01-10", - "author": [ - "Pushparaj P.", - "Nicoletto A.", - "Sheward D. J.", - "Das H.", - "Castro Dopico X." - ] - }, - { - "doi": "10.1186/s13049-022-01056-8", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Literature review data realted to disaster training programs for medical first responders.", - "data_type": [ - "Social science and humanities data" - ], - "data_url": "https://europepmc.org/article/MED/36566227#id696386" - } - ], - "title": "Preparing medical first responders for crises: a systematic literature review of disaster training programs and their effectiveness", - "issue": "1", - "volume": "30", - "publisher": "Springer Science and Business Media LLC", - "published": "2022-12-24", - "author": [ - "Baetzner A. S.", - "Wespi R.", - "Hill Y.", - "Gyllencreutz L.", - "Sauter T. C." - ] - }, - { - "doi": "10.1371/journal.pgen.1010367", - "available_items": [ - { - "type": "data", - "repo_name": "GWAS Catalog", - "accession_number": "GCST90132193", - "description": "Single variant association studies summary statistics", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://www.ebi.ac.uk/gwas/studies/GCST90132193" - }, - { - "type": "data", - "repo_name": "GWAS Catalog", - "accession_number": "GCST90132194", - "description": "Single variant association studies summary statistics", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://www.ebi.ac.uk/gwas/studies/GCST90132194" - }, - { - "type": "data", - "repo_name": "GWAS Catalog", - "accession_number": "GCST90132195", - "description": "Single variant association studies summary statistics", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://www.ebi.ac.uk/gwas/studies/GCST90132195" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Analysis scripts", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://github.com/DrGBL/WES.WGS" - } - ], - "title": "Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative", - "issue": "11", - "volume": "18", - "publisher": "Public Library of Science (PLoS)", - "published": "2022-11-03", - "author": [ - "Butler-Laporte G.", - "Povysil G.", - "Kosmicki J. A.", - "Cirulli E. T.", - "Drivas T." - ] - }, - { - "doi": "10.1371/journal.ppat.1010931", - "available_items": [ - { - "type": "data", - "repo_name": "Gene Expression Omnibus", - "accession_number": "GSE196472", - "description": "Raw sequencing data", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE196472" - }, - { - "type": "data", - "repo_name": "Gene Expression Omnibus", - "accession_number": "GSE196473", - "description": "Processed sequencing data", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE196473" - } - ], - "title": "Cross-protection against African swine fever virus upon intranasal vaccination is associated with an adaptive-innate immune crosstalk", - "issue": "11", - "volume": "18", - "publisher": "Public Library of Science (PLoS)", - "published": "2022-11-09", - "author": [ - "Bosch-Camós L.", - "Alonso U.", - "Esteve-Codina A.", - "Chang C.", - "Martín-Mur B." - ] - }, - { - "doi": "10.1038/s41598-022-23415-2", - "available_items": [ - { - "type": "data", - "repo_name": "Open Science Framework", - "accession_number": "", - "description": "All survey data and study material used in this project", - "data_type": [ - "Social science and humanities data" - ], - "data_url": "https://osf.io/c8zhn/" - }, - { - "type": "code", - "repo_name": "Open Science Framework", - "accession_number": "Code used for analysis", - "description": "", - "data_type": [ - "Social science and humanities data" - ], - "data_url": "https://osf.io/c8zhn/" - } - ], - "title": "Acute anxiety during the COVID-19 pandemic was associated with higher levels of everyday altruism", - "issue": "1", - "volume": "12", - "publisher": "Springer Science and Business Media LLC", - "published": "2022-11-03", - "author": [ - "Vieira J. B.", - "Pierzchajlo S.", - "Jangard S.", - "Marsh A. A.", - "Olsson A." - ] - }, - { - "doi": "10.1371/journal.pone.0277470", - "available_items": [ - { - "type": "data", - "repo_name": "Open Science Framework", - "accession_number": "", - "description": "Survey data from 321 early career dementia researchers, including relevant socialdemographic characteristics", - "data_type": [ - "Social science and humanities data" - ], - "data_url": "https://osf.io/fr8j2/" - } - ], - "title": "Impact of the COVID-19 pandemic on early career dementia researchers: A global online survey", - "issue": "11", - "volume": "17", - "publisher": "Public Library of Science (PLoS)", - "published": "2022-11-09", - "author": [ - "Bartels S. L.", - "Shaaban C. E.", - "Brum W. S.", - "Welikovitch L. A.", - "Folarin R." - ] - }, - { - "doi": "10.3389/fpubh.2022.996036", - "available_items": [ - { - "type": "data", - "repo_name": "OSF", - "accession_number": "", - "description": "Data for collectivism and mobility", - "data_type": [ - "Social science and humanities data" - ], - "data_url": "https://osf.io/xt5qs/?view_only=e7da6b6f69f24bc7b3a9656d00cebb10" - } - ], - "title": "Collectivism reduces objective mobility trends to public areas during the COVID-19 pandemic", - "issue": "", - "volume": "10", - "publisher": "Frontiers Media SA", - "published": "2022-09-28", - "author": [ - "Dang J.", - "Xiao S." - ] - }, - { - "doi": "10.1038/s41380-022-01786-2", - "available_items": [ - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Source code to reproduce the findings", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://github.com/SellgrenLab/organoid-Covid19" - } - ], - "title": "SARS-CoV-2 promotes microglial synapse elimination in human brain organoids", - "issue": "", - "volume": "", - "publisher": "Springer Science and Business Media LLC", - "published": "2022-10-05", - "author": [ - "Samudyata S.", - "Oliveira A. O.", - "Malwade S.", - "Rufino de Sousa N.", - "Goparaju S. K." - ] - }, - { - "doi": "10.1371/journal.pone.0275380", - "available_items": [ - { - "type": "protocol", - "repo_name": "OSF", - "accession_number": "", - "description": "The protocol for this study", - "data_type": [ - "Other data" - ], - "data_url": "https://osf.io/jgwvk/" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Data used to evaluate publications and model types, and the code used for analysis.", - "data_type": [ - "Other data" - ], - "data_url": "https://github.com/zavalis/transparency-indicators-inf-dis-models" - } - ], - "title": "A meta-epidemiological assessment of transparency indicators of infectious disease models", - "issue": "10", - "volume": "17", - "publisher": "Public Library of Science (PLoS)", - "published": "2022-10-07", - "author": [ - "Zavalis E. A.", - "Ioannidis J. P. A." - ] - }, - { - "doi": "10.1038/s41598-022-17303-y", - "available_items": [ - { - "type": "data", - "repo_name": "OSF", - "accession_number": "", - "description": "Processed and anonymised demographic and health data.", - "data_type": [ - "Social science and humanities data", - "Other data" - ], - "data_url": "https://osf.io/vr6p4/?view_only=070d364b489b43fca34bfcfd811ed22b" - } - ], - "title": "Development and cross-national investigation of a model explaining participation in WHO-recommended and placebo behaviours to prevent COVID-19 infection", - "issue": "1", - "volume": "12", - "publisher": "Springer Science and Business Media LLC", - "published": "2022-10-21", - "author": [ - "Kłosowska J.", - "Bajcar E. A.", - "Bieniek H.", - "Brączyk J.", - "Joshanloo M." - ] - }, - { - "doi": "10.1016/j.evolhumbehav.2022.09.003", - "available_items": [ - { - "type": "data", - "repo_name": "OSF", - "accession_number": "", - "description": "Data related to social motivation", - "data_type": [ - "Social science and humanities data", - "Other data" - ], - "data_url": "https://osf.io/p9z2a/" - } - ], - "title": "Family still matters: Human social motivation across 42 countries during a global pandemic", - "issue": "6", - "volume": "43", - "publisher": "Elsevier BV", - "published": "2022-11-02", - "author": [ - "Pick C. M.", - "Ko A.", - "Wormley A. S.", - "Wiezel A.", - "Kenrick D. T." - ] - }, - { - "doi": "10.1038/s41598-022-22711-1", - "available_items": [ - { - "type": "data", - "repo_name": "MR-base", - "accession_number": "ebi-a-GCST005536", - "description": "Exposure dataset for type 1 diabetes mellitus", - "data_type": [ - "Genomics & transcriptomics data", - "Other data" - ], - "data_url": "https://gwas.mrcieu.ac.uk/datasets/ebi-a-GCST005536" - }, - { - "type": "data", - "repo_name": "MR-base", - "accession_number": "ebi-a-GCST003156", - "description": "Exposure dataset for systemic lupus erythematosus", - "data_type": [ - "Genomics & transcriptomics data", - "Other data" - ], - "data_url": "https://gwas.mrcieu.ac.uk/datasets/ebi-a-GCST003156" - }, - { - "type": "data", - "repo_name": "MR-base", - "accession_number": "ebi-a-GCST005527", - "description": "Exposure dataset for psoriasis", - "data_type": [ - "Genomics & transcriptomics data", - "Other data" - ], - "data_url": "https://gwas.mrcieu.ac.uk/datasets/ebi-a-GCST005527" - }, - { - "type": "data", - "repo_name": "MR-base", - "accession_number": "ieu-b-18", - "description": "Exposure dataset for multiple sclerosis", - "data_type": [ - "Genomics & transcriptomics data", - "Other data" - ], - "data_url": "https://gwas.mrcieu.ac.uk/datasets/ieu-b-18" - }, - { - "type": "data", - "repo_name": "MR-base", - "accession_number": "ieu-a-1112", - "description": "Exposure dataset for primary sclerosing cholangitis", - "data_type": [ - "Genomics & transcriptomics data", - "Other data" - ], - "data_url": "https://gwas.mrcieu.ac.uk/datasets/ieu-a-1112" - }, - { - "type": "data", - "repo_name": "MR-base", - "accession_number": "ebi-a-GCST005581", - "description": "Exposure dataset for primary biliary cirrhosis", - "data_type": [ - "Genomics & transcriptomics data", - "Other data" - ], - "data_url": "https://gwas.mrcieu.ac.uk/datasets/ebi-a-GCST005581" - }, - { - "type": "data", - "repo_name": "COVID19-hg GWAS", - "accession_number": "", - "description": "Outcome datasets generated in the current study.", - "data_type": [ - "Genomics & transcriptomics data", - "Other data" - ], - "data_url": "https://www.covid19hg.org/results/r6/" - } - ], - "title": "A Mendelian randomization study of genetic predisposition to autoimmune diseases and COVID-19", - "issue": "1", - "volume": "12", - "publisher": "Springer Science and Business Media LLC", - "published": "2022-10-21", - "author": [ - "Li S.", - "Yuan S.", - "Schooling C. M.", - "Larsson S. C." - ] - }, - { - "doi": "10.1101/2022.10.06.22280777", - "available_items": [ - { - "type": "data", - "repo_name": "OSF", - "accession_number": "", - "description": "Anonymised databases with the individual participant data and the metadata for Bayesian analyses.", - "data_type": [ - "Social science and humanities data", - "Other data" - ], - "data_url": "https://osf.io/2xn5m/" - }, - { - "type": "code", - "repo_name": "OSF", - "accession_number": "", - "description": "Code used for data analysis.", - "data_type": [ - "Social science and humanities data", - "Other data" - ], - "data_url": "https://osf.io/2xn5m/" - } - ], - "title": "Treating intrusive memories after trauma in healthcare workers: a Bayesian adaptive randomised trial developing an imagery-competing task intervention", - "issue": "", - "volume": "", - "publisher": "Cold Spring Harbor Laboratory", - "published": "2022-10-07", - "author": [ - "Ramineni V.", - "Millroth P.", - "Iyadurai L.", - "Jaki T.", - "Kingslake J." - ] - }, - { - "doi": "10.15252/emmm.202215821", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Raw time series data related to vaccine efficacy, blood testing, and histology. ", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://ki.se/en/research/opencorona" - } - ], - "title": "A universal SARS‐CoV DNA vaccine inducing highly cross‐reactive neutralizing antibodies and T cells", - "issue": "", - "volume": "", - "publisher": "EMBO", - "published": "2022-09-02", - "author": [ - "Appelberg S.", - "Ahlén G.", - "Yan J.", - "Nikouyan N.", - "Weber S." - ] - }, - { - "doi": "10.12688/hrbopenres.13516.1", - "available_items": [ - { - "type": "data", - "repo_name": "FigShare", - "accession_number": "", - "description": "Long COVID Survey Data", - "data_type": [ - "Social science and humanities data" - ], - "data_url": "https://doi.org/10.6084/m9.figshare.19364828.v1" - }, - { - "type": "data", - "repo_name": "FigShare", - "accession_number": "", - "description": "Long COVID Survey questionnaire", - "data_type": [ - "Social science and humanities data" - ], - "data_url": "https://figshare.com/articles/online_resource/Long_COVID_Survey/19447919" - } - ], - "title": "Impact of Long COVID on health and quality of life", - "issue": "", - "volume": "5", - "publisher": "F1000 Research Ltd", - "published": "2022-04-22", - "author": [ - "O’ Mahony L.", - "Buwalda T.", - "Blair M.", - "Forde B.", - "Lunjani N." - ] - }, - { - "doi": "10.1038/s41598-022-19155-y", - "available_items": [ - { - "type": "data", - "repo_name": "GitHub", - "accession_number": "", - "description": "Data on direct and indirect indicators of transmission e.g. mobility data, number of calls to the national healthcare advice line and vaccination coverage.", - "data_type": [ - "Public health data" - ], - "data_url": "https://github.com/MolEpicUU/spatiotemporal_predictions_COVID19" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Code used to produce models.", - "data_type": [ - "Public health data" - ], - "data_url": "https://github.com/MolEpicUU/spatiotemporal_predictions_COVID19" - } - ], - "title": "Spatio-temporal predictions of COVID-19 test positivity in Uppsala County, Sweden: a comparative approach", - "issue": "1", - "volume": "12", - "publisher": "Springer Science and Business Media LLC", - "published": "2022-09-07", - "author": [ - "van Zoest V.", - "Varotsis G.", - "Menzel U.", - "Wigren A.", - "Kennedy B." - ] - }, - { - "doi": "10.1098/rsos.220440", - "available_items": [ - { - "type": "data", - "repo_name": "dryad", - "accession_number": "", - "description": "Survey responses collected through Qualtrix", - "data_type": [ - "Other data" - ], - "data_url": "https://datadryad.org/stash/dataset/doi:10.5061/dryad.rfj6q57d0" - }, - { - "type": "code", - "repo_name": "dryad", - "accession_number": "", - "description": "Code used for analysis (in R)", - "data_type": [ - "Other data" - ], - "data_url": "https://datadryad.org/stash/dataset/doi:10.5061/dryad.rfj6q57d0" - } - ], - "title": "Forecasting the publication and citation outcomes of COVID-19 preprints", - "issue": "9", - "volume": "9", - "publisher": "The Royal Society", - "published": "2022-09-28", - "author": [ - "Gordon M.", - "Bishop M.", - "Chen Y.", - "Dreber A.", - "Goldfedder B." - ] - }, - { - "doi": "10.1016/j.cels.2022.06.006", - "available_items": [ - { - "type": "data", - "repo_name": "FigShare", - "accession_number": "", - "description": "Metabolomics data", - "data_type": [ - "Health data", - "Other data" - ], - "data_url": "https://dx.doi.org/10.6084/m9.figshare.13336862" - }, - { - "type": "code", - "repo_name": "Zenodo", - "accession_number": "", - "description": "Analysis code", - "data_type": [ - "Health data", - "Other data" - ], - "data_url": "https://dx.doi.org/10.5281/zenodo.6706499" - } - ], - "title": "Multi-omics personalized network analyses highlight progressive disruption of central metabolism associated with COVID-19 severity", - "issue": "8", - "volume": "13", - "publisher": "Elsevier BV", - "published": "2022-08-20", - "author": [ - "Ambikan A. T.", - "Yang H.", - "Krishnan S.", - "Svensson Akusjärvi S.", - "Gupta S." - ] - }, - { - "doi": "10.1016/j.medj.2022.07.007", - "available_items": [ - { - "type": "data", - "repo_name": "GISAID", - "accession_number": "EPI_ISL_11414777-11415389 and EPI_ISL_11450500-11450677", - "description": "Assembled SARS-CoV-2 genomes", - "data_type": [ - "Biochemistry data", - "Health data", - "Genomics & transcriptomics data" - ], - "data_url": "https://gisaid.org/" - }, - { - "type": "data", - "repo_name": "ArrayExpress", - "accession_number": "E-MTAB-11650", - "description": "Raw sequencing data", - "data_type": [ - "Biochemistry data", - "Health data", - "Genomics & transcriptomics data" - ], - "data_url": "https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-11650/" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Computational code", - "data_type": [ - "Biochemistry data", - "Health data", - "Genomics & transcriptomics data" - ], - "data_url": "https://github.com/reiniuslab/OmicronWaves/" - } - ], - "title": "Monitoring of the SARS-CoV-2 Omicron BA.1/BA.2 lineage transition in the Swedish population reveals increased viral RNA levels in BA.2 cases", - "issue": "9", - "volume": "3", - "publisher": "Elsevier BV", - "published": "2022-09-11", - "author": [ - "Lentini A.", - "Pereira A.", - "Winqvist O.", - "Reinius B." - ] - }, - { - "doi": "10.1038/s41558-022-01426-1", - "available_items": [ - { - "type": "data", - "repo_name": "GitHub", - "accession_number": "", - "description": "All data collected as part of the literature search (list of considered diseases, and references for empirical cases.", - "data_type": [ - "Other data" - ], - "data_url": "https://github.com/Camilo-Mora/Diseases" - } - ], - "title": "Over half of known human pathogenic diseases can be aggravated by climate change", - "issue": "9", - "volume": "12", - "publisher": "Springer Science and Business Media LLC", - "published": "2022-08-08", - "author": [ - "Mora C.", - "McKenzie T.", - "Gaw I. M.", - "Dean J. M.", - "von Hammerstein H." - ] - }, - { - "doi": "10.1038/s41467-022-32357-2", - "available_items": [ - { - "type": "data", - "repo_name": "EGA", - "accession_number": "EGAS00001005304", - "description": "Genotype data generated (SPGRX cohort)", - "data_type": [ - "Biochemistry data", - "Genomics & transcriptomics data" - ], - "data_url": "https://ega-archive.org/studies/EGAS00001005304" - }, - { - "type": "data", - "repo_name": "Gene Expression Omnibus", - "accession_number": "GSE179325", - "description": "Methylation data", - "data_type": [ - "Biochemistry data", - "Genomics & transcriptomics data" - ], - "data_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE179325" - } - ], - "title": "Whole blood DNA methylation analysis reveals respiratory environmental traits involved in COVID-19 severity following SARS-CoV-2 infection", - "issue": "1", - "volume": "13", - "publisher": "Springer Science and Business Media LLC", - "published": "2022-08-06", - "author": [ - "Barturen G.", - "Carnero-Montoro E.", - "Martínez-Bueno M.", - "Rojo-Rello S.", - "Sobrino B." - ] - }, - { - "doi": "10.1016/j.immuni.2022.07.005", - "available_items": [ - { - "type": "data", - "repo_name": "ArrayExpress", - "accession_number": "E-MTAB-11845", - "description": "Processed scRNA-seq data", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-11845/" - } - ], - "title": "Immunodeficiency syndromes differentially impact the functional profile of SARS-CoV-2-specific T cells elicited by mRNA vaccination", - "issue": "9", - "volume": "55", - "publisher": "Elsevier BV", - "published": "2022-09-14", - "author": [ - "Gao Y.", - "Cai C.", - "Wullimann D.", - "Niessl J.", - "Rivera-Ballesteros O." - ] - }, - { - "doi": "10.3389/fimmu.2022.932388", - "available_items": [ - { - "type": "data", - "repo_name": "Gene Expression Omnibus", - "accession_number": "GSE201551", - "description": "Expression profiling by high throughput sequencing", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE201551" - } - ], - "title": "Type I Interferons Promote Germinal Centers Through B Cell Intrinsic Signaling and Dendritic Cell Dependent Th1 and Tfh Cell Lineages", - "issue": "", - "volume": "13", - "publisher": "Frontiers Media SA", - "published": "2022-07-13", - "author": [ - "Dahlgren M. W.", - "Plumb A. W.", - "Niss K.", - "Lahl K.", - "Brunak S." - ] - }, - { - "doi": "10.3389/fimmu.2022.924244", - "available_items": [ - { - "type": "data", - "repo_name": "Gene Expression Omnibus", - "accession_number": "GSE201772", - "description": "Expression profiling by high throughput sequencing", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE201772" - } - ], - "title": "Dynamically upregulated mast cell CPA3 patterns in chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis", - "issue": "", - "volume": "13", - "publisher": "Frontiers Media SA", - "published": "2022-08-02", - "author": [ - "Siddhuraj P.", - "Jönsson J.", - "Alyamani M.", - "Prabhala P.", - "Magnusson M." - ] - }, - { - "doi": "10.1057/s41599-022-01257-7", - "available_items": [ - { - "type": "data", - "repo_name": "Open Science Framework", - "accession_number": "", - "description": "Data related to herd immunity, willingness to get vaccinated, and demographic factors.", - "data_type": [ - "Social science and humanities data", - "Other data" - ], - "data_url": "https://osf.io/7nbzr/?view_only=1b1483f5ce494d809f08eaa529bed982" - } - ], - "title": "The effect of herd immunity thresholds on willingness to vaccinate", - "issue": "1", - "volume": "9", - "publisher": "Springer Science and Business Media LLC", - "published": "2022-07-18", - "author": [ - "Andersson P. A.", - "Tinghög G.", - "Västfjäll D." - ] - }, - { - "doi": "10.1007/s10664-022-10176-9", - "available_items": [ - { - "type": "code", - "repo_name": "Zenodo", - "accession_number": "", - "description": "R code for Bayesian analysis", - "data_type": [ - "Social science and humanities data", - "Other data" - ], - "data_url": "https://zenodo.org/record/5115661#.YymQIOxByX0" - } - ], - "title": "Agile software development one year into the COVID-19 pandemic", - "issue": "6", - "volume": "27", - "publisher": "Springer Science and Business Media LLC", - "published": "2022-06-22", - "author": [ - "Ågren P.", - "Knoph E.", - "Berntsson Svensson R." - ] - }, - { - "doi": "10.1038/s41598-022-13218-w", - "available_items": [ - { - "type": "data", - "repo_name": "Zenodo", - "accession_number": "", - "description": "A comparative dataset on public perceptions of multiple risks during the COVID-19 pandemic in Italy and Sweden.", - "data_type": [ - "Social science and humanities data", - "Other data" - ], - "data_url": "https://zenodo.org/record/5653322#.YymOvexByX2" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Code for processing and visualisations", - "data_type": [ - "Social science and humanities data", - "Other data" - ], - "data_url": "https://github.com/eleraf/epidemics-risk-perception" - } - ], - "title": "Epidemic risk perceptions in Italy and Sweden driven by authority responses to COVID-19", - "issue": "1", - "volume": "12", - "publisher": "Springer Science and Business Media LLC", - "published": "2022-06-03", - "author": [ - "Raffetti E.", - "Mondino E.", - "Di Baldassarre G." - ] - }, - { - "doi": "10.1590/1678-4685-gmb-2022-0034", - "available_items": [ - { - "type": "data", - "repo_name": "BioProject", - "accession_number": "PRJNA736341", - "description": "Beaudette genome sequencing and assembly", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://www.ebi.ac.uk/ena/browser/view/PRJNA736341?show=reads" - }, - { - "type": "data", - "repo_name": "ENA", - "accession_number": "MZ368698", - "description": "Avian coronavirus strain Beaudette, complete genome.", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://www.ebi.ac.uk/ena/browser/view/MZ368698" - } - ], - "title": "The order of events on Avian coronavirus life cycle shapes the order of quasispecies evolution during host switches", - "issue": "2", - "volume": "45", - "publisher": "FapUNIFESP (SciELO)", - "published": "2022-07-26", - "author": [ - "Brandão P. E.", - "Berg M.", - "Leite B. A.", - "Silva S. O.", - "Taniwaki S. A." - ] - }, - { - "doi": "10.1080/19490976.2022.2073131", - "available_items": [ - { - "type": "data", - "repo_name": "ENA", - "accession_number": "PRJEB50040", - "description": "Sequence data", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://www.ebi.ac.uk/ena/browser/view/PRJEB50040" - }, - { - "type": "data", - "repo_name": "FigShare", - "accession_number": "", - "description": "Metabolite data", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://figshare.com/articles/dataset/Metabolomics_Data_xlsx/18046400" - } - ], - "title": "A high-risk gut microbiota configuration associates with fatal hyperinflammatory immune and metabolic responses to SARS-CoV-2", - "issue": "1", - "volume": "14", - "publisher": "Informa UK Limited", - "published": "2022-05-15", - "author": [ - "Albrich W. C.", - "Ghosh T. S.", - "Ahearn-Ford S.", - "Mikaeloff F.", - "Lunjani N." - ] - }, - { - "doi": "10.1038/s41467-022-30340-5", - "available_items": [ - { - "type": "data", - "repo_name": "Zenodo", - "accession_number": "", - "description": "Data on the effect of an mRNA vaccine booster on immunogenicity in individuals vaccinated with two doses of inactivated vaccine.", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://zenodo.org/record/6305550#.Yyl_tuxByX1" - } - ], - "title": "Heterologous immunisation with inactivated vaccine followed by mRNA-booster elicits strong immunity against SARS-CoV-2 Omicron variant", - "issue": "1", - "volume": "13", - "publisher": "Springer Science and Business Media LLC", - "published": "2022-05-13", - "author": [ - "Zuo F.", - "Abolhassani H.", - "Du L.", - "Piralla A.", - "Bertoglio F." - ] - }, - { - "doi": "10.1128/mbio.00892-22", - "available_items": [ - { - "type": "data", - "repo_name": "ArrayExpress", - "accession_number": "E-MTAB-10687", - "description": "Bulk and single-cell RNA-Seq gene counts", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-10687" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "R and Python code used for analysis", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://github.com/henriksson-lab/covidali_r.git" - } - ], - "title": "Serine Protease Inhibitors Restrict Host Susceptibility to SARS-CoV-2 Infections", - "issue": "3", - "volume": "13", - "publisher": "American Society for Microbiology", - "published": "2022-06-28", - "author": [ - "Rosendal E.", - "Mihai I. S.", - "Becker M.", - "Das D.", - "Frängsmyr L." - ] - }, - { - "doi": "10.1371/journal.pmed.1003987", - "available_items": [ - { - "type": "data", - "repo_name": "GitHub", - "accession_number": "", - "description": "Data from the systematic review on asymptomatic and presymptomatic SARS-CoV-2 infection", - "data_type": [ - "Other data" - ], - "data_url": "https://github.com/leonieheron/LSR_Asymp_v5" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Code used to display and synthesise the results", - "data_type": [ - "Other data" - ], - "data_url": "https://github.com/leonieheron/LSR_Asymp_v5" - } - ], - "title": "Occurrence and transmission potential of asymptomatic and presymptomatic SARS-CoV-2 infections: Update of a living systematic review and meta-analysis", - "issue": "5", - "volume": "19", - "publisher": "Public Library of Science (PLoS)", - "published": "2022-05-26", - "author": [ - "Buitrago-Garcia D.", - "Ipekci A. M.", - "Heron L.", - "Imeri H.", - "Araujo-Chaveron L." - ] - }, - { - "doi": "10.1016/s2666-5247(21)00304-9", - "available_items": [ - { - "type": "data", - "repo_name": "BioProject", - "accession_number": "PRJNA748764", - "description": "Deidentified individual patient data and raw fastq microbial sequencing alignments", - "data_type": [ - "Health data", - "Genomics & transcriptomics data" - ], - "data_url": "https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA748764" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Background correction algorithm", - "data_type": [ - "Health data", - "Genomics & transcriptomics data" - ], - "data_url": "https://github.com/czbiohub/idseqr" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Rules-based model", - "data_type": [ - "Health data", - "Genomics & transcriptomics data" - ], - "data_url": "https://github.com/alexandra-t/rules_based_model" - } - ], - "title": "Lower respiratory tract infections in children requiring mechanical ventilation: a multicentre prospective surveillance study incorporating airway metagenomics", - "issue": "4", - "volume": "3", - "publisher": "Elsevier BV", - "published": "2022-03-30", - "author": [ - "Tsitsiklis A.", - "Osborne C. M.", - "Kamm J.", - "Williamson K.", - "Kalantar K." - ] - }, - { - "doi": "10.15252/embr.202154499", - "available_items": [ - { - "type": "data", - "repo_name": "ArrayExpress", - "accession_number": "E‐MTAB‐10679", - "description": "RNA-seq results", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-10679/" - } - ], - "title": "Myeloid cell‐specific topoisomerase 1 inhibition using DNA origami mitigates neuroinflammation", - "issue": "7", - "volume": "23", - "publisher": "EMBO", - "published": "2022-05-20", - "author": [ - "Zhu K.", - "Wang Y.", - "Sarlus H.", - "Geng K.", - "Nutma E." - ] - }, - { - "doi": "10.3390/biomedicines10050982", - "available_items": [ - { - "type": "data", - "repo_name": "BioProject", - "accession_number": "PRJNA781460", - "description": "Raw shotgun metagenome sequencing data", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA781460" - } - ], - "title": "Characterization of the Upper Respiratory Bacterial Microbiome in Critically Ill COVID-19 Patients", - "issue": "5", - "volume": "10", - "publisher": "MDPI AG", - "published": "2022-04-23", - "author": [ - "Bai X.", - "Narayanan A.", - "Skagerberg M.", - "Ceña-Diez R.", - "Giske C. G." - ] - }, - { - "doi": "10.1371/journal.pcbi.1009973", - "available_items": [ - { - "type": "data", - "repo_name": "Zenodo", - "accession_number": "", - "description": "Data time series of metereological factors, regional measures and mobility", - "data_type": [ - "Social science and humanities data", - "Other data" - ], - "data_url": "https://zenodo.org/record/6120655#.YyqzGexByX0" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Scripts for the model", - "data_type": [ - "Social science and humanities data", - "Other data" - ], - "data_url": "https://github.com/katharinaledebur/regional_differences_covid" - } - ], - "title": "Meteorological factors and non-pharmaceutical interventions explain local differences in the spread of SARS-CoV-2 in Austria", - "issue": "4", - "volume": "18", - "publisher": "Public Library of Science (PLoS)", - "published": "2022-04-04", - "author": [ - "Ledebur K.", - "Kaleta M.", - "Chen J.", - "Lindner S. D.", - "Matzhold C." - ] - }, - { - "doi": "10.1039/d0sc05064d", - "available_items": [ - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Structural ensembles of camostat, GBPA, and nafamostat", - "data_type": [ - "Protein data", - "Drug discovery data" - ], - "data_url": "https://github.com/noegroup/tmprss2_structures" - } - ], - "title": "Molecular mechanism of inhibiting the SARS-CoV-2 cell entry facilitator TMPRSS2 with camostat and nafamostat", - "issue": "3", - "volume": "12", - "publisher": "Royal Society of Chemistry (RSC)", - "published": "2022-02-24", - "author": [ - "Hempel T.", - "Raich L.", - "Olsson S.", - "Azouz N. P.", - "Klingler A. M." - ] - }, - { - "doi": "10.1038/s42003-022-03187-1 ", - "available_items": [ - { - "type": "data", - "repo_name": "PDB", - "accession_number": "6XN3", - "description": "Structure of the lactococcus lactis csm ctr_4:3 crispr-cas complex", - "data_type": [ - "Protein data" - ], - "data_url": "http://dx.doi.org/10.2210/pdb6xn3/pdb" - }, - { - "type": "data", - "repo_name": "PDB", - "accession_number": "6XN5", - "description": "Structure of the lactococcus lactis csm apo- crispr-cas complex", - "data_type": [ - "Protein data" - ], - "data_url": "https://dx.doi.org/10.2210/pdb6xn5/pdb" - }, - { - "type": "data", - "repo_name": "PDB", - "accession_number": "6XN4", - "description": "Structure of the lactococcus lactis csm ctr_3:2 crispr-cas complex", - "data_type": [ - "Protein data" - ], - "data_url": "https://dx.doi.org/10.2210/pdb6xn4/pdb" - }, - { - "type": "data", - "repo_name": "PDB", - "accession_number": "6XN7", - "description": "structure of the lactococcus lactis csm ntr crispr-cas complex", - "data_type": [ - "Protein data" - ], - "data_url": "https://dx.doi.org/10.2210/pdb6xn7/pdb" - } - ], - "title": "Structural and biochemical characterization of in vivo assembled Lactococcus lactis CRISPR-Csm complex", - "issue": "1", - "volume": "5", - "publisher": "Springer Science and Business Media LLC", - "published": "2022-03-29", - "author": [ - "Sridhara S.", - "Rai J.", - "Whyms C.", - "Goswami H.", - "He H." - ] - }, - { - "doi": "10.1161/CIRCULATIONAHA.121.056663", - "available_items": [ - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Code used in the main analysis", - "data_type": [ - "Health data" - ], - "data_url": "https://github.com/alhenry/cvd1-hf" - } - ], - "title": "Therapeutic Targets for Heart Failure Identified Using Proteomics and Mendelian Randomization", - "issue": "16", - "volume": "145", - "publisher": "Ovid Technologies (Wolters Kluwer Health)", - "published": "2022-04-19", - "author": [ - "Henry A.", - "Gordillo-Marañón M.", - "Finan C.", - "Schmidt A. F.", - "Ferreira J. P." - ] - }, - { - "doi": "10.1002/sim.9365", - "available_items": [ - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Code and simulated data", - "data_type": [ - "Social science and humanities data", - "Other data" - ], - "data_url": "https://github.com/jsheen/NPI" - } - ], - "title": "The required size of cluster randomized trials of nonpharmaceutical interventions in epidemic settings", - "issue": "13", - "volume": "41", - "publisher": "Wiley", - "published": "2022-03-07", - "author": [ - "Sheen J. K.", - "Haushofer J.", - "Metcalf C. J. E.", - "Kennedy‐Shaffer L." - ] - }, - { - "doi": "10.3389/fgene.2022.792090", - "available_items": [ - { - "type": "code", - "repo_name": "BitBucket", - "accession_number": "", - "description": "Dataset used to to assess cross-talk based approaches for drug repurposing", - "data_type": [ - "Drug discovery data" - ], - "data_url": "https://bitbucket.org/sonnhammergroup/drugrepurposingbench/src/master/" - }, - { - "type": "data", - "repo_name": "BitBucket", - "accession_number": "", - "description": "Code used for analysis", - "data_type": [ - "Drug discovery data" - ], - "data_url": "https://bitbucket.org/sonnhammergroup/drugrepurposingbench/src/master/" - } - ], - "title": "Network Crosstalk as a Basis for Drug Repurposing", - "issue": "", - "volume": "13", - "publisher": "Frontiers Media SA", - "published": "2022-03-08", - "author": [ - "Guala D.", - "Sonnhammer E. L. L." - ] - }, - { - "doi": "10.1126/sciadv.abm0220", - "available_items": [ - { - "type": "data", - "repo_name": "BioProject", - "accession_number": "PRJNA814713", - "description": "NGS data", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA814713/" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Implementation of the seqUMAP algorithm", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://github.com/MurrellGroup/SeqUMAP.jl" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Codes for processing NGS nanobody", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://github.com/MurrellGroup/FuNGS" - } - ], - "title": "Multivariate mining of an alpaca immune repertoire identifies potent cross-neutralizing SARS-CoV-2 nanobodies", - "issue": "12", - "volume": "8", - "publisher": "American Association for the Advancement of Science (AAAS)", - "published": "2022-03-25", - "author": [ - "Hanke L.", - "Sheward D. J.", - "Pankow A.", - "Vidakovics L. P.", - "Karl V." - ] - }, - { - "doi": "10.1038/s41467-022-28865-w", - "available_items": [ - { - "type": "data", - "repo_name": "FigShare", - "accession_number": "16866202.v1", - "description": "Raw data and predicted PDB files", - "data_type": [ - "Genomics & transcriptomics data", - "Protein data" - ], - "data_url": "https://scilifelab.figshare.com/articles/dataset/Data_and_most_relevant_results_for_the_FoldDock_project/16866202/1" - } - ], - "title": "Improved prediction of protein-protein interactions using AlphaFold2", - "issue": "1", - "volume": "13", - "publisher": "Springer Science and Business Media LLC", - "published": "2022-03-10", - "author": [ - "Bryant P.", - "Pozzati G.", - "Elofsson A." - ] - }, - { - "doi": "10.3390/ijerph19052558", - "available_items": [ - { - "type": "data", - "repo_name": "FigShare", - "accession_number": "", - "description": "Dataset including variables of physical activity and sedentary behavior during the COVID-19 pandemic", - "data_type": [ - "Social science and humanities data" - ], - "data_url": "https://doi.org/10.6084/m9.figshare.19208538" - } - ], - "title": "Changes in Physical Activity and Sedentary Behavior before and during the COVID-19 Pandemic: A Swedish Population Study", - "issue": "5", - "volume": "19", - "publisher": "MDPI AG", - "published": "2022-02-23", - "author": [ - "Elvén M.", - "Kerstis B.", - "Stier J.", - "Hellström C.", - "von Heideken Wågert P." - ] - }, - { - "doi": "10.7554/elife.64709", - "available_items": [ - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "SiteLocalization software for binding site localisation on non-homogeneous cell surfaces using topological image averaging", - "data_type": [ - "Imaging data" - ], - "data_url": "https://github.com/nordenfeltLab/SiteLocalization" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "FluoroDist.jl - software for simulated fluorescence images with accurate surface distances", - "data_type": [ - "Imaging data" - ], - "data_url": "https://github.com/nordenfeltLab/FluoroDist.jl" - }, - { - "type": "data", - "repo_name": "Dryad", - "accession_number": "", - "description": "Site localisation measurements data", - "data_type": [ - "Imaging data" - ], - "data_url": "https://doi.org/10.5061/dryad.h18931znn" - } - ], - "title": "Nanoscale binding site localization by molecular distance estimation on native cell surfaces using topological image averaging", - "issue": "", - "volume": "11", - "publisher": "eLife Sciences Publications, Ltd", - "published": "2022-02-24", - "author": [ - "Kumra Ahnlide V.", - "Kumra Ahnlide J.", - "Wrighton S.", - "Beech J. P.", - "Nordenfelt P." - ] - }, - { - "doi": "10.1038/s41598-022-05597-x", - "available_items": [ - { - "type": "data", - "repo_name": "Gene Expression Omnibus", - "accession_number": "GSE63229", - "description": "Expression profiling by array", - "data_type": [ - "Drug discovery data", - "Genomics & transcriptomics data" - ], - "data_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63229" - }, - { - "type": "data", - "repo_name": "Gene Expression Omnibus", - "accession_number": "GSE123574", - "description": "Genome binding/occupancy profiling by high throughput sequencing", - "data_type": [ - "Drug discovery data", - "Genomics & transcriptomics data" - ], - "data_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE123574" - } - ], - "title": "An in silico analysis identifies drugs potentially modulating the cytokine storm triggered by SARS-CoV-2 infection", - "issue": "1", - "volume": "12", - "publisher": "Springer Science and Business Media LLC", - "published": "2022-01-31", - "author": [ - "Sanchez-Burgos L.", - "Gómez-López G.", - "Al-Shahrour F.", - "Fernandez-Capetillo O." - ] - }, - { - "doi": "10.1073/pnas.2116435119", - "available_items": [ - { - "type": "data", - "repo_name": "dbSNP", - "accession_number": "RS17713054", - "description": "Reference single nucleotide polymorphism report", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://www.ncbi.nlm.nih.gov/snp/rs17713054" - }, - { - "type": "data", - "repo_name": "dbSNP", - "accession_number": "RS17764980", - "description": "Reference single nucleotide polymorphism report", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://www.ncbi.nlm.nih.gov/snp/rs17764980" - }, - { - "type": "data", - "repo_name": "dbSNP", - "accession_number": "RS17714101", - "description": "Reference single nucleotide polymorphism report", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://www.ncbi.nlm.nih.gov/snp/rs17714101" - }, - { - "type": "data", - "repo_name": "dbSNP", - "accession_number": "RS17714228", - "description": "Reference single nucleotide polymorphism report", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://www.ncbi.nlm.nih.gov/snp/rs17714228" - }, - { - "type": "data", - "repo_name": "dbSNP", - "accession_number": "RS71325092", - "description": "Reference single nucleotide polymorphism report", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://www.ncbi.nlm.nih.gov/snp/rs71325092" - } - ], - "title": "The major genetic risk factor for severe COVID-19 is associated with protection against HIV", - "issue": "9", - "volume": "119", - "publisher": "Proceedings of the National Academy of Sciences", - "published": "2022-02-22", - "author": [ - "Zeberg H." - ] - }, - { - "doi": "10.1186/s12915-021-01086-1", - "available_items": [ - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Data analysis code.", - "data_type": [ - "Drug discovery data" - ], - "data_url": "https://github.com/pharmbio/antiviral-phenomics" - }, - { - "type": "data", - "repo_name": "Figshare", - "accession_number": "", - "description": "Images, analysis pipelines, and feature data.", - "data_type": [ - "Drug discovery data" - ], - "data_url": "https://doi.org/10.17044/scilifelab.14188403.v1" - } - ], - "title": "A phenomics approach for antiviral drug discovery", - "issue": "1", - "volume": "19", - "publisher": "Springer Science and Business Media LLC", - "published": "2021-08-02", - "author": [ - "Rietdijk J.", - "Tampere M.", - "Pettke A.", - "Georgiev P.", - "Lapins M." - ] - }, - { - "doi": "10.1371/journal.pone.0255270", - "available_items": [ - { - "type": "data", - "repo_name": "GitHub", - "accession_number": "", - "description": "Information on interactions between proteins & human cells, potential drug targets, genes related to potential targets.", - "data_type": [ - "Drug discovery data" - ], - "data_url": "https://github.com/MahnazHabibi/Drug-repurposing" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Matlab analysis code required to process data.", - "data_type": [ - "Drug discovery data" - ], - "data_url": "https://github.com/MahnazHabibi/Drug-repurposing" - } - ], - "title": "Topological network based drug repurposing for coronavirus 2019", - "issue": "7", - "volume": "16", - "publisher": "Public Library of Science (PLoS)", - "published": "2021-07-29", - "author": [ - "Habibi M.", - "Taheri G." - ] - }, - { - "doi": "10.3390/md19070391", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "All data are included in the article or supplementary material (Sarcophyton cembranoid diterpenes metabolites).", - "data_type": [ - "Drug discovery data", - "Protein data" - ], - "data_url": "https://www.mdpi.com/1660-3397/19/7/391/htm" - } - ], - "title": "Blue Biotechnology: Computational Screening of Sarcophyton Cembranoid Diterpenes for SARS-CoV-2 Main Protease Inhibition", - "issue": "7", - "volume": "19", - "publisher": "MDPI AG", - "published": "2021-07-13", - "author": [ - "Ibrahim M. A. A.", - "Abdelrahman A. H. M.", - "Atia M. A. M.", - "Mohamed T. A.", - "Moustafa M. F." - ] - }, - { - "doi": "10.1038/s41586-021-03767-x", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Summary statistics by COVID-19 HGI.", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://www.covid19hg.org/results/r5/" - }, - { - "type": "data", - "repo_name": "GWAS", - "accession_number": "GCST011074", - "description": "GWAS catalog study.", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://www.ebi.ac.uk/gwas/studies/GCST011074" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Code for summary statistics, PCA pipeline with precomputed loadings and meta-analyses.", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://github.com/covid19-hg/" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Code for Mendelian randomization and genetic correlation pipeline.", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://github.com/marcoralab/MRcovid" - } - ], - "title": "Mapping the human genetic architecture of COVID-19", - "issue": "7889", - "volume": "600", - "publisher": "Springer Science and Business Media LLC", - "published": "2021-07-08", - "author": [ - "Niemi M. E. K.", - "Karjalainen J.", - "Liao R. G.", - "Neale B. M.", - "Daly M." - ] - }, - { - "doi": "10.1172/jci152386", - "available_items": [ - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Code for data management and analysis (commit 183ddb7).", - "data_type": [ - "Genomics & transcriptomics data", - "Health data" - ], - "data_url": "https://github.com/tomoconaka/COVID19-chr3" - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Data are held in multiple international repositories. Details about gaining access are contained in the paper.", - "data_type": [ - "Genomics & transcriptomics data", - "Health data" - ], - "data_url": "https://www.jci.org/articles/view/152386" - } - ], - "title": "Age-dependent impact of the major common genetic risk factor for COVID-19 on severity and mortality", - "issue": "23", - "volume": "131", - "publisher": "American Society for Clinical Investigation", - "published": "2021-12-01", - "author": [ - "Nakanishi T.", - "Pigazzini S.", - "Degenhardt F.", - "Cordioli M.", - "Butler-Laporte G." - ] - }, - { - "doi": "10.1038/s41588-021-00996-8", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "COVID-19 summary statistics for individuals of African ancestry.", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://www.covid19hg.org/results/r6/" - }, - { - "type": "data", - "repo_name": "Combined Annotation Dependent Depletion", - "accession_number": "", - "description": "CADD-scores v.1.6.", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://cadd.gs.washington.edu/score" - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Genomes from the 1000 Genomes Project.", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://www.internationalgenome.org/data" - }, - { - "type": "data", - "repo_name": "Zenodo", - "accession_number": "", - "description": "Fine-mapping association summary statistics produced in this study.", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://doi.org/10.5281/zenodo.5708333" - }, - { - "type": "code", - "repo_name": "Zenodo", - "accession_number": "", - "description": "Code used for the fine-mapping analysis.", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://doi.org/10.5281/zenodo.5708333" - } - ], - "title": "Multi-ancestry fine mapping implicates OAS1 splicing in risk of severe COVID-19", - "issue": "2", - "volume": "54", - "publisher": "Springer Science and Business Media LLC", - "published": "2022-01-13", - "author": [ - "Huffman J. E.", - "Butler-Laporte G.", - "Khan A.", - "Pairo-Castineira E.", - "Drivas T. G." - ] - }, - { - "doi": "10.1093/heapol/czab113", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "All data are available in the article, or in sources therein (e.g. information on healthcare and political systems).", - "data_type": [ - "Public health data", - "Social science and humanities data" - ], - "data_url": "https://academic.oup.com/heapol/article/37/3/297/6373138#341608669" - } - ], - "title": "Priority setting and equity in COVID-19 pandemic plans: a comparative analysis of 18 African countries", - "issue": "3", - "volume": "37", - "publisher": "Oxford University Press (OUP)", - "published": "2021-10-07", - "author": [ - "Kapiriri L.", - "Kiwanuka S.", - "Biemba G.", - "Velez C.", - "Razavi S. D." - ] - }, - { - "doi": "10.3390/jcm10194411", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Data on influenza/pneumonia deaths & hospitalisations due to sepsis, subdivided by mental health condition, physical comorbidities, and demographic features.", - "data_type": [ - "Health data", - "Public health data", - "Social science and humanities data" - ], - "data_url": "https://www.mdpi.com/2077-0383/10/19/4411/s1?version=1632654678" - } - ], - "title": "Increased Risks of Death and Hospitalization in Influenza/Pneumonia and Sepsis for Individuals Affected by Psychotic Disorders, Bipolar Disorders, and Single Manic Episodes: A Retrospective Cross-Sectional Study", - "issue": "19", - "volume": "10", - "publisher": "MDPI AG", - "published": "2021-09-26", - "author": [ - "Nilsson N.", - "Bendix M.", - "Öhlund L.", - "Widerström M.", - "Werneke U." - ] - }, - { - "doi": "10.3389/fpsyg.2021.736499", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Descriptive data on subjects included in the study, particularly focussed on the reasons behind limitations in ability to train.", - "data_type": [ - "Health data", - "Social science and humanities data" - ], - "data_url": "https://www.frontiersin.org/articles/10.3389/fpsyg.2021.736499/full#supplementary-material" - } - ], - "title": "Effects of the COVID-19 Health Crisis on Sports Practice, Life Quality, and Emotional Status in Spanish High-Performance Athletes", - "issue": "", - "volume": "12", - "publisher": "Frontiers Media SA", - "published": "2021-09-27", - "author": [ - "Conde E.", - "Martínez-Aranda L. M.", - "Sanz G.", - "López de Subijana C.", - "Sánchez-Pato A." - ] - }, - { - "doi": "10.1136/bmjopen-2021-052777", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Data related to literature requests available in the paper and supplementary materials.", - "data_type": [ - "Health data", - "Public health data" - ], - "data_url": "https://bmjopen.bmj.com/content/bmjopen/11/10/e049267/DC1/embed/inline-supplementary-material-1.pdf?download=true" - } - ], - "title": "Diabetes, hypertension, body mass index, smoking and COVID-19-related mortality: a systematic review and meta-analysis of observational studies", - "issue": "10", - "volume": "11", - "publisher": "BMJ", - "published": "2021-10-25", - "author": [ - "Mahamat-Saleh Y.", - "Fiolet T.", - "Rebeaud M. E.", - "Mulot M.", - "Guihur A." - ] - }, - { - "doi": "10.3390/ijerph182010680", - "available_items": [ - { - "type": "data", - "repo_name": "Open Science Framework", - "accession_number": "", - "description": "Raw data on physical activity and psychological well-being.", - "data_type": [ - "Health data", - "Public health data", - "Social science and humanities data" - ], - "data_url": "https://osf.io/w4gfe/" - } - ], - "title": "Changes in Physical Activity Are Associated with Corresponding Changes in Psychological Well-Being: A Pandemic Case Study", - "issue": "20", - "volume": "18", - "publisher": "MDPI AG", - "published": "2021-10-12", - "author": [ - "Dahlen M.", - "Thorbjørnsen H.", - "Sjåstad H.", - "von Heideken Wågert P.", - "Hellström C." - ] - }, - { - "doi": "10.3389/fpsyg.2021.708037", - "available_items": [ - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "R-code used for data analyses.", - "data_type": [ - "Public health data", - "Social science and humanities data" - ], - "data_url": "http://github.com/hakanwall/covid_study" - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Data cannot be made publicly available, but access can be requested for data with some personal details removed.", - "data_type": [ - "Public health data", - "Social science and humanities data" - ], - "data_url": "https://www.frontiersin.org/articles/10.3389/fpsyg.2021.708037/full#h7" - } - ], - "title": "A Longitudinal Study of Gambling Behaviors During the COVID-19 Pandemic in Sweden", - "issue": "", - "volume": "12", - "publisher": "Frontiers Media SA", - "published": "2021-10-14", - "author": [ - "Månsson V.", - "Wall H.", - "Berman A. H.", - "Jayaram-Lindström N.", - "Rosendahl I." - ] - }, - { - "doi": "10.1093/eurpub/ckab138", - "available_items": [ - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "The code of the individual-based epidemiological model.", - "data_type": [ - "Public health data", - "Social science and humanities data" - ], - "data_url": "https://github.com/ImperialCollegeLondon/covid19model" - }, - { - "type": "data", - "repo_name": "GitHub", - "accession_number": "", - "description": "The raw data from the Quarterly Labour Force Survey October to December 2019 used for the labour force model.", - "data_type": [ - "Public health data", - "Social science and humanities data" - ], - "data_url": "https://www.ukdataservice.ac.uk/" - } - ], - "title": "The impact of a COVID-19 lockdown on work productivity under good and poor compliance", - "issue": "5", - "volume": "31", - "publisher": "Oxford University Press (OUP)", - "published": "2021-08-06", - "author": [ - "Ohrnberger J.", - "Segal A. B.", - "Forchini G.", - "Miraldo M.", - "Skarp J." - ] - }, - { - "doi": "10.1021/jacs.1c08402", - "available_items": [ - { - "type": "data", - "repo_name": "Figshare", - "accession_number": "", - "description": "Information on methods, data on chemical structures and assay data", - "data_type": [ - "Drug discovery data" - ], - "data_url": "https://doi.org/10.1021/jacs.1c08402" - } - ], - "title": "Ultralarge Virtual Screening Identifies SARS-CoV-2 Main Protease Inhibitors with Broad-Spectrum Activity against Coronaviruses", - "issue": "7", - "volume": "144", - "publisher": "American Chemical Society (ACS)", - "published": "2022-02-10", - "author": [ - "Luttens A.", - "Gullberg H.", - "Abdurakhmanov E.", - "Vo D. D.", - "Akaberi D." - ] - }, - { - "doi": "10.1016/j.dib.2021.107698", - "available_items": [ - { - "type": "protocol", - "repo_name": "Zenodo", - "accession_number": "", - "description": "Chronological data on Swedish Governmental COVID-19 policy/actions", - "data_type": [ - "Public health data", - "Social science and humanities data", - "Other data" - ], - "data_url": "https://doi.org/10.5281/zenodo.5718432" - } - ], - "title": "Dataset: COVID-19 epidemic policy and events timeline (Sweden)", - "issue": "", - "volume": "40", - "publisher": "Elsevier BV", - "published": "2022-06-04", - "author": [ - "Olofsson T.", - "Vilhelmsson A." - ] - }, - { - "doi": "10.1371/journal.pone.0262169", - "available_items": [ - { - "type": "data", - "repo_name": "Figshare", - "accession_number": "", - "description": "Metadata record for dataset", - "data_type": [ - "Public health data", - "Serology data" - ], - "data_url": "https://doi.org/10.17044/scilifelab.13567355.v3" - } - ], - "title": "SARS-CoV-2 induces a durable and antigen specific humoral immunity after asymptomatic to mild COVID-19 infection", - "issue": "1", - "volume": "17", - "publisher": "Public Library of Science (PLoS)", - "published": "2022-01-12", - "author": [ - "Havervall S.", - "Jernbom Falk A.", - "Klingström J.", - "Ng H.", - "Greilert-Norin N." - ] - }, - { - "doi": "10.1038/s41588-021-00996-8", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "COVID-19 summary statistics for individuals of African ancestry", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://www.covid19hg.org/results/r6/" - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "CADD-scores v.1.6.", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://cadd.gs.washington.edu/score" - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Genomes from 1000 Genomes project", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://www.internationalgenome.org/data" - }, - { - "type": "data", - "repo_name": "Zenodo", - "accession_number": "", - "description": "Summary data for OAS1/2/3 multi-ancestry fine mapping", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://zenodo.org/record/5708333#.YnOVnS8Rqu4" - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Source data for LD in OAS1/2/3 region", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "10.1038/s41588-021-00996-8#Sec17" - }, - { - "type": "code", - "repo_name": "", - "accession_number": "", - "description": "Code for fine mapping", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://doi.org/10.5281/zenodo.5708333" - } - ], - "title": "Multi-ancestry fine mapping implicates OAS1 splicing in risk of severe COVID-19", - "issue": "2", - "volume": "54", - "publisher": "Springer Science and Business Media LLC", - "published": "2022-01-13", - "author": [ - "Huffman J. E.", - "Butler-Laporte G.", - "Khan A.", - "Pairo-Castineira E.", - "Drivas T. G." - ] - }, - { - "doi": "10.1038/s41467-021-27610-z", - "available_items": [ - { - "type": "data", - "repo_name": "Electron Microscopy Data Bank", - "accession_number": "EMD-12561", - "description": "cryo-EM density maps", - "data_type": [ - "Biochemistry data", - "Protein data" - ], - "data_url": "https://www.ebi.ac.uk/emdb/EMD-12561" - }, - { - "type": "data", - "repo_name": "Electron Microscopy Data Bank", - "accession_number": "EMD-12465", - "description": "cryo-EM density maps", - "data_type": [ - "Biochemistry data", - "Protein data" - ], - "data_url": "https://www.ebi.ac.uk/emdb/search/EMD-12465" - }, - { - "type": "data", - "repo_name": "Protein Data Bank", - "accession_number": "7NS6", - "description": "Atomic coordinates", - "data_type": [ - "Biochemistry data", - "Protein data" - ], - "data_url": "https://www.rcsb.org/structure/unreleased/7NS6" - }, - { - "type": "data", - "repo_name": "Protein Data Bank", - "accession_number": "7NLL", - "description": "Atomic coordinates", - "data_type": [ - "Biochemistry data", - "Protein data" - ], - "data_url": "https://www.rcsb.org/structure/unreleased/7NLL" - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Source Data for Study", - "data_type": [ - "Biochemistry data", - "Protein data" - ], - "data_url": "https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-021-27610-z/MediaObjects/41467_2021_27610_MOESM3_ESM.xlsx" - } - ], - "title": "A bispecific monomeric nanobody induces spike trimer dimers and neutralizes SARS-CoV-2 in vivo", - "issue": "1", - "volume": "13", - "publisher": "Springer Science and Business Media LLC", - "published": "2022-01-10", - "author": [ - "Hanke L.", - "Das H.", - "Sheward D. J.", - "Perez Vidakovics L.", - "Urgard E." - ] - }, - { - "doi": "10.1039/D1CB00135C", - "available_items": [ - { - "type": "data", - "repo_name": "Protein Data Bank", - "accession_number": "7ORW", - "description": "Protein model", - "data_type": [ - "Protein data", - "Public health data" - ], - "data_url": "https://www.rcsb.org/structure/7ORW" - }, - { - "type": "data", - "repo_name": "Protein Data Bank", - "accession_number": "7ORV", - "description": "Protein model", - "data_type": [ - "Protein data", - "Public health data" - ], - "data_url": "https://www.rcsb.org/structure/7ORV" - }, - { - "type": "data", - "repo_name": "Protein Data Bank", - "accession_number": "7ORU", - "description": "Protein model", - "data_type": [ - "Protein data", - "Public health data" - ], - "data_url": "https://www.rcsb.org/structure/7ORU" - }, - { - "type": "data", - "repo_name": "Protein Data Bank", - "accession_number": "7ORR", - "description": "Protein model", - "data_type": [ - "Protein data", - "Public health data" - ], - "data_url": "http://xlink.rsc.org/?pdb=7ORR" - }, - { - "type": "data", - "repo_name": "Zenodo", - "accession_number": "", - "description": "Crystallographic fragment screen", - "data_type": [ - "Protein data", - "Public health data" - ], - "data_url": "https://zenodo.org/record/5234009#.YnOdVS8RphE" - } - ], - "title": "Identification of fragments binding to SARS-CoV-2 nsp10 reveals ligand-binding sites in conserved interfaces between nsp10 and nsp14/nsp16", - "issue": "1", - "volume": "3", - "publisher": "Royal Society of Chemistry (RSC)", - "published": "2022-01-05", - "author": [ - "Kozielski F.", - "Sele C.", - "Talibov V. O.", - "Lou J.", - "Dong D." - ] - }, - { - "doi": "10.1098/rsif.2021.0819", - "available_items": [ - { - "type": "data", - "repo_name": "Figshare", - "accession_number": "", - "description": "Data related to respiratory events", - "data_type": [ - "Public health data" - ], - "data_url": "https://figshare.com/articles/dataset/An_Effective_Model_for_Evaluating_The_Direct_Infection_Risk_Associated_to_Respiratory_Events/16826374" - }, - { - "type": "code", - "repo_name": "Figshare", - "accession_number": "", - "description": "Code used to generate visualisations (Python)", - "data_type": [ - "Public health data" - ], - "data_url": "https://figshare.com/articles/dataset/An_Effective_Model_for_Evaluating_The_Direct_Infection_Risk_Associated_to_Respiratory_Events/16826374" - } - ], - "title": "Modelling the direct virus exposure risk associated with respiratory events", - "issue": "186", - "volume": "19", - "publisher": "The Royal Society", - "published": "2022-01-12", - "author": [ - "Wang J.", - "Dalla Barba F.", - "Roccon A.", - "Sardina G.", - "Soldati A." - ] - }, - { - "doi": "10.1016/j.celrep.2021.110242", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Patient VDJ data, raw FASTQ files", - "data_type": [ - "Public health data" - ], - "data_url": "http://www.ncbi.nlm.nih.gov/bioproject/782883" - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Enriched hybridoma NGS, raw FASTQ files", - "data_type": [ - "Public health data" - ], - "data_url": "http://www.ncbi.nlm.nih.gov/bioproject/782992" - }, - { - "type": "code", - "repo_name": "Github", - "accession_number": "", - "description": "Code for analysis", - "data_type": [ - "Public health data" - ], - "data_url": "https://github.com/LSSI-ETH" - } - ], - "title": "SARS-CoV-2 reactive and neutralizing antibodies discovered by single-cell sequencing of plasma cells and mammalian display", - "issue": "3", - "volume": "38", - "publisher": "Elsevier BV", - "published": "2022-01-25", - "author": [ - "Ehling R. A.", - "Weber C. R.", - "Mason D. M.", - "Friedensohn S.", - "Wagner B." - ] - }, - { - "doi": "10.7554/eLife.73641", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Molecular models and simulation trajectories", - "data_type": [ - "Drug discovery data" - ], - "data_url": "https://covid.bioexcel.eu/simulations/" - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Drug targeting modalities for COVID-19 drug discovery", - "data_type": [ - "Drug discovery data" - ], - "data_url": "https://covid.molssi.org//targets/#blocking-sars-cov-2-spike-protein-binding-to-human-ace2-receptor" - } - ], - "title": "Structure-guided glyco-engineering of ACE2 for improved potency as soluble SARS-CoV-2 decoy receptor", - "issue": "", - "volume": "10", - "publisher": "eLife Sciences Publications, Ltd", - "published": "2021-12-20", - "author": [ - "Capraz T.", - "Kienzl N. F.", - "Laurent E.", - "Perthold J. W.", - "Föderl-Höbenreich E." - ] - }, - { - "doi": "10.1371/journal.pone.0260453", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Pseudonymised, individual-level data", - "data_type": [ - "Public health data" - ], - "data_url": "https://b2share.eudat.eu" - }, - { - "type": "data", - "repo_name": "Figshare", - "accession_number": "", - "description": "Individual health care workers cohort data from KI Hospital", - "data_type": [ - "Public health data" - ], - "data_url": "https://doi.org/10.6084/m9.figshare.17114138" - }, - { - "type": "data", - "repo_name": "Figshare", - "accession_number": "", - "description": "Additional data from South Hospital in Stockholm", - "data_type": [ - "Public health data" - ], - "data_url": "https://doi.org/10.6084/m9.figshare.17117093" - } - ], - "title": "Potential SARS-CoV-2 infectiousness among asymptomatic healthcare workers", - "issue": "12", - "volume": "16", - "publisher": "Public Library of Science (PLoS)", - "published": "2021-12-17", - "author": [ - "Pimenoff V. N.", - "Elfström M.", - "Conneryd Lundgren K.", - "Klevebro S.", - "Melen E." - ] - }, - { - "doi": "10.3390/v13122537", - "available_items": [ - { - "type": "data", - "repo_name": "Gene Expression Omnibus", - "accession_number": "GSE185657", - "description": "Expression profiling by high throughput sequencing", - "data_type": [ - "Protein data" - ], - "data_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE185657" - } - ], - "title": "Differential Effect of SARS-CoV-2 Spike Glycoprotein 1 on Human Bronchial and Alveolar Lung Mucosa Models: Implications for Pathogenicity", - "issue": "12", - "volume": "13", - "publisher": "MDPI AG", - "published": "2021-12-17", - "author": [ - "Rahman M.", - "Irmler M.", - "Keshavan S.", - "Introna M.", - "Beckers J." - ] - }, - { - "doi": "10.1371/journal.pone.0261315#sec018", - "available_items": [ - { - "type": "data", - "repo_name": "Figshare", - "accession_number": "", - "description": "Data is sensitive and cannot be shared openly, but data transfer agreement could be established", - "data_type": [ - "Health data" - ], - "data_url": "https://scilifelab.figshare.com/articles/dataset/PRONMED_Uppsala_COVID-19_ICU_Biobank/14229410/1" - } - ], - "title": "ECG pathology and its association with death in critically ill COVID-19 patients, a cohort study", - "issue": "12", - "volume": "16", - "publisher": "Public Library of Science (PLoS)", - "published": "2021-12-14", - "author": [ - "Rosén J.", - "Noreland M.", - "Stattin K.", - "Lipcsey M.", - "Frithiof R." - ] - }, - { - "doi": "10.1371/journal.pone.0251834#sec006", - "available_items": [ - { - "type": "data", - "repo_name": "BioMagResBank", - "accession_number": "50915", - "description": "Chemical shifts of full-length SARS-CoV-2", - "data_type": [ - "Protein data" - ], - "data_url": "https://bmrb.io/data_library/summary/index.php?bmrbId=50915" - } - ], - "title": "1H, 13C and 15N resonance assignment of the SARS-CoV-2 full-length nsp1 protein and its mutants reveals its unique secondary structure features in solution", - "issue": "12", - "volume": "16", - "publisher": "Public Library of Science (PLoS)", - "published": "2021-12-07", - "author": [ - "Agback T.", - "Dominguez F.", - "Frolov I.", - "Frolova E. I.", - "Agback P." - ] - }, - { - "doi": "10.1038/s41467-021-23893-4", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Source Data (data on antibody titer, among other things)", - "data_type": [ - "Serology data" - ], - "data_url": "10.1038/s41467-021-23893-4#Sec25" - }, - { - "type": "code", - "repo_name": "Github", - "accession_number": "", - "description": "Code for analysis (R)", - "data_type": [ - "Serology data" - ], - "data_url": "https://github.com/Schwenk-Lab/covid19-serology/tree/v1.0.0" - } - ], - "title": "Multianalyte serology in home-sampled blood enables an unbiased assessment of the immune response against SARS-CoV-2", - "issue": "1", - "volume": "12", - "publisher": "Springer Science and Business Media LLC", - "published": "2021-06-17", - "author": [ - "Roxhed N.", - "Bendes A.", - "Dale M.", - "Mattsson C.", - "Hanke L." - ] - }, - { - "doi": "10.1038/s41467-021-22446-z", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Source Data (includes mortality data, among other things)", - "data_type": [ - "Public health data" - ], - "data_url": "10.1038/s41467-021-22446-z#Sec15" - }, - { - "type": "code", - "repo_name": "Open Science Framework", - "accession_number": "", - "description": "Code for metaanalysis", - "data_type": [ - "Public health data" - ], - "data_url": "https://osf.io/qesv4/" - } - ], - "title": "Mortality outcomes with hydroxychloroquine and chloroquine in COVID-19 from an international collaborative meta-analysis of randomized trials", - "issue": "1", - "volume": "12", - "publisher": "Springer Science and Business Media LLC", - "published": "2021-04-15", - "author": [ - "Axfors C.", - "Schmitt A. M.", - "Janiaud P.", - "van’t Hooft J.", - "Abd-Elsalam S." - ] - }, - { - "doi": "10.1002/eji.202149626", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Curated data are available for exploration via the Karolinska KI/K COVID-19 Immune Atlas", - "data_type": [ - "Health data", - "Other data" - ], - "data_url": "https://covid19cellatlas.com/#/" - } - ], - "title": "COVID‐19‐specific metabolic imprint yields insights into multiorgan system perturbations", - "issue": "3", - "volume": "52", - "publisher": "Wiley", - "published": "2021-12-16", - "author": [ - "Cornillet M.", - "Strunz B.", - "Rooyackers O.", - "Ponzetta A.", - "Chen P." - ] - }, - { - "doi": "10.1038/s41597-021-01071-x", - "available_items": [ - { - "type": "code", - "repo_name": "", - "accession_number": "", - "description": "Code used to generate synthetic evalutation datasets", - "data_type": [ - "Other data" - ], - "data_url": "https://github.com/KCL-BMEIS/ExeTeraEval" - }, - { - "type": "code", - "repo_name": "", - "accession_number": "", - "description": "Source code for ExeTera", - "data_type": [ - "Other data" - ], - "data_url": "https://github.com/KCL-BMEIS/ExeTera" - } - ], - "title": "Accessible data curation and analytics for international-scale citizen science datasets", - "issue": "1", - "volume": "8", - "publisher": "Springer Science and Business Media LLC", - "published": "2021-11-22", - "author": [ - "Murray B.", - "Kerfoot E.", - "Chen L.", - "Deng J.", - "Graham M. S." - ] - }, - { - "doi": "10.1186/s12879-021-06829-7", - "available_items": [ - { - "type": "data", - "repo_name": "Open Science Framework", - "accession_number": "", - "description": "Data from clinical trial registries used in the study", - "data_type": [ - "Health data", - "Public health data" - ], - "data_url": "https://osf.io/gr8jt/" - } - ], - "title": "Association between convalescent plasma treatment and mortality in COVID-19: a collaborative systematic review and meta-analysis of randomized clinical trials", - "issue": "1", - "volume": "21", - "publisher": "Springer Science and Business Media LLC", - "published": "2021-11-20", - "author": [ - "Axfors C.", - "Janiaud P.", - "Schmitt A. M.", - "van’t Hooft J.", - "Smith E. R." - ] - }, - { - "doi": "10.1016/j.xcrm.2021.100450", - "available_items": [ - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Data from clinical trial registries used in the study", - "data_type": [ - "Health data", - "Public health data", - "Biochemistry data" - ], - "data_url": "https://github.com/MurrellGroup/VOCfreq" - } - ], - "title": "Beta RBD boost broadens antibody-mediated protection against SARS-CoV-2 variants in animal models", - "issue": "11", - "volume": "2", - "publisher": "Elsevier BV", - "published": "2021-11-16", - "author": [ - "Sheward D. J.", - "Mandolesi M.", - "Urgard E.", - "Kim C.", - "Hanke L." - ] - }, - { - "doi": "10.7554/eLife.70843", - "available_items": [ - { - "type": "data", - "repo_name": "ProteomeXchange", - "accession_number": "PXD026366", - "description": "Proteomics data", - "data_type": [ - "Protein data" - ], - "data_url": "http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD026366" - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Mass spectrometry data generated", - "data_type": [ - "Protein data" - ], - "data_url": "https://panoramaweb.org/Panorama%20Public/2021/KTH%20Uhlen%20Lab%20-%20SARS-CoV-2%20SISCAPA/project-begin.view?" - } - ], - "title": "Rapid and sensitive detection of SARS-CoV-2 infection using quantitative peptide enrichment LC-MS analysis", - "issue": "", - "volume": "10", - "publisher": "eLife Sciences Publications, Ltd", - "published": "2021-11-08", - "author": [ - "Hober A.", - "Tran-Minh K. H.", - "Foley D.", - "McDonald T.", - "Vissers J. P." - ] - }, - { - "doi": "10.3390/ijms222111622", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Data available in the supplementary material", - "data_type": [ - "Health data", - "Imaging data" - ], - "data_url": "https://www.mdpi.com/article/10.3390/ijms222111622/s1" - } - ], - "title": "Infection of Brain Pericytes Underlying Neuropathology of COVID-19 Patients", - "issue": "21", - "volume": "22", - "publisher": "MDPI AG", - "published": "2021-10-27", - "author": [ - "Bocci M.", - "Oudenaarden C.", - "Sàenz-Sardà X.", - "Simrén J.", - "Edén A." - ] - }, - { - "doi": "10.1126/scitranslmed.abj7521", - "available_items": [ - { - "type": "data", - "repo_name": "ProteomeXchange", - "accession_number": "PXD025265", - "description": "Proteomics data", - "data_type": [ - "Genomics & transcriptomics data", - "Protein data", - "Health data" - ], - "data_url": "http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD025265" - }, - { - "type": "data", - "repo_name": "Gene Expression Omnibus", - "accession_number": "GSE172114", - "description": "RNA-seq datasets", - "data_type": [ - "Genomics & transcriptomics data", - "Protein data", - "Health data" - ], - "data_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE172114" - }, - { - "type": "code", - "repo_name": "Zenodo", - "accession_number": "", - "description": "Code to perform classification and structural causal modeling", - "data_type": [ - "Genomics & transcriptomics data", - "Protein data", - "Health data" - ], - "data_url": "https://zenodo.org/record/5557611#.YnjTii8Rqu5" - } - ], - "title": "Identification of driver genes for critical forms of COVID-19 in a deeply phenotyped young patient cohort", - "issue": "628", - "volume": "14", - "publisher": "American Association for the Advancement of Science (AAAS)", - "published": "2022-01-19", - "author": [ - "Carapito R.", - "Li R.", - "Helms J.", - "Carapito C.", - "Gujja S." - ] - }, - { - "doi": "10.1021/acs.jproteome.1c00657", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Union of proteins in both the plasma and blood extracellular vesicle PeptideAtlas builds", - "data_type": [ - "Health data", - "Protein data" - ], - "data_url": "https://pubs.acs.org/doi/10.1021/acs.jproteome.1c00657" - } - ], - "title": "Advances and Utility of the Human Plasma Proteome", - "issue": "12", - "volume": "20", - "publisher": "American Chemical Society (ACS)", - "published": "2021-10-21", - "author": [ - "Deutsch E. W.", - "Omenn G. S.", - "Sun Z.", - "Maes M.", - "Pernemalm M." - ] - }, - { - "doi": "10.1038/s41598-021-99721-y", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Raw and processed data available in Bitbucket", - "data_type": [ - "Health data", - "Drug discovery data" - ], - "data_url": "https://bitbucket.org/sonnhammergroup/unadrug" - }, - { - "type": "code", - "repo_name": "", - "accession_number": "", - "description": "Code for data processing and figure reproduction available in Bitbucket", - "data_type": [ - "Health data", - "Drug discovery data" - ], - "data_url": "https://bitbucket.org/sonnhammergroup/unadrug" - } - ], - "title": "Drug repurposing improves disease targeting 11-fold and can be augmented by network module targeting, applied to COVID-19", - "issue": "1", - "volume": "11", - "publisher": "Springer Science and Business Media LLC", - "published": "2021-10-19", - "author": [ - "Rivero-García I.", - "Castresana-Aguirre M.", - "Guglielmo L.", - "Guala D.", - "Sonnhammer E. L. L." - ] - }, - { - "doi": "10.1016/j.isci.2021.103185", - "available_items": [ - { - "type": "data", - "repo_name": "Mendeley", - "accession_number": "", - "description": "Clinical and raw data related to serological assay", - "data_type": [ - "Health data", - "Serology data" - ], - "data_url": "https://data.mendeley.com/datasets/69tvkst9ct/1" - } - ], - "title": "SARS-CoV-2 integral membrane proteins shape the serological responses of patients with COVID-19", - "issue": "10", - "volume": "24", - "publisher": "Elsevier BV", - "published": "2022-07-24", - "author": [ - "Martin S.", - "Heslan C.", - "Jégou G.", - "Eriksson L. A.", - "Le Gallo M." - ] - }, - { - "doi": "10.1080/15592294.2021.1969499", - "available_items": [ - { - "type": "code", - "repo_name": "", - "accession_number": "", - "description": "R scripts to analyse Alveolar macrophages (HLA-DR+/CD3-) and lymphocytes (CD3+) specific cell types from DNA methylation analysis.", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://github.com/JD2112/Alveolar-Cell-Type-Deconvolution" - } - ], - "title": "DNA methylome-based validation of induced sputum as an effective protocol to study lung immunity: construction of a classifier of pulmonary cell types", - "issue": "8", - "volume": "17", - "publisher": "Informa UK Limited", - "published": "2021-09-05", - "author": [ - "Das J.", - "Idh N.", - "Sikkeland L. I. B.", - "Paues J.", - "Lerm M." - ] - }, - { - "doi": "10.1016/j.cell.2021.09.003", - "available_items": [ - { - "type": "data", - "repo_name": "Zenodo", - "accession_number": "", - "description": "Initial release of SARS-CoV2 variation data", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://zenodo.org/record/5149112#.YnjZ_S8Rqu4" - }, - { - "type": "data, code", - "repo_name": "", - "accession_number": "", - "description": "Visualising selection analysis results for evolution of the B.1.351 clade", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://observablehq.com/@spond/n501y-clades@3752" - }, - { - "type": "data, code", - "repo_name": "", - "accession_number": "", - "description": "Frequency trends and selection detection of subsets of sites in SARS-CoV-2 genes", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://observablehq.com/@spond/sc2-selection-trends" - }, - { - "type": "data, code", - "repo_name": "", - "accession_number": "", - "description": "Temporal evolution of selective pressures on SARS-CoV-2 genes", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://observablehq.com/@spond/sc2-temporal-selection-trends" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Collection of result files and underlying sequence alignments processed by the RASCL SARS-CoV-2 clade analysis pipeline", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://github.com/spond/SARS-CoV-2-clade-analysis" - } - ], - "title": "The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages", - "issue": "20", - "volume": "184", - "publisher": "Elsevier BV", - "published": "2022-05-19", - "author": [ - "Martin D. P.", - "Weaver S.", - "Tegally H.", - "San J. E.", - "Shank S. D." - ] - }, - { - "doi": "10.1016/j.invent.2021.100402", - "available_items": [ - { - "type": "data", - "repo_name": "Figshare", - "accession_number": "", - "description": "Data and metadata from a randomised clinical trial, and the demographic questionaire ", - "data_type": [ - "Health data" - ], - "data_url": "https://figshare.com/articles/dataset/Efficacy_of_Internet-based_cognitive_behavioral_therapy_and_applied_relaxation_for_tinnitus_distress_in_the_United_States_ICBT_vs_IAR_study_A_Randomized_Clinical_Trial/13679179" - } - ], - "title": "Dismantling internet-based cognitive behavioral therapy for tinnitus. The contribution of applied relaxation: A randomized controlled trial", - "issue": "", - "volume": "25", - "publisher": "Elsevier BV", - "published": "2021-09-16", - "author": [ - "Beukes E. W.", - "Andersson G.", - "Fagelson M. A.", - "Manchaiah V." - ] - }, - { - "doi": "10.1002/cti2.1340", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "COVID-19 patients’ repertoire data: AIRR-seq data (iReceptor Study ID IR-Binder-000001)", - "data_type": [ - "Genomics & transcriptomics data", - "Health data" - ], - "data_url": "https://gateway.ireceptor.org/login" - }, - { - "type": "data", - "repo_name": "European Nucleotide Archive", - "accession_number": "PRJEB38339", - "description": "Raw FASTQ sequencing files are deposited in the European Nucleotide Archive", - "data_type": [ - "Genomics & transcriptomics data", - "Health data" - ], - "data_url": "https://www.ebi.ac.uk/ena/browser/view/PRJEB38339" - } - ], - "title": "Landscape of T‐cell repertoires with public COVID‐19‐associated T‐cell receptors in pre‐pandemic risk cohorts", - "issue": "9", - "volume": "10", - "publisher": "Wiley", - "published": "2021-09-27", - "author": [ - "Simnica D.", - "Schultheiß C.", - "Mohme M.", - "Paschold L.", - "Willscher E." - ] - }, - { - "doi": "10.1002/mpr.1892", - "available_items": [ - { - "type": "data", - "repo_name": "Figshare", - "accession_number": "", - "description": "Database with codebook for the European Alcohol Use and COVID-19 Survey", - "data_type": [ - "Public health data", - "Health data", - "Social science and humanities data" - ], - "data_url": "https://figshare.com/articles/dataset/ESAC_database/13580693/1" - } - ], - "title": "Measuring changes in alcohol use in Finland and Norway during the COVID‐19 pandemic: Comparison between data sources", - "issue": "4", - "volume": "30", - "publisher": "Wiley", - "published": "2021-08-27", - "author": [ - "Mäkelä P.", - "Rossow I.", - "Moan I. S.", - "Bye E. K.", - "Kilian C." - ] - }, - { - "doi": "10.1136/bmjopen-2020-048025", - "available_items": [ - { - "type": "data, code", - "repo_name": "Open Science Framework", - "accession_number": "", - "description": "Data on vaccine acceptance and code for analysis", - "data_type": [ - "Public health data", - "Social science and humanities data" - ], - "data_url": "https://osf.io/vgez2/" - }, - { - "type": "data", - "repo_name": "Figshare", - "accession_number": "", - "description": "Image data, the image analysis pipelines, and extracted features", - "data_type": [ - "Public health data", - "Social science and humanities data" - ], - "data_url": "https://scilifelab.figshare.com/articles/dataset/A_phenomics_approach_for_antiviral_drug_discovery_-_Images_analysis_pipelines_and_feature_data/14188403/1" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Code for analysis", - "data_type": [ - "Public health data", - "Social science and humanities data" - ], - "data_url": "https://github.com/pharmbio/antiviral-phenomics" - } - ], - "title": "Correlates of intended COVID-19 vaccine acceptance across time and countries: results from a series of cross-sectional surveys", - "issue": "8", - "volume": "11", - "publisher": "BMJ", - "published": "2021-08-02", - "author": [ - "Kerr J. R.", - "Schneider C. R.", - "Recchia G.", - "Dryhurst S.", - "Sahlin U." - ] - }, - { - "doi": "10.1038/s41562-021-01173-x", - "available_items": [ - { - "type": "data, code", - "repo_name": "Open Science Framework", - "accession_number": "", - "description": "Data (raw and processed) and analysis code related to emotion-regulation strategy testing", - "data_type": [ - "Public health data", - "Social science and humanities data" - ], - "data_url": "https://osf.io/jeu73/" - } - ], - "title": "A multi-country test of brief reappraisal interventions on emotions during the COVID-19 pandemic", - "issue": "8", - "volume": "5", - "publisher": "Springer Science and Business Media LLC", - "published": "2021-08-02", - "author": [ - "Wang K.", - "Goldenberg A.", - "Dorison C. A.", - "Miller J. K.", - "Uusberg A." - ] - }, - { - "doi": "https://doi.org/10.1038/s41467-021-24832-z", - "available_items": [ - { - "type": "data, code", - "repo_name": "Figshare", - "accession_number": "", - "description": "Data from different provinces and analysis code", - "data_type": [ - "Public health data", - "Social science and humanities data", - "Other data" - ], - "data_url": "https://figshare.com/articles/software/NatComm/14153351/1" - } - ], - "title": "Impact of tiered restrictions on human activities and the epidemiology of the second wave of COVID-19 in Italy", - "issue": "", - "volume": "12", - "publisher": "Nature Communications", - "published": "2021-07-27", - "author": [ - "Manica M.", - "Guzzetta G.", - "Riccardo F.", - "Valenti A.", - "Poletti P." - ] - }, - { - "doi": "10.1080/23744235.2021.1957143", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Data on subjects from first and second infection", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://www.tandfonline.com/doi/figure/10.1080/23744235.2021.1957143?scroll=top&needAccess=true" - } - ], - "title": "Recurrent and persistent infection with SARS-CoV-2 – epidemiological data and case reports from Western Sweden, 2020", - "issue": "12", - "volume": "53", - "publisher": "Informa UK Limited", - "published": "2021-07-24", - "author": [ - "Ringlander J.", - "Olausson J.", - "Nyström K.", - "Härnqvist T.", - "Jakobsson H. E." - ] - }, - { - "doi": "10.1098/rstb.2020.0267", - "available_items": [ - { - "type": "data, code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Data and code related to household-contact-tracing", - "data_type": [ - "Public health data", - "Social science and humanities data" - ], - "data_url": "https://github.com/martyn1fyles/HouseholdContactTracing" - } - ], - "title": "Using a household-structured branching process to analyse contact tracing in the SARS-CoV-2 pandemic", - "issue": "1829", - "volume": "376", - "publisher": "The Royal Society", - "published": "2021-05-31", - "author": [ - "Fyles M.", - "Fearon E.", - "Overton C.", - "Wingfield T.", - "Medley G. F." - ] - }, - { - "doi": "10.1038/s41591-021-01454-y", - "available_items": [ - { - "type": "data, code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Deidentified participant data, analysis code and replication files", - "data_type": [ - "Public health data", - "Social science and humanities data" - ], - "data_url": "https://github.com/wzb-ipi/covid_vaccines_nmed" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Analysis code and replication exercise", - "data_type": [ - "Public health data", - "Social science and humanities data" - ], - "data_url": "https://wzb-ipi.github.io/covid_vaccines_nmed/" - } - ], - "title": "COVID-19 vaccine acceptance and hesitancy in low- and middle-income countries", - "issue": "8", - "volume": "27", - "publisher": "Springer Science and Business Media LLC", - "published": "2021-07-16", - "author": [ - "Solís Arce J. S.", - "Warren S. S.", - "Meriggi N. F.", - "Scacco A.", - "McMurry N." - ] - }, - { - "doi": "10.1038/s41366-021-00893-4", - "available_items": [ - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Analysis code used by the CHARYBDIS study", - "data_type": [ - "Public health data" - ], - "data_url": "https://github.com/ohdsi-studies/Covid19CharacterizationCharybdis" - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Data produced and used by the CHARYBDIS study", - "data_type": [ - "Public health data" - ], - "data_url": "https://data.ohdsi.org/Covid19CharacterizationCharybdis/" - } - ], - "title": "Characteristics and outcomes of 627 044 COVID-19 patients living with and without obesity in the United States, Spain, and the United Kingdom", - "issue": "11", - "volume": "45", - "publisher": "Springer Science and Business Media LLC", - "published": "2021-07-15", - "author": [ - "Recalde M.", - "Roel E.", - "Pistillo A.", - "Sena A. G.", - "Prats-Uribe A." - ] - }, - { - "doi": "10.1016/j.janxdis.2021.102454", - "available_items": [ - { - "type": "data", - "repo_name": "Open Science Framework", - "accession_number": "", - "description": "Methods used and survey results on factors related to mental health issues related to COVID-19", - "data_type": [ - "Public health data", - "Social science and humanities data" - ], - "data_url": "https://osf.io/jcnf3/" - } - ], - "title": "Fear and anxiety in the face of COVID-19: Negative dispositions towards risk and uncertainty as vulnerability factors", - "issue": "", - "volume": "83", - "publisher": "Elsevier BV", - "published": "2021-09-09", - "author": [ - "Millroth P.", - "Frey R." - ] - }, - { - "doi": "10.1136/bmjopen-2021-049302", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Numbers of deaths by influenza and suicide and total population for 1910-1978", - "data_type": [ - "Public health data", - "Social science and humanities data" - ], - "data_url": "https://osf.io/jcnf3/" - } - ], - "title": "Swedish nationwide time series analysis of influenza and suicide deaths from 1910 to 1978", - "issue": "7", - "volume": "11", - "publisher": "BMJ", - "published": "2022-01-13", - "author": [ - "Rück C.", - "Mataix-Cols D.", - "Malki K.", - "Adler M.", - "Flygare O." - ] - }, - { - "doi": "10.1038/s41598-021-93390-7", - "available_items": [ - { - "type": "data", - "repo_name": "Zenodo", - "accession_number": "", - "description": "Proteomics dataset based on plasma samples from 1,388 subjects.", - "data_type": [ - "Public health data", - "Protein data", - "Genomics & transcriptomics data" - ], - "data_url": "https://zenodo.org/record/4280776#.YnkeOy8RpTZ" - } - ], - "title": "An artificial neural network approach integrating plasma proteomics and genetic data identifies PLXNA4 as a new susceptibility locus for pulmonary embolism", - "issue": "1", - "volume": "11", - "publisher": "Springer Science and Business Media LLC", - "published": "2021-07-07", - "author": [ - "Razzaq M.", - "Iglesias M. J.", - "Ibrahim-Kosta M.", - "Goumidi L.", - "Soukarieh O." - ] - }, - { - "doi": "10.1177/14034948211023633", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Perceived changes in capability during the COVID-19 pandemic (includes data on socioeconomic position, place of birth and regional residence)", - "data_type": [ - "Public health data", - "Health data", - "Social science and humanities data" - ], - "data_url": "https://snd.gu.se/sv/catalogue/study/2020-206/1/1#dataset" - } - ], - "title": "Perceived changes in capability during the COVID-19 pandemic: A Swedish cross-sectional study from June 2020", - "issue": "1", - "volume": "50", - "publisher": "SAGE Publications", - "published": "2021-07-02", - "author": [ - "Meili K. W.", - "Jonsson H.", - "Lindholm L.", - "Månsdotter A." - ] - }, - { - "doi": "10.1098/rsos.210386", - "available_items": [ - { - "type": "data", - "repo_name": "Figshare", - "accession_number": "", - "description": "Information on Matlab files, summary statistics, R0 values, and data visualisations", - "data_type": [ - "Public health data" - ], - "data_url": "https://rs.figshare.com/collections/Supplementary_material_from_The_risk_for_a_new_COVID-19_wave_and_how_it_depends_on_i_R_i_sub_0_sub_the_current_immunity_level_and_current_restrictions_/5526951" - } - ], - "title": "The risk for a new COVID-19 wave and how it depends on\n R\n 0\n , the current immunity level and current restrictions", - "issue": "7", - "volume": "8", - "publisher": "The Royal Society", - "published": "2021-07-28", - "author": [ - "Britton T.", - "Trapman P.", - "Ball F." - ] - }, - { - "doi": "10.1002/advs.202101222", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Raw, patient-level characteristics and data available in Supporting Information", - "data_type": [ - "Public health data", - "Health data" - ], - "data_url": "10.1002/advs.202101222" - } - ], - "title": "Combined Metabolic Activators Accelerates Recovery in Mild‐to‐Moderate COVID‐19", - "issue": "17", - "volume": "8", - "publisher": "Wiley", - "published": "2021-06-28", - "author": [ - "Altay O.", - "Arif M.", - "Li X.", - "Yang H.", - "Aydın M." - ] - }, - { - "doi": "10.1136/bmjopen-2020-048172", - "available_items": [ - { - "type": "data", - "repo_name": "Open Science Framework", - "accession_number": "", - "description": "Vaccine acceptance in Denmark, France, Germany, Hungary, Sweden, Italy, UK and USA; September 2020 to February 2021.", - "data_type": [ - "Public health data", - "Social science and humanities data" - ], - "data_url": "10.1002/advs.202101222" - } - ], - "title": "Public acceptance of COVID-19 vaccines: cross-national evidence on levels and individual-level predictors using observational data", - "issue": "6", - "volume": "11", - "publisher": "BMJ", - "published": "2021-06-15", - "author": [ - "Lindholt M. F.", - "Jørgensen F.", - "Bor A.", - "Petersen M. B." - ] - }, - { - "doi": "10.12688/wellcomeopenres.16661.2", - "available_items": [ - { - "type": "data", - "repo_name": "Zenodo", - "accession_number": "", - "description": "Data underlying cov-lineages.org website.", - "data_type": [ - "Public health data", - "Genomics & transcriptomics data" - ], - "data_url": "https://zenodo.org/record/4640140#.YntNOi8Rqu4" - }, - { - "type": "data", - "repo_name": "Zenodo", - "accession_number": "", - "description": "Accession IDs included in publication tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2.", - "data_type": [ - "Public health data", - "Genomics & transcriptomics data" - ], - "data_url": "https://zenodo.org/record/4642401#.YntNGC8Rqu4" - }, - { - "type": "data", - "repo_name": "Zenodo", - "accession_number": "", - "description": "Supplementary materials with group affiliations for tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2.", - "data_type": [ - "Public health data", - "Genomics & transcriptomics data" - ], - "data_url": "https://zenodo.org/record/4704471#.YntODS8Rqu4" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Current source code for grinch (global report investigating novel coronavirus haplotypes) software.", - "data_type": [ - "Public health data", - "Genomics & transcriptomics data" - ], - "data_url": "https://github.com/cov-lineages/grinch" - }, - { - "type": "data", - "repo_name": "GitHub", - "accession_number": "", - "description": "Data on global lineage reports (on variants of concern), lineages, and software tools.", - "data_type": [ - "Public health data", - "Genomics & transcriptomics data" - ], - "data_url": "https://cov-lineages.org/index.html#global_reports" - } - ], - "title": "Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch", - "issue": "", - "volume": "6", - "publisher": "F1000 Research Ltd", - "published": "2021-09-17", - "author": [ - "O'Toole Á.", - "Hill V.", - "Pybus O. G.", - "Watts A.", - "Bogoch I. I." - ] - }, - { - "doi": "10.1186/s12985-021-01556-6", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Summary swab results, and Ct values and RT-qPCR validation results for samples all included with the article", - "data_type": [ - "Public health data" - ], - "data_url": "https://virologyj.biomedcentral.com/articles/10.1186/s12985-021-01556-6" - } - ], - "title": "SARS-CoV-2 in hospital indoor environments is predominantly non-infectious", - "issue": "1", - "volume": "18", - "publisher": "Springer Science and Business Media LLC", - "published": "2021-06-02", - "author": [ - "Krambrich J.", - "Akaberi D.", - "Ling J.", - "Hoffman T.", - "Svensson L." - ] - }, - { - "doi": "10.1186/s12959-021-00272-z", - "available_items": [ - { - "type": "data", - "repo_name": "Figshare", - "accession_number": "", - "description": "Metadata record for PRONMED Uppsala COVID-19 ICU Biobank (facilitates data access requests)", - "data_type": [ - "Health data", - "Genomics & transcriptomics data" - ], - "data_url": "https://scilifelab.figshare.com/articles/dataset/PRONMED_Uppsala_COVID-19_ICU_Biobank/14229410/1" - } - ], - "title": "Point of care ultrasound screening for deep vein thrombosis in critically ill COVID-19 patients, an observational study", - "issue": "1", - "volume": "19", - "publisher": "Springer Science and Business Media LLC", - "published": "2021-06-02", - "author": [ - "Galien S.", - "Hultström M.", - "Lipcsey M.", - "Stattin K.", - "Frithiof R." - ] - }, - { - "doi": "10.1136/bmjnph-2021-000250", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "ZOE COVID Study website (providing information on raw data and data visualisations).", - "data_type": [ - "Health data", - "Public health data" - ], - "data_url": "https://covid.joinzoe.com" - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Supplementary Information (includes information on relevant survey questions, summary statistics and flowcharts about the study).", - "data_type": [ - "Health data", - "Public health data" - ], - "data_url": "https://nutrition.bmj.com/content/4/1/149#supplementary-materials" - } - ], - "title": "Modest effects of dietary supplements during the COVID-19 pandemic: insights from 445 850 users of the COVID-19 Symptom Study app", - "issue": "1", - "volume": "4", - "publisher": "BMJ", - "published": "2021-04-19", - "author": [ - "Louca P.", - "Murray B.", - "Klaser K.", - "Graham M. S.", - "Mazidi M." - ] - }, - { - "doi": "10.1016/S2589-7500(21)00077-7", - "available_items": [ - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Code for data processing, visualisation, and analysis.", - "data_type": [ - "Health data" - ], - "data_url": "https://github.com/brueggemann-lab/iris-ldh-2020" - } - ], - "title": "Changes in the incidence of invasive disease due to Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis during the COVID-19 pandemic in 26 countries and territories in the Invasive Respiratory Infection Surveillance Initiative: a prospective analysis of surveillance data", - "issue": "6", - "volume": "3", - "publisher": "Elsevier BV", - "published": "2022-07-24", - "author": [ - "Brueggemann A. B.", - "Jansen van Rensburg M. J.", - "Shaw D.", - "McCarthy N. D.", - "Jolley K. A." - ] - }, - { - "doi": "10.1016/j.jmb.2021.167118", - "available_items": [ - { - "type": "data", - "repo_name": "Protein Data Bank", - "accession_number": "7KFI", - "description": "7KFI SARS-CoV-2 Main protease immature form - apo structure", - "data_type": [ - "Genomics & transcriptomics data", - "Protein data" - ], - "data_url": "https://www.rcsb.org/structure/7KFI" - }, - { - "type": "data", - "repo_name": "Protein Data Bank", - "accession_number": "7MBG", - "description": "7MBG SARS-CoV-2 Main protease in orthorhombic space group", - "data_type": [ - "Genomics & transcriptomics data", - "Protein data" - ], - "data_url": "https://www.rcsb.org/structure/7MBG" - }, - { - "type": "data", - "repo_name": "Protein Data Bank", - "accession_number": "7KPH", - "description": "7KPH SARS-CoV-2 Main Protease in mature form", - "data_type": [ - "Genomics & transcriptomics data", - "Protein data" - ], - "data_url": "https://www.rcsb.org/structure/7KPH" - }, - { - "type": "data", - "repo_name": "Protein Data Bank", - "accession_number": "7N6N", - "description": "7N6N SARS-CoV-2 Main protease C145S mutant in complex with N and C-terminal residues", - "data_type": [ - "Genomics & transcriptomics data", - "Protein data" - ], - "data_url": "https://www.rcsb.org/structure/7N6N" - }, - { - "type": "data", - "repo_name": "Protein Data Bank", - "accession_number": "7LFE", - "description": "7LFE SARS-CoV-2 Main protease immature form - F2X Entry Library E03 fragment", - "data_type": [ - "Genomics & transcriptomics data", - "Protein data" - ], - "data_url": "https://www.rcsb.org/structure/7LFE" - }, - { - "type": "data", - "repo_name": "Protein Data Bank", - "accession_number": "7LDX", - "description": "7LDX SARS-CoV-2 Main protease immature form - F2X Entry Library E06 fragment", - "data_type": [ - "Genomics & transcriptomics data", - "Protein data" - ], - "data_url": "https://www.rcsb.org/structure/7LDX" - }, - { - "type": "data", - "repo_name": "Protein Data Bank", - "accession_number": "7LFP", - "description": "7LFP SARS-CoV-2 Main protease immature form - F2X Entry Library G05 fragment", - "data_type": [ - "Genomics & transcriptomics data", - "Protein data" - ], - "data_url": "https://www.rcsb.org/structure/7LFP" - }, - { - "type": "data", - "repo_name": "Protein Data Bank", - "accession_number": "7KVL", - "description": "7KVL SARS-CoV-2 Main protease immature form - FMAX Library E01 fragment", - "data_type": [ - "Genomics & transcriptomics data", - "Protein data" - ], - "data_url": "https://www.rcsb.org/structure/7KVL" - }, - { - "type": "data", - "repo_name": "Protein Data Bank", - "accession_number": "7N5Z", - "description": "7N5Z SARS-CoV-2 Main protease C145S mutant", - "data_type": [ - "Genomics & transcriptomics data", - "Protein data" - ], - "data_url": "https://www.rcsb.org/structure/7N5Z" - }, - { - "type": "data", - "repo_name": "Protein Data Bank", - "accession_number": "7KVR", - "description": "7KVR SARS-CoV-2 Main protease immature form - FMAX Library E09 fragment", - "data_type": [ - "Genomics & transcriptomics data", - "Protein data" - ], - "data_url": "https://www.rcsb.org/structure/7KVR" - } - ], - "title": "A Crystallographic Snapshot of SARS-CoV-2 Main Protease Maturation Process", - "issue": "18", - "volume": "433", - "publisher": "Elsevier BV", - "published": "2022-06-23", - "author": [ - "Noske G.", - "Nakamura A.", - "Gawriljuk V.", - "Fernandes R.", - "Lima G." - ] - }, - { - "doi": "10.1101/2021.05.28.446179", - "available_items": [ - { - "type": "data", - "repo_name": "Zenodo", - "accession_number": "", - "description": "Biophysical characterisation of the SARS-CoV-2 E protein.", - "data_type": [ - "Protein data" - ], - "data_url": "https://zenodo.org/record/4818292#.YntbbC8RpTY" - } - ], - "title": "Probing effects of the SARS-CoV-2 E protein on membrane curvature and intracellular calcium", - "issue": "", - "volume": "", - "publisher": "Cold Spring Harbor Laboratory", - "published": "2021-05-28", - "author": [ - "Mehregan A.", - "Pérez-Conesa S.", - "Zhuang Y.", - "Elbahnsi A.", - "Pasini D." - ] - }, - { - "doi": "10.1038/s41467-021-22664-5", - "available_items": [ - { - "type": "data", - "repo_name": "Gene Expression Omnibus", - "accession_number": "GSE163688", - "description": "Sequencing data for all experiments.", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE163688" - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Primer sequences are in Supplementary Data 2.", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-021-22664-5/MediaObjects/41467_2021_22664_MOESM5_ESM.xlsx" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "code to analyse Next-Generation Sequencing (NGS) data.", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://github.com/alex-stark-imp/SARSeq" - } - ], - "title": "Multiplexed detection of SARS-CoV-2 and other respiratory infections in high throughput by SARSeq", - "issue": "1", - "volume": "12", - "publisher": "Springer Science and Business Media LLC", - "published": "2021-05-25", - "author": [ - "Yelagandula R.", - "Bykov A.", - "Vogt A.", - "Heinen R.", - "Özkan E." - ] - }, - { - "doi": "10.1038/s41420-021-00487-z", - "available_items": [ - { - "type": "data", - "repo_name": "ProteomeXchange", - "accession_number": "PXD023450", - "description": "Raw mass spectromic data.", - "data_type": [ - "Protein data" - ], - "data_url": "http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD023450" - }, - { - "type": "data", - "repo_name": "GitHub", - "accession_number": "", - "description": "bioinformatic analysis codes.", - "data_type": [ - "Protein data" - ], - "data_url": "https://github.com/neogilab/COVID_IFN" - } - ], - "title": "Type-I interferon signatures in SARS-CoV-2 infected Huh7 cells", - "issue": "1", - "volume": "7", - "publisher": "Springer Science and Business Media LLC", - "published": "2021-05-18", - "author": [ - "Chen X.", - "Saccon E.", - "Appelberg K. S.", - "Mikaeloff F.", - "Rodriguez J. E." - ] - }, - { - "doi": "10.1371/journal.pone.0251151", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Dataset on the COVID-19 pandemic and serious psychological consequences in Bangladesh: a population-based nationwide study.", - "data_type": [ - "Social science and humanities data", - "Health data" - ], - "data_url": "https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/YKH9C1" - } - ], - "title": "Knowledge and preventive behaviors regarding COVID-19 in Bangladesh: A nationwide distribution", - "issue": "5", - "volume": "16", - "publisher": "Public Library of Science (PLoS)", - "published": "2021-05-03", - "author": [ - "Hosen I.", - "Pakpour A. H.", - "Sakib N.", - "Hussain N.", - "al Mamun F." - ] - }, - { - "doi": "10.1038/s41598-021-88481-4", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "OxCOVID19 Database to download", - "data_type": [ - "Public health data" - ], - "data_url": "https://covid19.eng.ox.ac.uk/" - }, - { - "type": "data", - "repo_name": "GitHub", - "accession_number": "", - "description": "CSV extracts from the OxCOVID19 Database", - "data_type": [ - "Public health data" - ], - "data_url": "https://github.com/covid19db/data" - }, - { - "type": "data", - "repo_name": "Figshare", - "accession_number": "", - "description": "Complete OxCOVID19 Database in CSV format as of 2020-07-31", - "data_type": [ - "Public health data" - ], - "data_url": "https://doi.org/10.6084/m9.figshare.12746150" - } - ], - "title": "OxCOVID19 Database, a multimodal data repository for better understanding the global impact of COVID-19", - "issue": "1", - "volume": "11", - "publisher": "Springer Science and Business Media LLC", - "published": "2021-04-29", - "author": [ - "Mahdi A.", - "Błaszczyk P.", - "Dłotko P.", - "Salvi D.", - "Chan T." - ] - }, - { - "doi": "10.1186/s12889-021-10897-4", - "available_items": [ - { - "type": "data", - "repo_name": "Figshare", - "accession_number": "", - "description": "Individual-level demographic, occupational, COVID-19 data", - "data_type": [ - "Social science and humanities data", - "Health data" - ], - "data_url": "https://figshare.com/articles/dataset/QUAN_Strand_Dataset_-_Occupational_Burnout_and_Job_Satisfaction_Among_Physicians_in_Times_of_COVID-19_Crisis_A_Convergent_Parallel_Mixed-Method_Study/14058185/1" - } - ], - "title": "Occupational burnout and job satisfaction among physicians in times of COVID-19 crisis: a convergent parallel mixed-method study", - "issue": "1", - "volume": "21", - "publisher": "Springer Science and Business Media LLC", - "published": "2021-04-28", - "author": [ - "Alrawashdeh H. M.", - "Al-Tammemi A. B.", - "Alzawahreh M. K.", - "Al-Tamimi A.", - "Elkholy M." - ] - }, - { - "doi": "10.1038/s41598-021-85877-0", - "available_items": [ - { - "type": "data", - "repo_name": "BioStudies", - "accession_number": "S-BSST416", - "description": "Proteomic data", - "data_type": [ - "Protein data" - ], - "data_url": "https://www.ebi.ac.uk/biostudies/studies/S-BSST416?query=S-BSST416" - }, - { - "type": "code", - "repo_name": "Zenodo", - "accession_number": "", - "description": "Application related to proteomic data analysis", - "data_type": [ - "Protein data" - ], - "data_url": "https://zenodo.org/record/3895886#.Yo3E_S8RpTY" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Code behind application related to proteomic data analysis", - "data_type": [ - "Protein data" - ], - "data_url": "https://github.com/hamelpatel/COVID19_proteomic/blob/v1.0" - } - ], - "title": "Proteomic blood profiling in mild, severe and critical COVID-19 patients", - "issue": "1", - "volume": "11", - "publisher": "Springer Science and Business Media LLC", - "published": "2021-03-18", - "author": [ - "Patel H.", - "Ashton N. J.", - "Dobson R. J. B.", - "Andersson L.", - "Yilmaz A." - ] - }, - { - "doi": "10.1007/s40279-021-01438-5", - "available_items": [ - { - "type": "data", - "repo_name": "Open Science Framework", - "accession_number": "", - "description": "Raw data, plots, surveys", - "data_type": [ - "Health data", - "Social science and humanities data" - ], - "data_url": "https://osf.io/xhryf/" - } - ], - "title": "The Impact of Coronavirus (COVID-19) Related Public-Health Measures on Training Behaviours of Individuals Previously Participating in Resistance Training: A Cross-Sectional Survey Study", - "issue": "7", - "volume": "51", - "publisher": "Springer Science and Business Media LLC", - "published": "2021-04-19", - "author": [ - "Steele J.", - "Androulakis-Korakakis P.", - "Carlson L.", - "Williams D.", - "Phillips S." - ] - }, - { - "doi": "10.21203/rs.3.rs-419853/v1", - "available_items": [ - { - "type": "data", - "repo_name": "Figshare", - "accession_number": "", - "description": "Metadata record detailing data access requirements", - "data_type": [ - "Health data" - ], - "data_url": "https://scilifelab.figshare.com/articles/dataset/PRONMED_Uppsala_COVID-19_ICU_Biobank/14229410/1" - } - ], - "title": "ECG with Prior Myocardial Infarction Pattern or acute ST-T Pathology is Associated with Death in Critically Ill COVID-19 Patients", - "issue": "", - "volume": "", - "publisher": "Research Square Platform LLC", - "published": "2021-04-19", - "author": [ - "Rosen J.", - "Noreland M.", - "Stattin K.", - "Lipcsey M.", - "Frithiof R." - ] - }, - { - "doi": "10.1101/2021.04.03.438330", - "available_items": [ - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Code to acquire and analyse data", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://github.com/MurrellGroup/VOCfreq" - } - ], - "title": "Driving potent neutralization of a SARS-CoV-2 Variant of Concern with a heterotypic boost", - "issue": "", - "volume": "", - "publisher": "Cold Spring Harbor Laboratory", - "published": "2021-04-05", - "author": [ - "Sheward D. J.", - "Mandolesi M.", - "Urgard E.", - "Kim C.", - "Hanke L." - ] - }, - { - "doi": "10.2807/1560-7917.ES.2021.26.16.2100348", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Data in supplementary materials/appendices - data on genetic data divided by demogaphic factors", - "data_type": [ - "Genomics & transcriptomics data", - "Other data" - ], - "data_url": "https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2021.26.16.2100348" - } - ], - "title": "Characteristics of SARS-CoV-2 variants of concern B.1.1.7, B.1.351 or P.1: data from seven EU/EEA countries, weeks 38/2020 to 10/2021", - "issue": "16", - "volume": "26", - "publisher": "European Centre for Disease Control and Prevention (ECDC)", - "published": "2021-04-22", - "author": [ - "Funk T.", - "Pharris A.", - "Spiteri G.", - "Bundle N.", - "Melidou A." - ] - }, - { - "doi": "10.1038/s41587-021-00860-4", - "available_items": [ - { - "type": "data", - "repo_name": "ProteomeXchange", - "accession_number": "PXD023613", - "description": "The data generated for the benchmarks and the drug response screen in yeast", - "data_type": [ - "Protein data" - ], - "data_url": "http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD023613" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Open-source algorithms made available through the DIA–NN software suite", - "data_type": [ - "Protein data" - ], - "data_url": "https://github.com/vdemichev/diann" - } - ], - "title": "Ultra-fast proteomics with Scanning SWATH", - "issue": "7", - "volume": "39", - "publisher": "Springer Science and Business Media LLC", - "published": "2021-03-25", - "author": [ - "Messner C. B.", - "Demichev V.", - "Bloomfield N.", - "Yu J. S. L.", - "White M." - ] - }, - { - "doi": "10.1017/S0950268821000649", - "available_items": [ - { - "type": "data", - "repo_name": "Zenodo", - "accession_number": "", - "description": "Datasets of the original ECDC data and the curve fits", - "data_type": [ - "Public health data" - ], - "data_url": "https://zenodo.org/record/4454173#.Yo3Rby8RpTY" - } - ], - "title": "A simple model for the total number of SARS-CoV-2 infections on a national level", - "issue": "", - "volume": "149", - "publisher": "Cambridge University Press (CUP)", - "published": "2021-04-06", - "author": [ - "Blanco N.", - "Stafford K. A.", - "Lavoie M. C.", - "Brandenburg A.", - "Górna M. W." - ] - }, - { - "doi": "10.1136/bmjopen-2021-058422", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Data are from the SNAC-K Project, a population-based study on ageing and dementia. Need approval for access.", - "data_type": [ - "Public health data", - "Other data", - "Social science and humanities data" - ], - "data_url": "https://www.snac-k.se" - } - ], - "title": "COVID-19 collateral damage—psychological burden and behavioural changes among older adults during the first outbreak in Stockholm, Sweden: a cross-sectional study", - "issue": "1", - "volume": "12", - "publisher": "BMJ", - "published": "2022-01-07", - "author": [ - "Beridze G.", - "Triolo F.", - "Grande G.", - "Fratiglioni L.", - "Calderón-Larrañaga A." - ] - }, - { - "doi": "10.1016/j.celrep.2021.108852", - "available_items": [ - { - "type": "data", - "repo_name": "Mendeley", - "accession_number": "", - "description": "Data required to produce the figures, includes data on proteomics and immunology", - "data_type": [ - "Serology data", - "Protein data" - ], - "data_url": "https://data.mendeley.com/datasets/stxwzbyfsc/1?__hstc=25856994.201473a88516d23766c33b93f465990b.1653472457683.1653472457683.1653472457683.1&__hssc=25856994.1.1653472457683&__hsfp=1159211105" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "R code for multi-omics factor analyses, correlations, and plots", - "data_type": [ - "Serology data", - "Protein data" - ], - "data_url": "https://github.com/GRP92/PRNT_manuscript" - } - ], - "title": "Virological and immunological features of SARS-CoV-2-infected children who develop neutralizing antibodies", - "issue": "11", - "volume": "34", - "publisher": "Elsevier BV", - "published": "2021-06-24", - "author": [ - "Cotugno N.", - "Ruggiero A.", - "Bonfante F.", - "Petrara M. R.", - "Zicari S." - ] - }, - { - "doi": "10.1101/2021.03.10.21252820", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Summary statistics generated by COVID-19 HGI", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://www.covid19hg.org/results/r5/" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Code for Mendelian randomization and genetic correlation pipeline", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://github.com/marcoralab/MRcovid" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Code for summary statistics liftover and meta-analysis and PCA pipeline", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://github.com/covid19-hg/" - } - ], - "title": "Mapping the human genetic architecture of COVID-19 by worldwide meta-analysis", - "issue": "", - "volume": "", - "publisher": "Cold Spring Harbor Laboratory", - "published": "2021-03-12", - "author": [ - "Ganna A." - ] - }, - { - "doi": "10.1136/bmjopen-2020-042387", - "available_items": [ - { - "type": "code", - "repo_name": "GitLab", - "accession_number": "", - "description": "R and Stata code related to COVID-19 mortality assessment", - "data_type": [ - "Health data", - "Social science and humanities data", - "Other data" - ], - "data_url": "https://gitlab.switch.ch/torsten.hothorn/relative_covid-19_mortality" - } - ], - "title": "Assessing relative COVID-19 mortality: a Swiss population-based study", - "issue": "3", - "volume": "11", - "publisher": "BMJ", - "published": "2021-03-08", - "author": [ - "Hothorn T.", - "Bopp M.", - "Günthard H.", - "Keiser O.", - "Roelens M." - ] - }, - { - "doi": "10.1038/s41598-021-84356-w", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Pseudonymised, individual-level data that allow full replication of the results in this article are freely available from joakim.dillner@sll.se or from the Karolinska University Hospital data analysis department: tableau.karolinska@sll.se.", - "data_type": [ - "Public health data", - "Serology data" - ], - "data_url": "https://www.nature.com/articles/s41598-021-84356-w" - } - ], - "title": "Antibodies to SARS-CoV-2 and risk of past or future sick leave", - "issue": "1", - "volume": "11", - "publisher": "Springer Science and Business Media LLC", - "published": "2021-03-04", - "author": [ - "Dillner J.", - "Elfström K. M.", - "Blomqvist J.", - "Eklund C.", - "Lagheden C." - ] - }, - { - "doi": "10.1073/pnas.2020834118", - "available_items": [ - { - "type": "code", - "repo_name": "Open Science Framework", - "accession_number": "", - "description": "Analysis code", - "data_type": [ - "Health data", - "Other data", - "Social science and humanities data" - ], - "data_url": "https://osf.io/4zegu/" - } - ], - "title": "The effects of school closures on SARS-CoV-2 among parents and teachers", - "issue": "9", - "volume": "118", - "publisher": "Proceedings of the National Academy of Sciences", - "published": "2021-02-11", - "author": [ - "Vlachos J.", - "Hertegård E.", - "B. Svaleryd H." - ] - }, - { - "doi": "10.1017/S0950268821000510", - "available_items": [ - { - "type": "code", - "repo_name": "", - "accession_number": "", - "description": "Analysis code (R)", - "data_type": [ - "Health data", - "Other data" - ], - "data_url": "https://static.cambridge.org/content/id/urn:cambridge.org:id:article:S0950268821000510/resource/name/S0950268821000510sup001.zip" - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Data related to incubation period and patient.", - "data_type": [ - "Health data", - "Other data" - ], - "data_url": "https://static.cambridge.org/content/id/urn:cambridge.org:id:article:S0950268821000510/resource/name/S0950268821000510sup001.zip" - } - ], - "title": "Epidemiology and transmission characteristics of early COVID-19 cases, 20 January–19 March 2020, in Bavaria, Germany", - "issue": "", - "volume": "149", - "publisher": "Cambridge University Press (CUP)", - "published": "2021-03-15", - "author": [ - "Böhm S.", - "Woudenberg T.", - "Chen D.", - "Marosevic D. V.", - "Böhmer M. M." - ] - }, - { - "doi": "10.1016/j.ebiom.2021.103259", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Possible to apply for access to deidentified patient data and samples", - "data_type": [ - "Serology data" - ], - "data_url": "https://covid-consortium.com/application-for-samples/" - } - ], - "title": "Time series analysis and mechanistic modelling of heterogeneity and sero-reversion in antibody responses to mild SARS‑CoV-2 infection", - "issue": "", - "volume": "65", - "publisher": "Elsevier BV", - "published": "2021-05-29", - "author": [ - "Manisty C.", - "Treibel T. A.", - "Jensen M.", - "Semper A.", - "Joy G." - ] - }, - { - "doi": "10.3390/jcm10050896", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Patient characteristics, medical treatment regiments, symptoms, laboratory findings, ophthalmic findings, systemic symtoms for each patient", - "data_type": [ - "Other data" - ], - "data_url": "https://www.mdpi.com/2077-0383/10/5/896/s1" - } - ], - "title": "Ophthalmic Screening in Patients with Coronavirus Disease 2019: A Prospective Cohort Study", - "issue": "5", - "volume": "10", - "publisher": "MDPI AG", - "published": "2021-02-24", - "author": [ - "Papazoglou A.", - "Conen A.", - "Haubitz S.", - "Tschopp M.", - "Guignard V. J." - ] - }, - { - "doi": "10.1101/2021.02.18.21251422", - "available_items": [ - { - "type": "data", - "repo_name": "Gitlab", - "accession_number": "", - "description": "Data related to olfaction tests", - "data_type": [ - "Public health data", - "Other data" - ], - "data_url": "https://gitlab.com/snitz/smelltracker_article" - }, - { - "type": "code", - "repo_name": "Gitlab", - "accession_number": "", - "description": "Analysis code (Matlab)", - "data_type": [ - "Public health data", - "Other data" - ], - "data_url": "https://gitlab.com/snitz/smelltracker_article" - } - ], - "title": "A Novel Olfactory Self-Test Effectively Screens for COVID-19", - "issue": "", - "volume": "", - "publisher": "Cold Spring Harbor Laboratory", - "published": "2021-02-23", - "author": [ - "Snitz K.", - "Honigstein D.", - "Weissgross R.", - "Ravia A.", - "Mishor E." - ] - }, - { - "doi": "10.3389/fpubh.2021.579948", - "available_items": [ - { - "type": "data", - "repo_name": "GitHub", - "accession_number": "", - "description": "Data held on daily death counts for Sweden from 1860 to 31.08.2020; the total population of Sweden for the years 1860 to 2019 (from Statistics Sweden).", - "data_type": [ - "Public health data" - ], - "data_url": "https://github.com/aledberg/outbreaks" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Code to do analysis and produce figures.", - "data_type": [ - "Public health data" - ], - "data_url": "https://github.com/aledberg/outbreaks" - } - ], - "title": "Mortality of the COVID-19 Outbreak in Sweden in Relation to Previous Severe Disease Outbreaks", - "issue": "", - "volume": "9", - "publisher": "Frontiers Media SA", - "published": "2021-02-18", - "author": [ - "Ledberg A." - ] - }, - { - "doi": "10.1371/journal.pone.0244924", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Knowledge, attitudes, and practices (KAP) survey results.", - "data_type": [ - "Public health data", - "Other data", - "Social science and humanities data" - ], - "data_url": "https://reshare.ukdataservice.ac.uk/854605/" - } - ], - "title": "Community health worker knowledge, attitudes and practices towards COVID-19: Learnings from an online cross-sectional survey using a digital health platform, UpSCALE, in Mozambique", - "issue": "2", - "volume": "16", - "publisher": "Public Library of Science (PLoS)", - "published": "2021-02-10", - "author": [ - "Feldman M.", - "Lacey Krylova V.", - "Farrow P.", - "Donovan L.", - "Zandamela E." - ] - }, - { - "doi": "10.1016/j.imu.2021.100529", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Results of the efficacy of FDA approved antiviral drugs on SARS-CoV-2 spike glycoprotein.", - "data_type": [ - "Protein data", - "Drug discovery data" - ], - "data_url": "http://fulir.irb.hr/6161/" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "The Vini in silico model of cancer.", - "data_type": [ - "Protein data", - "Drug discovery data" - ], - "data_url": "https://github.com/draskot/Vini" - } - ], - "title": "The screening and evaluation of potential clinically significant HIV drug combinations against the SARS-CoV-2 virus", - "issue": "", - "volume": "23", - "publisher": "Elsevier BV", - "published": "2022-07-23", - "author": [ - "Tomić D.", - "Davidović D.", - "Szasz A. M.", - "Rezeli M.", - "Pirkić B." - ] - }, - { - "doi": "10.1038/s41598-020-80352-8", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Raw data for amplification curves, and Ct values for clinical samples.", - "data_type": [ - "Genomics & transcriptomics data", - "Other data" - ], - "data_url": "https://static-content.springer.com/esm/art%3A10.1038%2Fs41598-020-80352-8/MediaObjects/41598_2020_80352_MOESM2_ESM.xlsx" - } - ], - "title": "Direct detection of SARS-CoV-2 using non-commercial RT-LAMP reagents on heat-inactivated samples", - "issue": "1", - "volume": "11", - "publisher": "Springer Science and Business Media LLC", - "published": "2021-01-19", - "author": [ - "Alekseenko A.", - "Barrett D.", - "Pareja-Sanchez Y.", - "Howard R. J.", - "Strandback E." - ] - }, - { - "doi": "10.1073/pnas.2020732118", - "available_items": [ - { - "type": "data", - "repo_name": "Protein Data Bank", - "accession_number": "7AJP", - "description": "Crystal Structure of Human Adenovirus 56 Fiber Knob.", - "data_type": [ - "Protein data", - "Biochemistry data" - ], - "data_url": "https://www.rcsb.org/structure/7AJP" - } - ], - "title": "Human species D adenovirus hexon capsid protein mediates cell entry through a direct interaction with CD46", - "issue": "3", - "volume": "118", - "publisher": "Proceedings of the National Academy of Sciences", - "published": "2020-12-31", - "author": [ - "Persson B. D.", - "John L.", - "Rafie K.", - "Strebl M.", - "Frängsmyr L." - ] - }, - { - "doi": "10.1101/2021.01.13.21249429", - "available_items": [ - { - "type": "data", - "repo_name": "Figshare", - "accession_number": "", - "description": "Most data in paper, but metadata record is available as an access point for individual data requests.", - "data_type": [ - "Health data" - ], - "data_url": "https://doi.org/10.17044/scilifelab.14229410" - } - ], - "title": "Elevated Angiopoietin-2 inhibits thrombomodulin-mediated anticoagulation in critically ill COVID-19 patients", - "issue": "", - "volume": "", - "publisher": "Cold Spring Harbor Laboratory", - "published": "2021-01-15", - "author": [ - "Hultstrom M.", - "Fromell K.", - "Larsson A.", - "Quaggin S. E.", - "Betsholtz C." - ] - }, - { - "doi": "10.1038/s41467-020-20653-8", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Source data behind study.", - "data_type": [ - "Biochemistry data", - "Drug discovery data" - ], - "data_url": "https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-020-20653-8/MediaObjects/41467_2020_20653_MOESM4_ESM.xlsx" - } - ], - "title": "SARS-CoV-2 spike glycoprotein vaccine candidate NVX-CoV2373 immunogenicity in baboons and protection in mice", - "issue": "1", - "volume": "12", - "publisher": "Springer Science and Business Media LLC", - "published": "2021-01-14", - "author": [ - "Tian J.", - "Patel N.", - "Haupt R.", - "Zhou H.", - "Weston S." - ] - }, - { - "doi": "10.1186/s12912-021-00540-3", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Data cannot be publicly shared, but applications can be made for access.", - "data_type": [ - "Public health data", - "Other data" - ], - "data_url": "https://bmcnurs.biomedcentral.com/articles/10.1186/s12912-021-00540-3#availability-of-data-and-materials" - } - ], - "title": "Malpractice claimed calls within the Swedish Healthcare Direct: a descriptive – comparative case study", - "issue": "1", - "volume": "20", - "publisher": "Springer Science and Business Media LLC", - "published": "2021-01-14", - "author": [ - "Björkman A.", - "Engström M.", - "Winblad U.", - "Holmström I. K." - ] - }, - { - "doi": "10.1016/j.ijid.2021.01.023", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Patient demographics, management and outcome in 42 kidney recipients with COVID-19.", - "data_type": [ - "Health data" - ], - "data_url": "https://www.ijidonline.com/cms/10.1016/j.ijid.2021.01.023/attachment/10ccf84a-9c50-4457-b428-6a46ea9babe3/mmc1.docx" - } - ], - "title": "COVID-19 after kidney transplantation: Early outcomes and renal function following antiviral treatment", - "issue": "", - "volume": "104", - "publisher": "Elsevier BV", - "published": "2021-06-12", - "author": [ - "Elec A. D.", - "Oltean M.", - "Goldis P.", - "Cismaru C.", - "Lupse M." - ] - }, - { - "doi": "10.1038/s41598-021-95968-7", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Data cannot be shared publicly, but applications can be made for access.", - "data_type": [ - "Health data", - "Biochemistry data" - ], - "data_url": "https://www.nature.com/articles/s41598-021-95968-7#data-availability" - } - ], - "title": "Acquired olfactory loss alters functional connectivity and morphology", - "issue": "1", - "volume": "11", - "publisher": "Springer Science and Business Media LLC", - "published": "2021-08-12", - "author": [ - "Iravani B.", - "Peter M. G.", - "Arshamian A.", - "Olsson M. J.", - "Hummel T." - ] - }, - { - "doi": "10.1126/science.abe6230", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Data generated/analysed are in the article or supplementary materials.", - "data_type": [ - "Protein data", - "Biochemistry data", - "Imaging data" - ], - "data_url": "https://www.science.org/doi/10.1126/science.abe6230" - }, - { - "type": "data", - "repo_name": "Protein Data Bank", - "accession_number": "7KN5", - "description": "Crystal structure of SARS-CoV-2 receptor binding domain complexed with nanobodies VHH E and U.", - "data_type": [ - "Protein data", - "Biochemistry data", - "Imaging data" - ], - "data_url": "https://www.rcsb.org/structure/7KN5" - }, - { - "type": "data", - "repo_name": "Protein Data Bank", - "accession_number": "7KN6", - "description": "Crystal structure of SARS-CoV-2 receptor binding domain complexed with nanobody VHH V and antibody Fab CC12.3.", - "data_type": [ - "Protein data", - "Biochemistry data", - "Imaging data" - ], - "data_url": "https://www.rcsb.org/structure/7KN6" - }, - { - "type": "data", - "repo_name": "Protein Data Bank", - "accession_number": "7KN7", - "description": "Crystal structure of SARS-CoV-2 receptor binding domain complexed with nanobody VHH W and antibody Fab CC12.3.", - "data_type": [ - "Protein data", - "Biochemistry data", - "Imaging data" - ], - "data_url": "https://www.rcsb.org/structure/7KN7" - }, - { - "type": "data", - "repo_name": "Protein Data Bank", - "accession_number": "7KSG", - "description": "SARS-CoV-2 spike in complex with nanobodies E.", - "data_type": [ - "Protein data", - "Biochemistry data", - "Imaging data" - ], - "data_url": "https://www.rcsb.org/structure/7KSG" - }, - { - "type": "data", - "repo_name": "Protein Data Bank", - "accession_number": "7B14", - "description": "Nanobody E bound to Spike-RBD in a localized reconstruction.", - "data_type": [ - "Protein data", - "Biochemistry data", - "Imaging data" - ], - "data_url": "https://www.rcsb.org/structure/7B14" - }, - { - "type": "data", - "repo_name": "Protein Data Bank", - "accession_number": "7B11", - "description": "SARS-CoV-spike with two RBDs up bound to VHH V on all RBDs.", - "data_type": [ - "Protein data", - "Biochemistry data", - "Imaging data" - ], - "data_url": "https://www.rcsb.org/structure/unreleased/7B11" - }, - { - "type": "data", - "repo_name": "Protein Data Bank", - "accession_number": "7B18", - "description": "SARS-CoV-spike bound to two neutralising nanobodies.", - "data_type": [ - "Protein data", - "Biochemistry data", - "Imaging data" - ], - "data_url": "https://www.rcsb.org/structure/7B18" - }, - { - "type": "data", - "repo_name": "Protein Data Bank", - "accession_number": "7B17", - "description": "SARS-CoV-spike RBD bound to two neutralising nanobodies.", - "data_type": [ - "Protein data", - "Biochemistry data", - "Imaging data" - ], - "data_url": "https://www.rcsb.org/structure/7B17" - }, - { - "type": "data", - "repo_name": "Electron Microscopy Data Bank", - "accession_number": "EMD-23018", - "description": "SARS-CoV-2 spike in complex with nanobodies E.", - "data_type": [ - "Protein data", - "Biochemistry data", - "Imaging data" - ], - "data_url": "https://www.ebi.ac.uk/emdb/EMD-23018" - }, - { - "type": "data", - "repo_name": "Electron Microscopy Data Bank", - "accession_number": "EMD-11978", - "description": "Nanobody E bound to Spike-RBD in a localized reconstruction.", - "data_type": [ - "Protein data", - "Biochemistry data", - "Imaging data" - ], - "data_url": "https://www.ebi.ac.uk/emdb/EMD-11978" - }, - { - "type": "data", - "repo_name": "Electron Microscopy Data Bank", - "accession_number": "EMD-11981", - "description": "SARS-CoV-spike bound to two neutralising nanobodies.", - "data_type": [ - "Protein data", - "Biochemistry data", - "Imaging data" - ], - "data_url": "https://www.ebi.ac.uk/emdb/EMD-11981" - }, - { - "type": "data", - "repo_name": "Electron Microscopy Data Bank", - "accession_number": "EMD-11980", - "description": "SARS-CoV-spike RBD bound to two neutralising nanobodies.", - "data_type": [ - "Protein data", - "Biochemistry data", - "Imaging data" - ], - "data_url": "https://www.ebi.ac.uk/emdb/EMD-11980" - }, - { - "type": "data", - "repo_name": "BioProject", - "accession_number": "PRJNA679438", - "description": "Structure-guided multivalent nanobodies block SARS-CoV-2 infection and suppress mutational escape.", - "data_type": [ - "Protein data", - "Biochemistry data", - "Imaging data" - ], - "data_url": "https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA679438" - } - ], - "title": "Structure-guided multivalent nanobodies block SARS-CoV-2 infection and suppress mutational escape", - "issue": "6530", - "volume": "371", - "publisher": "American Association for the Advancement of Science (AAAS)", - "published": "2021-02-12", - "author": [ - "Koenig P.", - "Das H.", - "Liu H.", - "Kümmerer B. M.", - "Gohr F. N." - ] - }, - { - "doi": "10.3390/vaccines9010042", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Data cannot be shared publicly, but applications can be made for access.", - "data_type": [ - "Public health data", - "Social science and humanities data" - ], - "data_url": "https://www.mdpi.com/2076-393X/9/1/42/htm" - } - ], - "title": "High Rates of COVID-19 Vaccine Hesitancy and Its Association with Conspiracy Beliefs: A Study in Jordan and Kuwait among Other Arab Countries", - "issue": "1", - "volume": "9", - "publisher": "MDPI AG", - "published": "2021-01-12", - "author": [ - "Sallam M.", - "Dababseh D.", - "Eid H.", - "Al-Mahzoum K.", - "Al-Haidar A." - ] - }, - { - "doi": "10.1186/s12931-020-01605-8", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Data cannot be shared publicly, but applications can be made for access.", - "data_type": [ - "Biochemistry data", - "Health data" - ], - "data_url": "https://respiratory-research.biomedcentral.com/articles/10.1186/s12931-020-01605-8" - } - ], - "title": "Sputum ACE2, TMPRSS2 and FURIN gene expression in severe neutrophilic asthma", - "issue": "1", - "volume": "22", - "publisher": "Springer Science and Business Media LLC", - "published": "2021-01-07", - "author": [ - "Kermani N. Z.", - "Song W.", - "Badi Y.", - "Versi A.", - "Guo Y." - ] - }, - { - "doi": "10.1371/journal.pone.0244824", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Data are available in the article and supplementary materials (including Ct values & gel images).", - "data_type": [ - "Genomics & transcriptomics data", - "Health data" - ], - "data_url": "https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0244824" - } - ], - "title": "A direct RT-qPCR approach to test large numbers of individuals for SARS-CoV-2", - "issue": "12", - "volume": "15", - "publisher": "Public Library of Science (PLoS)", - "published": "2020-12-31", - "author": [ - "Maricic T.", - "Nickel O.", - "Aximu-Petri A.", - "Essel E.", - "Gansauge M." - ] - }, - { - "doi": "10.3390/v13010037", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Data are available in the article and supplementary materials (effect of novel antiviral compounds against ZIKV in several cell models).", - "data_type": [ - "Biochemistry data", - "Other data" - ], - "data_url": "https://www.mdpi.com/1999-4915/13/1/37/s1" - } - ], - "title": "Broadly Active Antiviral Compounds Disturb Zika Virus Progeny Release Rescuing Virus-Induced Toxicity in Brain Organoids", - "issue": "1", - "volume": "13", - "publisher": "MDPI AG", - "published": "2020-12-29", - "author": [ - "Pettke A.", - "Tampere M.", - "Pronk R.", - "Wallner O.", - "Falk A." - ] - }, - { - "doi": "10.1111/joim.13304", - "available_items": [ - { - "type": "data", - "repo_name": "GitHub", - "accession_number": "", - "description": "Data related to discriminative bayesian seroprevalence", - "data_type": [ - "Health data", - "Serology data" - ], - "data_url": "https://github.com/MurrellGroup/DiscriminativeSeroprevalence" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Code related to discriminative bayesian seroprevalence (see notebook).", - "data_type": [ - "Health data", - "Serology data" - ], - "data_url": "https://github.com/MurrellGroup/DiscriminativeSeroprevalence" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Code used in analysis of seroprevalence data (R)", - "data_type": [ - "Health data", - "Serology data" - ], - "data_url": "https://github.com/chr1swallace/seroprevalence-paper" - }, - { - "type": "data", - "repo_name": "GitHub", - "accession_number": "", - "description": "Seroprevalence data related to R code", - "data_type": [ - "Health data", - "Serology data" - ], - "data_url": "https://github.com/chr1swallace/seroprevalence-paper" - } - ], - "title": "Seropositivity in blood donors and pregnant women during the first year of SARS‐CoV‐2 transmission in Stockholm, Sweden", - "issue": "3", - "volume": "290", - "publisher": "Wiley", - "published": "2021-05-18", - "author": [ - "Castro Dopico X.", - "Muschiol S.", - "Christian M.", - "Hanke L.", - "Sheward D. J." - ] - }, - { - "doi": "10.1093/rheumatology/keaa771", - "available_items": [ - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Study protocol and analysis source code", - "data_type": [ - "Drug discovery data", - "Health data", - "Social science and humanities data" - ], - "data_url": "https://github.com/ohdsi-studies/Covid19EstimationHydroxychloroquine2" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Analysis tools used in study", - "data_type": [ - "Drug discovery data", - "Health data", - "Social science and humanities data" - ], - "data_url": "https://github.com/OHDSI/" - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Data and results artefacts that do not include patient-level health information", - "data_type": [ - "Drug discovery data", - "Health data", - "Social science and humanities data" - ], - "data_url": "http://data.ohdsi.org/Covid19EstimationHydroxychloroquine2" - } - ], - "title": "Risk of depression, suicide and psychosis with hydroxychloroquine treatment for rheumatoid arthritis: a multinational network cohort study", - "issue": "", - "volume": "", - "publisher": "Oxford University Press (OUP)", - "published": "2020-12-25", - "author": [ - "Lane J. C. E.", - "Weaver J.", - "Kostka K.", - "Duarte-Salles T.", - "Abrahao M. T. F." - ] - }, - { - "doi": "10.1016/j.ebiom.2021.103277", - "available_items": [ - { - "type": "data", - "repo_name": "GitHub", - "accession_number": "", - "description": "Data on collaborative genetic studies of idiopathic pulmonary fibrosis.", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://github.com/genomicsITER/PFgenetics" - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "COVID19-hg GWAS meta-analyses data.", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://github.com/genomicsITER/PFgenetics" - } - ], - "title": "Shared genetic etiology between idiopathic pulmonary fibrosis and COVID-19 severity", - "issue": "", - "volume": "65", - "publisher": "Elsevier BV", - "published": "2022-07-22", - "author": [ - "Fadista J.", - "Kraven L. M.", - "Karjalainen J.", - "Andrews S. J.", - "Geller F." - ] - }, - { - "doi": "10.1101/2020.12.15.20248247", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Data cannot be made publicly available, but those with written permission from the Swedish Ethical Review Authority may be granted access.", - "data_type": [ - "Health data" - ], - "data_url": "https://www.medrxiv.org/node/189563.external-links.html" - } - ], - "title": "Large differences in community COVID-19 testing across geographic areas in a Swedish region with 385,000 inhabitants", - "issue": "", - "volume": "", - "publisher": "Cold Spring Harbor Laboratory", - "published": "2020-12-16", - "author": [ - "Kennedy B.", - "Martinell M.", - "Hammar U.", - "van Zoest V.", - "Kristiansson R. S." - ] - }, - { - "doi": "10.1101/2020.12.13.20248122", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Data cannot be made publicly available, but applications can be made for individual-level pseudonymised data.", - "data_type": [ - "Health data" - ], - "data_url": "https://www.medrxiv.org/node/189563.external-links.html" - } - ], - "title": "Screening for high amounts of SARS-CoV-2 identifies pre-symptomatic subjects among healthy healthcare workers", - "issue": "", - "volume": "", - "publisher": "Cold Spring Harbor Laboratory", - "published": "2020-12-14", - "author": [ - "Dillner J.", - "Elfström K. M.", - "Blomqvist J.", - "Engstrand L.", - "Uhlén M." - ] - }, - { - "doi": "10.1101/2020.12.11.422139", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Croatian Neandertal genome.", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "http://cdna.eva.mpg.de/neandertal/Vindija/VCF/" - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Croatian Neandertal genome (alternate source).", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://bioinf.eva.mpg.de/jbrowse/" - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Modern human genome.", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/" - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "GWAS summary statistics (round 4 release: A/B2_ALL_eur_leave_23andme).", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://www.covid19hg.org/results/" - } - ], - "title": "The MERS-CoV receptor gene is among COVID-19 risk factors inherited from Neandertals", - "issue": "", - "volume": "", - "publisher": "Cold Spring Harbor Laboratory", - "published": "2020-12-12", - "author": [ - "Zeberg H.", - "Pääbo S." - ] - }, - { - "doi": "10.1002/jcp.30206", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "All data are included in the paper.", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://onlinelibrary.wiley.com/doi/10.1002/jcp.30206" - } - ], - "title": "Thermal inactivation of COVID‐19 specimens improves RNA quality and quantity", - "issue": "7", - "volume": "236", - "publisher": "Wiley", - "published": "2020-12-11", - "author": [ - "Hemati M.", - "Soosanabadi M.", - "Ghorashi T.", - "Ghaffari H.", - "Vahedi A." - ] - }, - { - "doi": "10.1038/s41597-020-00778-7", - "available_items": [ - { - "type": "data", - "repo_name": "Zenodo", - "accession_number": "", - "description": "Raw dataset: perceived likelihoods and impacts, individual and authorities’ preparedness and knowledge, socio-demographic characteristics in August 2020 (N=2,033 in Italy, N=2,121 in Sweden)", - "data_type": [ - "Public health data", - "Social science and humanities data" - ], - "data_url": "https://zenodo.org/record/4034277#.YsfjOS8RpTY" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Code for reading, processing and graphically representing the data", - "data_type": [ - "Public health data", - "Social science and humanities data" - ], - "data_url": "https://github.com/elenamondino/nationwide_survey" - } - ], - "title": "Public perceptions of multiple risks during the COVID-19 pandemic in Italy and Sweden", - "issue": "1", - "volume": "7", - "publisher": "Springer Science and Business Media LLC", - "published": "2021-12-02", - "author": [ - "Mondino E.", - "Di Baldassarre G.", - "Mård J.", - "Ridolfi E.", - "Rusca M." - ] - }, - { - "doi": "10.1080/2162402X.2020.1857112", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Allelic frequencies of FPR1 SNPs and characteristics of patient population from Hôpital Cochin and Hôpital Européen George Pompidou", - "data_type": [ - "Genomics & transcriptomics data", - "Health data" - ], - "data_url": "https://www.tandfonline.com/doi/figure/10.1080/2162402X.2020.1857112?scroll=top&needAccess=true" - } - ], - "title": "No impact of cancer and plague-relevant FPR1 polymorphisms on COVID-19", - "issue": "1", - "volume": "9", - "publisher": "Informa UK Limited", - "published": "2020-01-01", - "author": [ - "Petrazzuolo A.", - "Le Naour J.", - "Vacchelli E.", - "Gaussem P.", - "Ellouze S." - ] - }, - { - "doi": "10.3390/v12121423", - "available_items": [ - { - "type": "data", - "repo_name": "Figshare", - "accession_number": "", - "description": "Thermal Proteome Profiling dataset from Hazara virus infected SW13 cells treated with DMSO or antiviral inhibitor 20 µM TH6744", - "data_type": [ - "Genomics & transcriptomics data", - "Biochemistry data", - "Protein data", - "Drug discovery data" - ], - "data_url": "https://scilifelab.figshare.com/articles/dataset/Thermal_Proteome_Profiling_dataset_from_Hazara_virus_infected_SW13_cells_treated_with_DMSO_or_antiviral_inhibitor_20_M_TH6744_/13089023" - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Antiviral screening; Dose-response treatment of TH6744 and TH3289; List of proteins from 2D-TPP analysis in U87 cells (FDR); List of proteins from 2D-TPP analysis in U87 cells (Fold-change); Uniprot annotation of overlapping TPP-TR and 2D-TPP hits", - "data_type": [ - "Genomics & transcriptomics data", - "Biochemistry data", - "Protein data", - "Drug discovery data" - ], - "data_url": "https://www.mdpi.com/1999-4915/12/12/1423/s1" - }, - { - "type": "data", - "repo_name": "ProteomeXchange Consortium", - "accession_number": "PXD021494", - "description": "Raw mass spectrometry data", - "data_type": [ - "Genomics & transcriptomics data", - "Biochemistry data", - "Protein data", - "Drug discovery data" - ], - "data_url": "http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD021494" - } - ], - "title": "Novel Broad-Spectrum Antiviral Inhibitors Targeting Host Factors Essential for Replication of Pathogenic RNA Viruses", - "issue": "12", - "volume": "12", - "publisher": "MDPI AG", - "published": "2020-12-10", - "author": [ - "Tampere M.", - "Pettke A.", - "Salata C.", - "Wallner O.", - "Koolmeister T." - ] - }, - { - "doi": "10.1007/s10875-020-00928-x", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "General laboratory tests, immunologic investigation, computed tomographies of the chest of 17 primary immunodeficient patients infected with COVID-19", - "data_type": [ - "Genomics & transcriptomics data", - "Public health data" - ], - "data_url": "https://static-content.springer.com/esm/art%3A10.1007%2Fs10875-020-00928-x/MediaObjects/10875_2020_928_MOESM1_ESM.docx" - } - ], - "title": "Impact of SARS-CoV-2 Pandemic on Patients with Primary Immunodeficiency", - "issue": "2", - "volume": "41", - "publisher": "Springer Science and Business Media LLC", - "published": "2020-12-01", - "author": [ - "Delavari S.", - "Abolhassani H.", - "Abolnezhadian F.", - "Babaha F.", - "Iranparast S." - ] - }, - { - "doi": "10.1016/s2589-7500(20)30289-2", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Much of the data cannot be shared publicly, but applications can be made for access", - "data_type": [ - "Health data" - ], - "data_url": "https://data.ohdsi.org/IcariusSusceptibility/" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "start-to-finish open and executable source code", - "data_type": [ - "Health data" - ], - "data_url": "https://github.com/ohdsi-studies/Covid19Icarius" - } - ], - "title": "Renin–angiotensin system blockers and susceptibility to COVID-19: an international, open science, cohort analysis", - "issue": "2", - "volume": "3", - "publisher": "Elsevier BV", - "published": "2022-07-24", - "author": [ - "Morales D. R.", - "Conover M. M.", - "You S. C.", - "Pratt N.", - "Kostka K." - ] - }, - { - "doi": "10.1002/psp4.12568", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Experimental data are in the supplementary material", - "data_type": [ - "Biochemistry data", - "Other data" - ], - "data_url": "https://ascpt.onlinelibrary.wiley.com/action/downloadSupplement?doi=10.1002%2Fpsp4.12568&file=psp412568-sup-0002-Suppinfo2.zip" - }, - { - "type": "code", - "repo_name": "GitLab", - "accession_number": "", - "description": "Code for macrophage model (matlab)", - "data_type": [ - "Biochemistry data", - "Other data" - ], - "data_url": "https://gitlab.liu.se/eliny61/macrophage-model" - } - ], - "title": "Mechanisms of a Sustained Anti‐inflammatory Drug Response in Alveolar Macrophages Unraveled with Mathematical Modeling", - "issue": "12", - "volume": "9", - "publisher": "Wiley", - "published": "2020-12-26", - "author": [ - "Nyman E.", - "Lindh M.", - "Lövfors W.", - "Simonsson C.", - "Persson A." - ] - }, - { - "doi": "10.1080/22221751.2020.1799723", - "available_items": [ - { - "type": "data", - "repo_name": "BioProject", - "accession_number": "", - "description": "Raw RNAseq data", - "data_type": [ - "Genomics & transcriptomics data", - "Protein data", - "Health data" - ], - "data_url": "https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA627100" - }, - { - "type": "data", - "repo_name": "Zenodo", - "accession_number": "", - "description": "Proteomics data", - "data_type": [ - "Genomics & transcriptomics data", - "Protein data", - "Health data" - ], - "data_url": "https://zenodo.org/record/3754719#.Ysf11C8RrOR" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "All pre-processing and analysis code", - "data_type": [ - "Genomics & transcriptomics data", - "Protein data", - "Health data" - ], - "data_url": "https://github.com/neogilab/COVID19" - } - ], - "title": "Dysregulation in Akt/mTOR/HIF-1 signaling identified by proteo-transcriptomics of SARS-CoV-2 infected cells", - "issue": "1", - "volume": "9", - "publisher": "Informa UK Limited", - "published": "2020-01-01", - "author": [ - "Appelberg S.", - "Gupta S.", - "Svensson Akusjärvi S.", - "Ambikan A. T.", - "Mikaeloff F." - ] - }, - { - "doi": "10.1111/nan.12677", - "available_items": [ - { - "type": "data", - "repo_name": "Figshare", - "accession_number": "", - "description": "Whole slide scans of ACE2 immunohistochemistry from 4 COVID-19 patients and 3 pre-pandemic controls (named PAT1-4 and CONT1-4, respectively)", - "data_type": [ - "Health data" - ], - "data_url": "https://doi.org/10.6084/m9.figshare.13089383" - }, - { - "type": "data", - "repo_name": "Figshare", - "accession_number": "", - "description": "R script to analyze ACE2 expression in basal ganglian from GTEx project", - "data_type": [ - "Health data" - ], - "data_url": "https://doi.org/10.6084/m9.figshare.13089383" - } - ], - "title": "Intracerebral endotheliitis and microbleeds are neuropathological features of COVID‐19", - "issue": "3", - "volume": "47", - "publisher": "Wiley", - "published": "2020-12-14", - "author": [ - "Kirschenbaum D.", - "Imbach L. L.", - "Rushing E. J.", - "Frauenknecht K. B. M.", - "Gascho D." - ] - }, - { - "doi": "10.1016/j.dib.2020.106621", - "available_items": [ - { - "type": "data", - "repo_name": "Harvard Dataverse", - "accession_number": "", - "description": "Raw dataset: socio-demographic characteristics, sources of information regarding COVID-19, knowledge concerning COVID-19, behavior in preventing COVID-19, etc. (n=10,067)", - "data_type": [ - "Public health data", - "Social science and humanities data" - ], - "data_url": "https://doi.org/10.7910/DVN/YKH9C1" - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Detailed description of all study variables", - "data_type": [ - "Public health data", - "Social science and humanities data" - ], - "data_url": "https://ars.els-cdn.com/content/image/1-s2.0-S2352340920315018-mmc1.docx" - } - ], - "title": "A population-based nationwide dataset concerning the COVID-19 pandemic and serious psychological consequences in Bangladesh", - "issue": "", - "volume": "33", - "publisher": "Elsevier BV", - "published": "2021-03-20", - "author": [ - "Pakpour A. H.", - "Al Mamun F.", - "Hosen I.", - "Griffiths M. D.", - "Mamun M. A." - ] - }, - { - "doi": "10.3389/fpubh.2020.571364", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Data cannot be publicly shared, though it is is possible to apply for access.", - "data_type": [ - "Public health data", - "Social science and humanities data" - ], - "data_url": "https://www.frontiersin.org/articles/10.3389/fpubh.2020.571364/full" - } - ], - "title": "Social Determinants Predict Outcomes in Data From a Multi-Ethnic Cohort of 20,899 Patients Investigated for COVID-19", - "issue": "", - "volume": "8", - "publisher": "Frontiers Media SA", - "published": "2020-11-24", - "author": [ - "Lundon D. J.", - "Mohamed N.", - "Lantz A.", - "Goltz H. H.", - "Kelly B. D." - ] - }, - { - "doi": "10.1186/s13054-020-03375-7", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Data cannot be publicly shared, though it is is possible to apply for access.", - "data_type": [ - "Health data" - ], - "data_url": "https://ccforum.biomedcentral.com/articles/10.1186/s13054-020-03375-7#availability-of-data-and-materials" - } - ], - "title": "Dosing of thromboprophylaxis and mortality in critically ill COVID-19 patients", - "issue": "1", - "volume": "24", - "publisher": "Springer Science and Business Media LLC", - "published": "2020-11-23", - "author": [ - "Jonmarker S.", - "Hollenberg J.", - "Dahlberg M.", - "Stackelberg O.", - "Litorell J." - ] - }, - { - "doi": "10.1101/2020.11.18.20233767", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Supplementary materials include a list of GISAID accession numbers for the sequences used, and a summary of public intervention actions adopted in Nordic countries.", - "data_type": [ - "Health data", - "Social science and humanities data" - ], - "data_url": "https://www.medrxiv.org/content/10.1101/2020.11.18.20233767v2.supplementary-material" - } - ], - "title": "The impact of early public health interventions on SARS-CoV-2 transmission and evolution", - "issue": "", - "volume": "", - "publisher": "Cold Spring Harbor Laboratory", - "published": "2020-11-18", - "author": [ - "Duchene S.", - "Featherstone L.", - "de Blasio B. F.", - "Holmes E. C.", - "Bohlin J." - ] - }, - { - "doi": "10.1101/2020.07.03.20145649", - "available_items": [ - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Code for modeling the impact of NPI implementations and lifting in all US states", - "data_type": [ - "Social science and humanities data", - "Health data" - ], - "data_url": "https://github.com/patrickbryant1/COVID19.github.io/tree/master/simulations/mobility/dev/US" - }, - { - "type": "data", - "repo_name": "GitHub", - "accession_number": "", - "description": "Data for modeling the impact of NPI implementations and lifting in all US states", - "data_type": [ - "Social science and humanities data", - "Health data" - ], - "data_url": "https://github.com/patrickbryant1/COVID19.github.io/tree/master/simulations/mobility/dev/US" - } - ], - "title": "The effect of opening up the US on COVID-19 spread", - "issue": "", - "volume": "", - "publisher": "Cold Spring Harbor Laboratory", - "published": "2020-07-04", - "author": [ - "Bryant P.", - "Elofsson A." - ] - }, - { - "doi": "10.1111/ejh.13502", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Provided in the article: Characteristics, treatments, COVID-19-related outcomes, additional laboratory and clinical data for 9 patients", - "data_type": [ - "Health data" - ], - "data_url": "https://onlinelibrary.wiley.com/doi/10.1111/ejh.13502" - } - ], - "title": "Outcome of COVID‐19 in multiple myeloma patients in relation to treatment", - "issue": "6", - "volume": "105", - "publisher": "Wiley", - "published": "2020-08-18", - "author": [ - "Susek K. H.", - "Gran C.", - "Ljunggren H.", - "Alici E.", - "Nahi H." - ] - }, - { - "doi": "10.1101/2020.10.19.20215046", - "available_items": [ - { - "type": "data", - "repo_name": "GitHub", - "accession_number": "", - "description": "Code related to modelling the spread of COVID-19 on a dynamic social network with spread reduction according to Google mobility changes", - "data_type": [ - "Genomics & transcriptomics data", - "Social science and humanities data" - ], - "data_url": "https://github.com/patrickbryant1/epidemic_net" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Raw data and results related to modelling the spread of COVID-19 on a dynamic social network with spread reduction according to Google mobility changes", - "data_type": [ - "Genomics & transcriptomics data", - "Social science and humanities data" - ], - "data_url": "https://github.com/patrickbryant1/epidemic_net" - } - ], - "title": "Modelling the dispersion of SARS-CoV-2 on a dynamic network graph", - "issue": "", - "volume": "", - "publisher": "Cold Spring Harbor Laboratory", - "published": "2020-10-21", - "author": [ - "Bryant P.", - "Elofsson A." - ] - }, - { - "doi": "10.1073/pnas.2012331117", - "available_items": [ - { - "type": "data", - "repo_name": "GitHub", - "accession_number": "", - "description": "Data & circos plots related to multiple sequence alignments", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://github.com/hlzeng/Filtered_MSA_SARS_CoV_2" - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Data on GISAID accession numbers and multiple sequence alignments also available in the paper", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://www.pnas.org/doi/full/10.1073/pnas.2012331117" - } - ], - "title": "Global analysis of more than 50,000 SARS-CoV-2 genomes reveals epistasis between eight viral genes", - "issue": "49", - "volume": "117", - "publisher": "Proceedings of the National Academy of Sciences", - "published": "2020-11-17", - "author": [ - "Zeng H.", - "Dichio V.", - "Rodríguez Horta E.", - "Thorell K.", - "Aurell E." - ] - }, - { - "doi": "10.1111/apa.15673", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Case report of 5 Swedish children aged 9-15, as well as parental reported symptoms occurring over 2 months after diagnosis.", - "data_type": [ - "Health data" - ], - "data_url": "https://onlinelibrary.wiley.com/doi/10.1111/apa.15673" - } - ], - "title": "Case report and systematic review suggest that children may experience similar long‐term effects to adults after clinical COVID‐19", - "issue": "3", - "volume": "110", - "publisher": "Wiley", - "published": "2020-12-03", - "author": [ - "Ludvigsson J. F." - ] - }, - { - "doi": "10.1126/sciadv.abe4724", - "available_items": [ - { - "type": "data", - "repo_name": "ArrayExpress", - "accession_number": "E-MTAB-9711", - "description": "RNA-seq of SARS-CoV-2-infected human primary hepatocyte-derived spheroids upon interferon a2 and baricitinib treatment.", - "data_type": [ - "Biochemistry data", - "Genomics & transcriptomics data", - "Health data" - ], - "data_url": "https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-9711/" - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Patient information are contained in the paper and supplementary information.", - "data_type": [ - "Biochemistry data", - "Genomics & transcriptomics data", - "Health data" - ], - "data_url": "https://www.science.org/doi/10.1126/sciadv.abe4724" - } - ], - "title": "JAK inhibition reduces SARS-CoV-2 liver infectivity and modulates inflammatory responses to reduce morbidity and mortality", - "issue": "1", - "volume": "7", - "publisher": "American Association for the Advancement of Science (AAAS)", - "published": "2022-01-14", - "author": [ - "Stebbing J.", - "Sánchez Nievas G.", - "Falcone M.", - "Youhanna S.", - "Richardson P." - ] - }, - { - "doi": "10.1016/j.watres.2020.116620", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Amount of SARS-CoV-2 in wastewater in Gothenburg per week between February and June 2020 (data available in the article).", - "data_type": [ - "Public health data" - ], - "data_url": "https://www.sciencedirect.com/science/article/pii/S0043135420311556?via%3Dihub" - } - ], - "title": "Surveillance of wastewater revealed peaks of SARS-CoV-2 preceding those of hospitalized patients with COVID-19", - "issue": "", - "volume": "189", - "publisher": "Elsevier BV", - "published": "2021-01-19", - "author": [ - "Saguti F.", - "Magnil E.", - "Enache L.", - "Churqui M. P.", - "Johansson A." - ] - }, - { - "doi": "10.1093/nar/gkaa1013", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Nuclear magnetic resonance (NMR) experimental data deposited in COVID19-NMR project", - "data_type": [ - "Biochemistry data", - "Other data" - ], - "data_url": "http://covid19-nmr.de" - }, - { - "type": "data", - "repo_name": "BioMagResBank", - "accession_number": "", - "description": "Chemical shift data deposited in BMRB (multiple accession numbers, given in Table 1 in the article).", - "data_type": [ - "Biochemistry data", - "Other data" - ], - "data_url": "http://www.bmrb.wisc.edu/" - } - ], - "title": "Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy", - "issue": "22", - "volume": "48", - "publisher": "Oxford University Press (OUP)", - "published": "2020-11-10", - "author": [ - "Wacker A.", - "Weigand J. E.", - "Akabayov S. R.", - "Altincekic N.", - "Bains J. K." - ] - }, - { - "doi": "10.1038/s41467-020-19204-y", - "available_items": [ - { - "type": "data", - "repo_name": "GitHub", - "accession_number": "", - "description": "Microscale thermophoresis (MST) and biolayer interferometry (BLI) data.", - "data_type": [ - "Biochemistry data", - "Protein data", - "Other data" - ], - "data_url": "https://github.com/tania-custodio/Sb23" - }, - { - "type": "data", - "repo_name": "SASBDB", - "accession_number": "SASDJF4", - "description": "Synthetic nanobody Sybody 23 (Sy23).", - "data_type": [ - "Biochemistry data", - "Protein data", - "Other data" - ], - "data_url": "https://www.sasbdb.org/data/SASDJF4/" - }, - { - "type": "data", - "repo_name": "SASBDB", - "accession_number": "SASDJG4", - "description": "SARS-CoV-2 spike protein ACE2 receptor binding domain (RBD).", - "data_type": [ - "Biochemistry data", - "Protein data", - "Other data" - ], - "data_url": "https://www.sasbdb.org/data/SASDJG4/" - }, - { - "type": "data", - "repo_name": "SASBDB", - "accession_number": "SASDJH4", - "description": "SARS-CoV-2 spike protein ACE2 receptor binding domain (RBD) bound to the synthetic nanobody Sybody 23 (Sy23).", - "data_type": [ - "Biochemistry data", - "Protein data", - "Other data" - ], - "data_url": "https://www.sasbdb.org/data/SASDJH4/" - }, - { - "type": "data", - "repo_name": "Electron Microscopy Data Bank", - "accession_number": "EMD-11616", - "description": "Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing sybodies (Sb23).", - "data_type": [ - "Biochemistry data", - "Protein data", - "Other data" - ], - "data_url": "https://www.ebi.ac.uk/emdb/EMD-11616" - }, - { - "type": "data", - "repo_name": "Electron Microscopy Data Bank", - "accession_number": "EMD-11617", - "description": "Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing sybodies (Sb23) 2-up conformation.", - "data_type": [ - "Biochemistry data", - "Protein data", - "Other data" - ], - "data_url": "https://www.ebi.ac.uk/emdb/EMD-11617" - }, - { - "type": "data", - "repo_name": "Protein Data Bank", - "accession_number": "7A25", - "description": "Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing sybodies (Sb23).", - "data_type": [ - "Biochemistry data", - "Protein data", - "Other data" - ], - "data_url": "https://www.rcsb.org/structure/7A25" - }, - { - "type": "data", - "repo_name": "Protein Data Bank", - "accession_number": "7A29", - "description": "Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing sybodies (Sb23) 2-up conformation.", - "data_type": [ - "Biochemistry data", - "Protein data", - "Other data" - ], - "data_url": "https://www.rcsb.org/structure/7A29" - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Sequences of all the selected sybodies.", - "data_type": [ - "Biochemistry data", - "Protein data", - "Other data" - ], - "data_url": "https://www.nature.com/articles/s41467-020-19204-y#MOESM4" - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Source data.", - "data_type": [ - "Biochemistry data", - "Protein data", - "Other data" - ], - "data_url": "https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-020-19204-y/MediaObjects/41467_2020_19204_MOESM6_ESM.xlsx" - } - ], - "title": "Selection, biophysical and structural analysis of synthetic nanobodies that effectively neutralize SARS-CoV-2", - "issue": "1", - "volume": "11", - "publisher": "Springer Science and Business Media LLC", - "published": "2020-11-04", - "author": [ - "Custódio T. F.", - "Das H.", - "Sheward D. J.", - "Hanke L.", - "Pazicky S." - ] - }, - { - "doi": "10.1002/cti2.1224", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Karolinska KI/K Covid19 Immune atlas.", - "data_type": [ - "Biochemistry data", - "Health data" - ], - "data_url": "https://covid19cellatlas.com/#/" - } - ], - "title": "Innate lymphoid cell composition associates with COVID‐19 disease severity", - "issue": "12", - "volume": "9", - "publisher": "Wiley", - "published": "2021-02-08", - "author": [ - "García M.", - "Kokkinou E.", - "Carrasco García A.", - "Parrot T.", - "Palma Medina L. M." - ] - }, - { - "doi": "10.1186/s13054-020-03351-1", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Data cannot be shared publicly due to issues with sensitivity, but it is possible to request access.", - "data_type": [ - "Health data" - ], - "data_url": "https://ccforum.biomedcentral.com/articles/10.1186/s13054-020-03351-1#availability-of-data-materials" - } - ], - "title": "Circulating bioactive adrenomedullin as a marker of sepsis, septic shock and critical illness", - "issue": "1", - "volume": "24", - "publisher": "Springer Science and Business Media LLC", - "published": "2020-11-04", - "author": [ - "Lundberg O. H. M.", - "Lengquist M.", - "Spångfors M.", - "Annborn M.", - "Bergmann D." - ] - }, - { - "doi": "10.1016/S2665-9913(20)30276-9", - "available_items": [ - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "All analysis tools used by Observational Health Data Sciences and Informatics.", - "data_type": [ - "Health data" - ], - "data_url": "https://github.com/OHDSI/" - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Data and results artefacts that do not include patient-level health information.", - "data_type": [ - "Health data" - ], - "data_url": "http://evidence.ohdsi.org:3838/Covid19EstimationHydroxychloroquine/" - } - ], - "title": "Risk of hydroxychloroquine alone and in combination with azithromycin in the treatment of rheumatoid arthritis: a multinational, retrospective study", - "issue": "11", - "volume": "2", - "publisher": "Elsevier BV", - "published": "2022-07-24", - "author": [ - "Lane J. C. E.", - "Weaver J.", - "Kostka K.", - "Duarte-Salles T.", - "Abrahao M. T. F." - ] - }, - { - "doi": "10.3389/fdata.2020.00032", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Data related to Austrian social media during COVID-19.", - "data_type": [ - "Social science and humanities data", - "Public health data" - ], - "data_url": "https://mpellert.at/covid19_monitor_austria/" - } - ], - "title": "Dashboard of Sentiment in Austrian Social Media During COVID-19", - "issue": "", - "volume": "3", - "publisher": "Frontiers Media SA", - "published": "2020-10-26", - "author": [ - "Pellert M.", - "Lasser J.", - "Metzler H.", - "Garcia D." - ] - }, - { - "doi": "10.1126/science.abd4570", - "available_items": [ - { - "type": "data", - "repo_name": "dbGaP", - "accession_number": "phs002245.v1.p1", - "description": "Genetic Determinants of Susceptibility to Severe COVID-19 Infection.", - "data_type": [ - "Genomics & transcriptomics data", - "Health data" - ], - "data_url": "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs002245.v1.p1" - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Plasma, cells, genomic DNA, and other materials/samples are available upon request from authors or the Amsterdam UMC Covid-19 Biobank.", - "data_type": [ - "Genomics & transcriptomics data", - "Health data" - ], - "data_url": "https://www.science.org/doi/10.1126/science.abd4570" - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "All additional data are in the supplementary material.", - "data_type": [ - "Genomics & transcriptomics data", - "Health data" - ], - "data_url": "https://www.science.org/doi/10.1126/science.abd4570" - } - ], - "title": "Inborn errors of type I IFN immunity in patients with life-threatening COVID-19", - "issue": "6515", - "volume": "370", - "publisher": "American Association for the Advancement of Science (AAAS)", - "published": "2020-10-23", - "author": [ - "Zhang Q.", - "Bastard P.", - "Liu Z.", - "Le Pen J.", - "Moncada-Velez M." - ] - }, - { - "doi": "10.1126/science.abd4585", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Plasma, cells, and genomic DNA, as well as other materials can be provided via material transfer agreements.", - "data_type": [ - "Genomics & transcriptomics data", - "Health data" - ], - "data_url": "https://www.science.org/doi/10.1126/science.abd4585" - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Clinical, epidemiological characteristics of 101 patients, as well as information on neutralising capacity and assays are provided in the article and supplementary materials.", - "data_type": [ - "Genomics & transcriptomics data", - "Health data" - ], - "data_url": "https://www.science.org/doi/10.1126/science.abd4585" - } - ], - "title": "Autoantibodies against type I IFNs in patients with life-threatening COVID-19", - "issue": "6515", - "volume": "370", - "publisher": "American Association for the Advancement of Science (AAAS)", - "published": "2020-10-23", - "author": [ - "Bastard P.", - "Rosen L. B.", - "Zhang Q.", - "Michailidis E.", - "Hoffmann H." - ] - }, - { - "doi": "10.1371/journal.pone.0241104", - "available_items": [ - { - "type": "data", - "repo_name": "Zenodo", - "accession_number": "", - "description": "Serum-IgG responses to SARS-CoV-2 after mild and severe COVID-19 infection.", - "data_type": [ - "Biochemistry data", - "Serology data", - "Health data" - ], - "data_url": "https://zenodo.org/record/3994670#.YsveGC8RpTY" - } - ], - "title": "Serum-IgG responses to SARS-CoV-2 after mild and severe COVID-19 infection and analysis of IgG non-responders", - "issue": "10", - "volume": "15", - "publisher": "Public Library of Science (PLoS)", - "published": "2020-10-21", - "author": [ - "Marklund E.", - "Leach S.", - "Axelsson H.", - "Nyström K.", - "Norder H." - ] - }, - { - "doi": "10.1101/2020.07.17.20155937", - "available_items": [ - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Code for discriminative bayesian seroprevalence.", - "data_type": [ - "Serology data", - "Biochemistry data", - "Health data" - ], - "data_url": "https://github.com/MurrellGroup/DiscriminativeSeroprevalence/" - }, - { - "type": "data", - "repo_name": "GitHub", - "accession_number": "", - "description": "Data for discriminative bayesian seroprevalence.", - "data_type": [ - "Serology data", - "Biochemistry data", - "Health data" - ], - "data_url": "https://github.com/MurrellGroup/DiscriminativeSeroprevalence/" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Code used in analysis of seroprevalence data.", - "data_type": [ - "Serology data", - "Biochemistry data", - "Health data" - ], - "data_url": "https://github.com/chr1swallace/seroprevalence-paper" - }, - { - "type": "data", - "repo_name": "GitHub", - "accession_number": "", - "description": "Seroprevalence data.", - "data_type": [ - "Serology data", - "Biochemistry data", - "Health data" - ], - "data_url": "https://github.com/chr1swallace/seroprevalence-paper" - } - ], - "title": "Probabilistic approaches for classifying highly variable anti-SARS-CoV-2 antibody responses", - "issue": "", - "volume": "", - "publisher": "Cold Spring Harbor Laboratory", - "published": "2020-07-17", - "author": [ - "Dopico X. C.", - "Hanke L.", - "Sheward D. J.", - "Muschiol S.", - "Aleman S." - ] - }, - { - "doi": "10.1007/s11239-020-02312-3", - "available_items": [ - { - "type": "data", - "repo_name": "Swedish national dataservice", - "accession_number": "", - "description": "All raw data underlying the study.", - "data_type": [ - "Health data" - ], - "data_url": "https://snd.gu.se/sv/catalogue/study/2020-43/1/1#dataset" - } - ], - "title": "Rotational thromboelastometry results are associated with care level in COVID-19", - "issue": "2", - "volume": "51", - "publisher": "Springer Science and Business Media LLC", - "published": "2020-10-17", - "author": [ - "Almskog L. M.", - "Wikman A.", - "Svensson J.", - "Wanecek M.", - "Bottai M." - ] - }, - { - "doi": "10.1038/s41467-020-18848-0", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Source data related to symptoms and some aggregated patient data.", - "data_type": [ - "Serology data", - "Health data" - ], - "data_url": "https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-020-18848-0/MediaObjects/41467_2020_18848_MOESM4_ESM.xlsx" - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Data cannot be made publicly available, but can be made available upon request.", - "data_type": [ - "Serology data", - "Health data" - ], - "data_url": "https://www.nature.com/articles/s41467-020-18848-0#data-availability" - } - ], - "title": "SARS-CoV-2 exposure, symptoms and seroprevalence in healthcare workers in Sweden", - "issue": "1", - "volume": "11", - "publisher": "Springer Science and Business Media LLC", - "published": "2020-10-08", - "author": [ - "Rudberg A.", - "Havervall S.", - "Månberg A.", - "Jernbom Falk A.", - "Aguilera K." - ] - }, - { - "doi": "10.1038/s41467-020-18849-z", - "available_items": [ - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Data analysis code used in the study.", - "data_type": [ - "Public health data" - ], - "data_url": "https://github.com/ohdsi-studies/Covid19HospitalizationCharacterization." - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Aggregated results are available. Individual patient-level data cannot be made publicly available, but requests may be submitted for access.", - "data_type": [ - "Public health data" - ], - "data_url": "http://evidence.ohdsi.org/Covid19CharacterizationHospitalization/" - } - ], - "title": "Deep phenotyping of 34,128 adult patients hospitalised with COVID-19 in an international network study", - "issue": "1", - "volume": "11", - "publisher": "Springer Science and Business Media LLC", - "published": "2020-10-06", - "author": [ - "Burn E.", - "You S. C.", - "Sena A. G.", - "Kostka K.", - "Abedtash H." - ] - }, - { - "doi": "10.3390/ijms21197375", - "available_items": [ - { - "type": "data", - "repo_name": "Protein Data Bank", - "accession_number": "6ZPE", - "description": "Nonstructural protein 10 (nsp10) from SARS CoV-2, 1.58Å resolution.", - "data_type": [ - "Protein data" - ], - "data_url": "https://www.rcsb.org/structure/6ZPE" - }, - { - "type": "data", - "repo_name": "Protein Data Bank", - "accession_number": "6ZCT", - "description": "Nonstructural protein 10 (nsp10) from SARS CoV-2, 2.55Å resolution.", - "data_type": [ - "Protein data" - ], - "data_url": "https://www.rcsb.org/structure/6ZCT" - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Nsp10 unfolding temperatures determined by DSF.", - "data_type": [ - "Protein data" - ], - "data_url": "http://www.mdpi.com/1422-0067/21/19/7375/s1" - } - ], - "title": "Crystal Structure of Non-Structural Protein 10 from Severe Acute Respiratory Syndrome Coronavirus-2", - "issue": "19", - "volume": "21", - "publisher": "MDPI AG", - "published": "2020-10-06", - "author": [ - "Rogstam A.", - "Nyblom M.", - "Christensen S.", - "Sele C.", - "Talibov V. O." - ] - }, - { - "doi": "10.1016/j.cell.2020.08.017", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "All data generated during the study (predicted binding affinities, donor characteristics, sample information, and some analyses) are available in the article.", - "data_type": [ - "Genomics & transcriptomics data", - "Protein data", - "Other data" - ], - "data_url": "https://www.cell.com/cell/fulltext/S0092-8674(20)31008-4?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867420310084%3Fshowall%3Dtrue#secsectitle0060" - } - ], - "title": "Robust T Cell Immunity in Convalescent Individuals with Asymptomatic or Mild COVID-19", - "issue": "1", - "volume": "183", - "publisher": "Elsevier BV", - "published": "2020-10-01", - "author": [ - "Sekine T.", - "Perez-Potti A.", - "Rivera-Ballesteros O.", - "Strålin K.", - "Gorin J." - ] - }, - { - "doi": "10.1212/WNL.0000000000010977", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Data cannot be made publicly available, but access to anonymised data can be requested.", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://n.neurology.org/content/96/2/e294/tab-figures-data" - } - ], - "title": "CSF biomarkers in patients with COVID-19 and neurological symptoms", - "issue": "", - "volume": "", - "publisher": "Ovid Technologies (Wolters Kluwer Health)", - "published": "2020-10-01", - "author": [ - "Edén A.", - "Kanberg N.", - "Gostner J.", - "Fuchs D.", - "Hagberg L." - ] - }, - { - "doi": "10.1038/s41586-020-2818-3", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Summary statistics of the genome-wide association study are available from the COVID-19 Host Genetics Initiative (round 3, ANA_B2_V2: hospitalized patients with COVID-19 compared with population controls).", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://www.covid19hg.org/" - } - ], - "title": "The major genetic risk factor for severe COVID-19 is inherited from Neanderthals", - "issue": "7835", - "volume": "587", - "publisher": "Springer Science and Business Media LLC", - "published": "2020-09-30", - "author": [ - "Zeberg H.", - "Pääbo S." - ] - }, - { - "doi": "10.1126/sciimmunol.abe1670", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Curated flow cytometry data are available for exploration via the Karolinska COVID-19 Immune Atlas.", - "data_type": [ - "Health data", - "Protein data", - "Genomics & transcriptomics data" - ], - "data_url": "https://covid19cellatlas.com/#/" - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "All other data are available in the article itself or the supplementary materials.", - "data_type": [ - "Health data", - "Protein data", - "Genomics & transcriptomics data" - ], - "data_url": "https://www.science.org/doi/10.1126/sciimmunol.abe1670" - } - ], - "title": "MAIT cell activation and dynamics associated with COVID-19 disease severity", - "issue": "51", - "volume": "5", - "publisher": "American Association for the Advancement of Science (AAAS)", - "published": "2020-09-18", - "author": [ - "Parrot T.", - "Gorin J.", - "Ponzetta A.", - "Maleki K. T.", - "Kammann T." - ] - }, - { - "doi": "10.1074/jbc.AC120.015967", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Color light micrographs of autopsy lung tissue from the three Covid-19 cases, all included in the article.", - "data_type": [ - "Imaging data", - "Genomics & transcriptomics data" - ], - "data_url": "https://www.jbc.org/article/S0021-9258(17)50371-3/fulltext#seccestitle40" - } - ], - "title": "Presence of hyaluronan in lung alveoli in severe Covid-19: An opening for new treatment options?", - "issue": "45", - "volume": "295", - "publisher": "Elsevier BV", - "published": "2021-12-18", - "author": [ - "Hellman U.", - "Karlsson M. G.", - "Engström-Laurent A.", - "Cajander S.", - "Dorofte L." - ] - }, - { - "doi": "10.1038/s41467-020-18611-5", - "available_items": [ - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Analysis code used in the study.", - "data_type": [ - "Public health data", - "Genomics & transcriptomics data" - ], - "data_url": "https://github.com/reiniuslab/COVID19" - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Source data, including all raw data (primarily Ct values) are included in the article.", - "data_type": [ - "Public health data", - "Genomics & transcriptomics data" - ], - "data_url": "https://www.nature.com/articles/s41467-020-18611-5" - } - ], - "title": "Massive and rapid COVID-19 testing is feasible by extraction-free SARS-CoV-2 RT-PCR", - "issue": "1", - "volume": "11", - "publisher": "Springer Science and Business Media LLC", - "published": "2020-09-23", - "author": [ - "Smyrlaki I.", - "Ekman M.", - "Lentini A.", - "Rufino de Sousa N.", - "Papanicolaou N." - ] - }, - { - "doi": "10.1212/WNL.0000000000010111", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Data cannot be publicly shared, but applications can be made for access to anonymised data.", - "data_type": [ - "Health data", - "Biochemistry data" - ], - "data_url": "https://github.com/reiniuslab/COVID19" - } - ], - "title": "Neurochemical evidence of astrocytic and neuronal injury commonly found in COVID-19", - "issue": "12", - "volume": "95", - "publisher": "Ovid Technologies (Wolters Kluwer Health)", - "published": "2020-06-16", - "author": [ - "Kanberg N.", - "Ashton N. J.", - "Andersson L.", - "Yilmaz A.", - "Lindh M." - ] - }, - { - "doi": "10.7717/peerj.9879", - "available_items": [ - { - "type": "data", - "repo_name": "GitHub", - "accession_number": "", - "description": "Data required to reproduce the results. The data was largely produced using Google mobility data.", - "data_type": [ - "Biochemistry data", - "Health data" - ], - "data_url": "https://github.com/patrickbryant1/COVID19.github.io/tree/master/simulations/mobility" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Analysis code required for modelliing (primarily using R).", - "data_type": [ - "Biochemistry data", - "Health data" - ], - "data_url": "https://github.com/patrickbryant1/COVID19.github.io/tree/master/simulations/mobility" - } - ], - "title": "Estimating the impact of mobility patterns on COVID-19 infection rates in 11 European countries", - "issue": "", - "volume": "8", - "publisher": "PeerJ", - "published": "2020-09-15", - "author": [ - "Bryant P.", - "Elofsson A." - ] - }, - { - "doi": "10.3390/v12091026", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Supplementary materials include information about phylogenetic models, mutational profiles, and spatio-temporal appearance of each variant.", - "data_type": [ - "Biochemistry data", - "Genomics & transcriptomics data", - "Health data" - ], - "data_url": "https://www.mdpi.com/1999-4915/12/9/1026/htm" - } - ], - "title": "Spatio-Temporal Mutational Profile Appearances of Swedish SARS-CoV-2 during the Early Pandemic", - "issue": "9", - "volume": "12", - "publisher": "MDPI AG", - "published": "2020-09-14", - "author": [ - "Ling J.", - "Hickman R. A.", - "Li J.", - "Lu X.", - "Lindahl J. F." - ] - }, - { - "doi": "10.1128/mSphere.00224-21", - "available_items": [ - { - "type": "data", - "repo_name": "GitHub", - "accession_number": "", - "description": "Input data related to ELISA tests.", - "data_type": [ - "Biochemistry data", - "Serology data", - "Health data" - ], - "data_url": "https://github.com/chandranlab/Ig_titer_sigmoid_fit" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Code related to modelling antibody titer quantification from single dilution points.", - "data_type": [ - "Biochemistry data", - "Serology data", - "Health data" - ], - "data_url": "https://github.com/chandranlab/Ig_titer_sigmoid_fit" - } - ], - "title": "Single-Dilution COVID-19 Antibody Test with Qualitative and Quantitative Readouts", - "issue": "2", - "volume": "6", - "publisher": "American Society for Microbiology", - "published": "2021-04-28", - "author": [ - "Bortz R. H.", - "Florez C.", - "Laudermilch E.", - "Wirchnianski A. S.", - "Lasso G." - ] - }, - { - "doi": "10.1212/wnl.0000000000010250", - "available_items": [ - { - "type": "data", - "repo_name": "Dryad", - "accession_number": "", - "description": "Proteomics data.", - "data_type": [ - "Health data", - "Protein data" - ], - "data_url": "https://datadryad.org/stash/dataset/doi:10.5061/dryad.xwdbrv1bb" - } - ], - "title": "Acute necrotizing encephalopathy with SARS-CoV-2 RNA confirmed in cerebrospinal fluid", - "issue": "10", - "volume": "95", - "publisher": "Ovid Technologies (Wolters Kluwer Health)", - "published": "2020-06-25", - "author": [ - "Virhammar J.", - "Kumlien E.", - "Fällmar D.", - "Frithiof R.", - "Jackmann S." - ] - }, - { - "doi": "10.1016/j.cell.2020.09.016", - "available_items": [ - { - "type": "data", - "repo_name": "Mendeley", - "accession_number": "", - "description": "Data organised by figures presented in the article.", - "data_type": [ - "Serology data", - "Protein data", - "Health data" - ], - "data_url": "https://data.mendeley.com/datasets/ds6g796xyg/1" - }, - { - "type": "data", - "repo_name": "Figshare", - "accession_number": "", - "description": "Plasma protein expression (Olink - NPX values), FACS, Autoantibodies.", - "data_type": [ - "Serology data", - "Protein data", - "Health data" - ], - "data_url": "https://doi.org/10.17044/scilifelab.13181273" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Scripts to complete analyses and produce figures.", - "data_type": [ - "Serology data", - "Protein data", - "Health data" - ], - "data_url": "https://doi.org/10.17044/scilifelab.13181273" - } - ], - "title": "The Immunology of Multisystem Inflammatory Syndrome in Children with COVID-19", - "issue": "4", - "volume": "183", - "publisher": "Elsevier BV", - "published": "2022-06-25", - "author": [ - "Consiglio C. R.", - "Cotugno N.", - "Sardh F.", - "Pou C.", - "Amodio D." - ] - }, - { - "doi": "10.1038/s41467-020-18174-5", - "available_items": [ - { - "type": "data", - "repo_name": "GenBank", - "accession_number": "MT784731", - "description": "Sequence of Ty1.", - "data_type": [ - "Biochemistry data", - "Protein data", - "Genomics & transcriptomics data" - ], - "data_url": "https://www.ncbi.nlm.nih.gov/nuccore/MT784731" - }, - { - "type": "data", - "repo_name": "GitHub", - "accession_number": "", - "description": "Bio layer interferometry (BLI) data.", - "data_type": [ - "Biochemistry data", - "Protein data", - "Genomics & transcriptomics data" - ], - "data_url": "https://github.com/derpaule/Ty1_octet_itc" - }, - { - "type": "data", - "repo_name": "GitHub", - "accession_number": "", - "description": "Isothermal titration calorimetry (ITC) data.", - "data_type": [ - "Biochemistry data", - "Protein data", - "Genomics & transcriptomics data" - ], - "data_url": "https://github.com/derpaule/Ty1_octet_itc/tree/master/data_itc" - }, - { - "type": "data", - "repo_name": "BioProject", - "accession_number": "PRJNA638614", - "description": "Next generation sequencing (NGS) data.", - "data_type": [ - "Biochemistry data", - "Protein data", - "Genomics & transcriptomics data" - ], - "data_url": "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA638614" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Jupyter notebooks to reproduce next generation sequencing (NGS) data.", - "data_type": [ - "Biochemistry data", - "Protein data", - "Genomics & transcriptomics data" - ], - "data_url": "https://github.com/MurrellGroup/Ty1" - }, - { - "type": "data", - "repo_name": "Electron Microscopy Data Bank", - "accession_number": "EMD-11526", - "description": "Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing nanobodies (Ty1).", - "data_type": [ - "Biochemistry data", - "Protein data", - "Genomics & transcriptomics data" - ], - "data_url": "https://www.ebi.ac.uk/emdb/EMD-11526" - }, - { - "type": "data", - "repo_name": "Protein Data Bank", - "accession_number": "6ZXN", - "description": "Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing nanobodies (Ty1).", - "data_type": [ - "Biochemistry data", - "Protein data", - "Genomics & transcriptomics data" - ], - "data_url": "https://www.rcsb.org/structure/6zxn" - } - ], - "title": "An alpaca nanobody neutralizes SARS-CoV-2 by blocking receptor interaction", - "issue": "1", - "volume": "11", - "publisher": "Springer Science and Business Media LLC", - "published": "2020-09-04", - "author": [ - "Hanke L.", - "Vidakovics Perez L.", - "Sheward D. J.", - "Das H.", - "Schulte T." - ] - }, - { - "doi": "10.1371/journal.pone.0238217", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Number of COVID-19 deaths contributed by specific age group and population characteristics for 14 countries and 13 US states.", - "data_type": [ - "Social science and humanities data", - "Public health data" - ], - "data_url": "https://ars.els-cdn.com/content/image/1-s2.0-S0013935120307854-mmc2.pdf" - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Healthcare professionals’ responses about perceptions, exposure, and workload during the COVID-19 pandemic.", - "data_type": [ - "Social science and humanities data", - "Public health data" - ], - "data_url": "https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0238217#sec011" - } - ], - "title": "Factors contributing to healthcare professional burnout during the COVID-19 pandemic: A rapid turnaround global survey", - "issue": "9", - "volume": "15", - "publisher": "Public Library of Science (PLoS)", - "published": "2020-09-03", - "author": [ - "Morgantini L. A.", - "Naha U.", - "Wang H.", - "Francavilla S.", - "Acar Ö." - ] - }, - { - "doi": "10.1016/j.xcrm.2020.100078", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Raw mass cytometry data and the Olink protein data generated during this study.", - "data_type": [ - "Protein data", - "Health data" - ], - "data_url": "https://brodinlab.com/data-repository/" - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Immunoglobulin G (IgG) data.", - "data_type": [ - "Protein data", - "Health data" - ], - "data_url": "https://www.cell.com/cms/10.1016/j.xcrm.2020.100078/attachment/53aca693-33e7-4b26-881f-ea11c7c15ad1/mmc1" - }, - { - "type": "data", - "repo_name": "GitHub", - "accession_number": "", - "description": "SARS-CoV2 longitudinal systems-level analyses code.", - "data_type": [ - "Protein data", - "Health data" - ], - "data_url": "https://github.com/rodriluc/SARS-CoV2_study" - } - ], - "title": "Systems-Level Immunomonitoring from Acute to Recovery Phase of Severe COVID-19", - "issue": "5", - "volume": "1", - "publisher": "Elsevier BV", - "published": "2020-08-25", - "author": [ - "Rodriguez L.", - "Pekkarinen P. T.", - "Lakshmikanth T.", - "Tan Z.", - "Consiglio C. R." - ] - }, - { - "doi": "10.1126/sciimmunol.abd6832", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Curated flow cytometry data available via the Karolinska COVID-19 Immune Atlas.", - "data_type": [ - "Protein data", - "Biochemistry data", - "Genomics & transcriptomics data", - "Health data", - "Imaging data", - "Other data" - ], - "data_url": "https://covid19cellatlas.com/#/" - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Raw data, clinical characteristics of patients, and various results files are available in supplementary data.", - "data_type": [ - "Protein data", - "Biochemistry data", - "Genomics & transcriptomics data", - "Health data", - "Imaging data", - "Other data" - ], - "data_url": "https://www.science.org/doi/10.1126/sciimmunol.abd6832" - } - ], - "title": "Natural killer cell immunotypes related to COVID-19 disease severity", - "issue": "50", - "volume": "5", - "publisher": "American Association for the Advancement of Science (AAAS)", - "published": "2020-08-14", - "author": [ - "Maucourant C.", - "Filipovic I.", - "Ponzetta A.", - "Aleman S.", - "Cornillet M." - ] - }, - { - "doi": "10.1101/2020.08.06.20169854", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Supplementary information contains information on publicly available data sources used, instruments used, data on loci associated with risk factors, and genetic correlations between lifespan-related traits and COVID-19.", - "data_type": [ - "Genomics & transcriptomics data", - "Health data" - ], - "data_url": "https://www.medrxiv.org/content/10.1101/2020.08.06.20169854v2.supplementary-material" - } - ], - "title": "Genetic and Phenotypic Evidence for the Causal Relationship Between Aging and COVID-19", - "issue": "", - "volume": "", - "publisher": "Cold Spring Harbor Laboratory", - "published": "2020-08-07", - "author": [ - "Ying K.", - "Zhai R.", - "Pyrkov T. V.", - "Mariotti M.", - "Fedichev P. O." - ] - }, - { - "doi": "10.1080/20008686.2020.1789036", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Serological responses of 1,005 employees to SARS-CoV-2 at 22 different elderly care homes in Stockholm, Sweden, and the number of employees that reported known contacts with COVID-19.", - "data_type": [ - "Serology data", - "Health data" - ], - "data_url": "https://www.tandfonline.com/action/downloadTable?id=t0001&doi=10.1080%2F20008686.2020.1789036&downloadType=CSV" - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Prevalence of IgM (either only IgM or combined with IgG) or only IgG among elderly care home employees with or without reported symptoms.", - "data_type": [ - "Serology data", - "Health data" - ], - "data_url": "https://www.tandfonline.com/doi/figure/10.1080/20008686.2020.1789036?scroll=top&needAccess=true#" - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Predictors for seropositivity in both univariable and multivariable analyses.", - "data_type": [ - "Serology data", - "Health data" - ], - "data_url": "https://www.tandfonline.com/action/downloadTable?id=t0003&doi=10.1080%2F20008686.2020.1789036&downloadType=CSV" - } - ], - "title": "High seroprevalence of SARS-CoV-2 in elderly care employees in Sweden", - "issue": "1", - "volume": "10", - "publisher": "Informa UK Limited", - "published": "2020-01-01", - "author": [ - "Lindahl J. F.", - "Hoffman T.", - "Esmaeilzadeh M.", - "Olsen B.", - "Winter R." - ] - }, - { - "doi": "10.1016/S1473-3099(20)30314-5", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Data on single nucleotide polymorphisms and characteristics of 16 laboratory-confirmed COVID-19 cases included in the article.", - "data_type": [ - "Health data", - "Genomics & transcriptomics data" - ], - "data_url": "https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(20)30314-5/fulltext" - } - ], - "title": "Investigation of a COVID-19 outbreak in Germany resulting from a single travel-associated primary case: a case series", - "issue": "8", - "volume": "20", - "publisher": "Elsevier BV", - "published": "2020-11-02", - "author": [ - "Böhmer M. M.", - "Buchholz U.", - "Corman V. M.", - "Hoch M.", - "Katz K." - ] - }, - { - "doi": "10.1097/HJH.0000000000002531", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Biochemistry of patients ordered by days after intensive care admission (n = 9), included in the article.", - "data_type": [ - "Biochemistry data", - "Health data" - ], - "data_url": "https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(20)30314-5/fulltext" - } - ], - "title": "Hyperreninemia and low total body water may contribute to acute kidney injury in COVID-19 patients in intensive care", - "issue": "8", - "volume": "38", - "publisher": "Ovid Technologies (Wolters Kluwer Health)", - "published": "2020-05-28", - "author": [ - "Hultström M.", - "von Seth M.", - "Frithiof R." - ] - }, - { - "doi": "10.1038/s41467-021-21085-8", - "available_items": [ - { - "type": "data", - "repo_name": "Figshare", - "accession_number": "", - "description": "Raw data with demographic and clinical characteristics of the patients, progress of treatment and control groups.", - "data_type": [ - "Biochemistry data", - "Drug discovery data" - ], - "data_url": "https://figshare.com/articles/dataset/Source_Data_xls/13482810" - }, - { - "type": "code", - "repo_name": "Figshare", - "accession_number": "", - "description": "All relevant codes used in SAS software for statistical analysis.", - "data_type": [ - "Biochemistry data", - "Drug discovery data" - ], - "data_url": "https://figshare.com/articles/dataset/Source_Data_xls/13482810" - } - ], - "title": "Efficacy and tolerability of bevacizumab in patients with severe Covid-19", - "issue": "1", - "volume": "12", - "publisher": "Springer Science and Business Media LLC", - "published": "2021-02-05", - "author": [ - "Pang J.", - "Xu F.", - "Aondio G.", - "Li Y.", - "Fumagalli A." - ] - }, - { - "doi": "10.1101/2020.07.27.224063", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Due to risk of de-identification, the pseudonymised RNA sequencing data will not be made publicly available, but it is possible to apply for access.", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://www.biorxiv.org/content/10.1101/2020.07.27.224063v2.full" - }, - { - "type": "data", - "repo_name": "ArrayExpress", - "accession_number": "E-MTAB-9357", - "description": "Processed data: RNA-seq of coding RNA from single cells.", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-9357/" - }, - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Data are integrated for further visualization and analysis in ISB COVID-19 data explorer.", - "data_type": [ - "Genomics & transcriptomics data" - ], - "data_url": "https://atlas.fredhutch.org/isb/covid/" - } - ], - "title": "Multiomic Immunophenotyping of COVID-19 Patients Reveals Early Infection Trajectories", - "issue": "", - "volume": "", - "publisher": "Cold Spring Harbor Laboratory", - "published": "2020-07-28", - "author": [ - "Su Y.", - "Chen D.", - "Lausted C.", - "Yuan D.", - "Choi J." - ] - }, - { - "doi": "10.3389/fmed.2020.00349", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Data are in the article, including exposure history and characterists of COVID-19 patients during hospitalisation and discharge, as well as information from a follow-up.", - "data_type": [ - "Health data" - ], - "data_url": "https://www.frontiersin.org/articles/10.3389/fmed.2020.00349/full#h6" - } - ], - "title": "Re-positive Cases of Nucleic Acid Tests in Discharged Patients With COVID-19: A Follow-Up Study", - "issue": "", - "volume": "7", - "publisher": "Frontiers Media SA", - "published": "2020-06-23", - "author": [ - "Qiao X.", - "Xu X.", - "Zi H.", - "Liu G.", - "Li B." - ] - }, - { - "doi": "10.1038/s41586-020-2284-y", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Population outflow data from Wuhan from January 1-24, 2020; COVID-19 case counts as of February 19 and other data for 296 prefectures in mainland China (additional data in the article).", - "data_type": [ - "Health data" - ], - "data_url": "https://static-content.springer.com/esm/art%3A10.1038%2Fs41586-020-2284-y/MediaObjects/41586_2020_2284_MOESM3_ESM.xlsx" - }, - { - "type": "code", - "repo_name": "", - "accession_number": "", - "description": "Analysis code included alongside other data in spplementary information.", - "data_type": [ - "Health data" - ], - "data_url": "https://static-content.springer.com/esm/art%3A10.1038%2Fs41586-020-2284-y/MediaObjects/41586_2020_2284_MOESM1_ESM.pdf" - } - ], - "title": "Population flow drives spatio-temporal distribution of COVID-19 in China", - "issue": "7812", - "volume": "582", - "publisher": "Springer Science and Business Media LLC", - "published": "2020-04-29", - "author": [ - "Jia J. S.", - "Lu X.", - "Yuan Y.", - "Xu G.", - "Jia J." - ] - }, - { - "doi": "10.1186/s12931-020-01363-7", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Provided in the article: CT images for 2 patients over 12 days.", - "data_type": [ - "Imaging data", - "Health data" - ], - "data_url": "https://respiratory-research.biomedcentral.com/articles/10.1186/s12931-020-01363-7#availability-of-data-and-materials" - } - ], - "title": "The unsynchronized changes of CT image and nucleic acid detection in COVID-19: reports the two cases from Gansu, China", - "issue": "1", - "volume": "21", - "publisher": "Springer Science and Business Media LLC", - "published": "2020-04-22", - "author": [ - "Gao J.", - "Liu J.", - "Wen H.", - "Liu H.", - "Hu W." - ] - }, - { - "doi": "10.1371/journal.pone.0291146", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Data related to PCR probes, assessments of infectivity and RNA integrity, and ex-vivo challenges are included in the study.", - "data_type": [ - "Genomics & transcriptomics data", - "Health data" - ], - "data_url": "https://europepmc.org/article/MED/37769001#sec015" - } - ], - "title": "Evaluation of a human mucosal tissue explant model for SARS-CoV-2 replication", - "issue": "9", - "volume": "18", - "publisher": "Public Library of Science (PLoS)", - "published": "2023-09-28", - "author": [ - "Gordhan B. G.", - "Herrera C.", - "Pillay A.", - "Seiphetlo T.", - "Ealand C. S." - ] - }, - { - "doi": "10.1038/s41467-023-41146-4", - "available_items": [ - { - "type": "data", - "repo_name": "PRIDE", - "accession_number": "PXD038394", - "description": "AKI DIA samples for generalized peakgroup scoring model application", - "data_type": [ - "Genomics & transcriptomics data", - "Health data", - "Protein data", - "Other data" - ], - "data_url": "https://www.ebi.ac.uk/pride/archive/projects/PXD038394" - }, - { - "type": "data", - "repo_name": "PRIDE", - "accession_number": "PXD025752", - "description": "A time-resolved proteomic and prognostic map of COVID-19", - "data_type": [ - "Genomics & transcriptomics data", - "Health data", - "Protein data", - "Other data" - ], - "data_url": "https://www.ebi.ac.uk/pride/archive/projects/PXD025752" - }, - { - "type": "data", - "repo_name": "Figshare", - "accession_number": "", - "description": "Olink Dataset", - "data_type": [ - "Genomics & transcriptomics data", - "Health data", - "Protein data", - "Other data" - ], - "data_url": "https://figshare.com/articles/dataset/dx_doi_org_10_6084_m9_figshare_6025748/6025748" - }, - { - "type": "data", - "repo_name": "PRIDE", - "accession_number": "PXD044264", - "description": "56 samples from acute kidney injury patients (DIA-MS septic AKI dataset).", - "data_type": [ - "Genomics & transcriptomics data", - "Health data", - "Protein data", - "Other data" - ], - "data_url": "https://www.ebi.ac.uk/pride/archive/projects/PXD044264" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Biologically Informed Neural Network (BINN) code", - "data_type": [ - "Genomics & transcriptomics data", - "Health data", - "Protein data", - "Other data" - ], - "data_url": "https://github.com/InfectionMedicineProteomics/BINN" - }, - { - "type": "code", - "repo_name": "Zenodo", - "accession_number": "", - "description": "InfectionMedicineProteomics/BINN: First release", - "data_type": [ - "Genomics & transcriptomics data", - "Health data", - "Protein data", - "Other data" - ], - "data_url": "https://zenodo.org/record/8207421" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "DE-score algorithm has been implemented into the data processing package DPKS", - "data_type": [ - "Genomics & transcriptomics data", - "Health data", - "Protein data", - "Other data" - ], - "data_url": "https://github.com/InfectionMedicineProteomics/DPKS" - } - ], - "title": "Interpreting biologically informed neural networks for enhanced proteomic biomarker discovery and pathway analysis", - "issue": "1", - "volume": "14", - "publisher": "Springer Science and Business Media LLC", - "published": "2023-09-02", - "author": [ - "Hartman E.", - "Scott A. M.", - "Karlsson C.", - "Mohanty T.", - "Vaara S. T." - ] - }, - { - "doi": "10.1038/s41467-023-41541-x", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Data cannot be shared publicly, but those with appropriate ethical permissions can apply for access via helsedata.no/en.", - "data_type": [ - "Health data" - ], - "data_url": "" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Code used for analysis (in R)", - "data_type": [ - "Health data" - ], - "data_url": "https://github.com/remebjornatle/post_covid" - } - ], - "title": "Predictors of the post-COVID condition following mild SARS-CoV-2 infection", - "issue": "1", - "volume": "14", - "publisher": "Springer Science and Business Media LLC", - "published": "2023-09-20", - "author": [ - "Reme B.", - "Gjesvik J.", - "Magnusson K." - ] - }, - { - "doi": "10.1038/s41467-023-41159-z", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Results of the meta-analysis are available in a Shiny app.", - "data_type": [ - "Protein data" - ], - "data_url": "https://figshare.com/articles/online_resource/CoViD-19_Meta-Analysis_of_Plasma_Proteins_CoViMAPP_app/22293148" - }, - { - "type": "data", - "repo_name": "ProteomeXchange", - "accession_number": "PXD037486", - "description": "In-depth serum proteomics of hospitalized COVID-19 patients and PCR-negative healthy controls with HiRIEF LC-MS/MS", - "data_type": [ - "Protein data" - ], - "data_url": "https://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD037486" - }, - { - "type": "data", - "repo_name": "ProteomeXchange", - "accession_number": "PXD037451", - "description": "Mass-spectrometry proteomics of Calu-3 cell lines infected with SARS-CoV-2, in comparison to non-infected and UV mock-treated cell lines", - "data_type": [ - "Protein data" - ], - "data_url": "https://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD037451" - }, - { - "type": "data", - "repo_name": "ProteomeXchange", - "accession_number": "PXD040982", - "description": "Mass-spectrometry phosphoproteomics of Calu-3 cell lines infected with SARS-CoV-2, in comparison to non-infected and UV mock-treated cell lines", - "data_type": [ - "Protein data" - ], - "data_url": "https://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD040982" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Custom code for the Nextflow proteomics workflow", - "data_type": [ - "Protein data" - ], - "data_url": "https://europepmc.org/article/MED/37739942#id339581" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "R code used for analyses", - "data_type": [ - "Protein data" - ], - "data_url": "https://europepmc.org/article/MED/37739942#id339581" - } - ], - "title": "Comprehensive proteomics and meta-analysis of COVID-19 host response", - "issue": "1", - "volume": "14", - "publisher": "Springer Science and Business Media LLC", - "published": "2023-09-22", - "author": [ - "Babačić H.", - "Christ W.", - "Araújo J. E.", - "Mermelekas G.", - "Sharma N." - ] - }, - { - "doi": "10.1038/s41598-023-42127-9", - "available_items": [ - { - "type": "data", - "repo_name": "GitHub", - "accession_number": "", - "description": "Unsupervised learning methods to Identify essential genes associated with SARS-CoV-2", - "data_type": [ - "Genomics & transcriptomics data", - "Drug discovery data" - ], - "data_url": "https://github.com/MahnazHabibi/Gene_analysis" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Unsupervised learning methods to Identify essential genes associated with SARS-CoV-2", - "data_type": [ - "Genomics & transcriptomics data", - "Drug discovery data" - ], - "data_url": "https://github.com/MahnazHabibi/Gene_analysis" - } - ], - "title": "Identification of essential genes associated with SARS-CoV-2 infection as potential drug target candidates with machine learning algorithms", - "issue": "1", - "volume": "13", - "publisher": "Springer Science and Business Media LLC", - "published": "2023-09-13", - "author": [ - "Taheri G.", - "Habibi M." - ] - }, - { - "doi": "10.1038/s41598-023-43412-3", - "available_items": [ - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Workflow developed during the COVID-19 pandemic with the purpose of COVID-19 vaccination Phase III trial data analysis and support through data quality control and automated reporting", - "data_type": [ - "Health data" - ], - "data_url": "https://github.com/rcvanwijk/ReproducibilityPMX" - } - ], - "title": "Reproducibility in pharmacometrics applied in a phase III trial of BCG-vaccination for COVID-19", - "issue": "1", - "volume": "13", - "publisher": "Springer Science and Business Media LLC", - "published": "2023-09-28", - "author": [ - "van Wijk R. C.", - "Mockeliunas L.", - "van den Hoogen G.", - "Upton C. M.", - "Diacon A. H." - ] - }, - { - "doi": "10.1371/journal.pone.0290974", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "All vaccination data are available on Ireland's COVID-19 Data Hub", - "data_type": [ - "Public health data" - ], - "data_url": "https://covid19ireland-geohive.hub.arcgis.com/" - }, - { - "type": "code", - "repo_name": "GitHub", - "accession_number": "", - "description": "Code to simulate the evolution of the COVID-19 pandemic with and without optimal vaccination.", - "data_type": [ - "Public health data" - ], - "data_url": "https://github.com/elenizavrakli/Optimal-Age-Specific-Vaccination-Control" - } - ], - "title": "Optimal age-specific vaccination control for COVID-19: An Irish case study", - "issue": "9", - "volume": "18", - "publisher": "Public Library of Science (PLoS)", - "published": "2023-09-05", - "author": [ - "Zavrakli E.", - "Parnell A.", - "Malone D.", - "Duffy K.", - "Dey S." - ] - }, - { - "doi": "10.1038/s41467-023-41312-8", - "available_items": [ - { - "type": "data", - "repo_name": "", - "accession_number": "", - "description": "Library designs including the proteins, peptides and statistics", - "data_type": [ - "Protein data", - "Biochemistry data" - ], - "data_url": "http://slim.icr.ac.uk/phage_libraries/human/" - } - ], - "title": "Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral targets", - "issue": "1", - "volume": "14", - "publisher": "Springer Science and Business Media LLC", - "published": "2023-09-13", - "author": [ - "Mihalič F.", - "Benz C.", - "Kassa E.", - "Lindqvist R.", - "Simonetti L." - ] - }, - { - "doi": "10.1038/s41398-023-02578-0", - "available_items": [ - { - "type": "data", - "repo_name": "Open Science Framework", - "accession_number": "", - "description": "Anonymised data, dictionary, analytical code, study protocol and frequentist statistical analysis plan", - "data_type": [ - "Social science and humanities data" - ], - "data_url": "https://osf.io/j9v2z/" - }, - { - "type": "code", - "repo_name": "Open Science Framework", - "accession_number": "", - "description": "Anonymised data, dictionary, analytical code, study protocol and frequentist statistical analysis plan", - "data_type": [ - "Social science and humanities data" - ], - "data_url": "https://osf.io/j9v2z/" - } - ], - "title": "Reducing intrusive memories after trauma via an imagery-competing task intervention in COVID-19 intensive care staff: a randomised controlled trial", - "issue": "1", - "volume": "13", - "publisher": "Springer Science and Business Media LLC", - "published": "2023-09-01", - "author": [ - "Iyadurai L.", - "Highfield J.", - "Kanstrup M.", - "Markham A.", - "Ramineni V." - ] - } - ] + "last_updated": "2024-01-18", + "datasets": [ + { + "doi": "10.1038/s41522-023-00461-w", + "available_items": [ + { + "type": "data", + "repo_name": "EU Clinical Trials Register", + "accession_number": "", + "description": "Immunological Responses after Vaccination for COVID-19 with the mRNA Vaccine Comirnaty in Immunosuppressed and Immunocompetent Individuals. An open, non-randomized , phase IV multicenter study", + "data_type": ["Serology data"], + "data_url": "https://www.clinicaltrialsregister.eu/ctr-search/search?query=2021-000175-37" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "All codes used for analysis are available in R markdown format.", + "data_type": ["Serology data"], + "data_url": "https://github.com/Asw614/Gut-microbiome-on-immunological-responses-to-COVID-vaccination/tree/main" + } + ], + "title": "Impact of the gut microbiome on immunological responses to COVID-19 vaccination in healthy controls and people living with HIV", + "issue": "1", + "volume": "9", + "publisher": "Springer Science and Business Media LLC", + "published": "2023-12-20", + "author": [ + "Ray S.", + "Narayanan A.", + "Vesterbacka J.", + "Blennow O.", + "Chen P." + ] + }, + { + "doi": "10.1016/j.bbih.2023.100708", + "available_items": [ + { + "type": "data", + "repo_name": "OSF HOME", + "accession_number": "", + "description": "Results of the Sickness Questionnaire (SicknessQ) in France, assessing symptoms of sickness behavior, including somatic, behavioral, and affective dimensions.", + "data_type": [ + "Public health data", + "Health data", + "Social science and humanities data" + ], + "data_url": "https://osf.io/x69j2/?view_only=82b9a879e8064edfad8f4a651d9acf9a" + } + ], + "title": "Assessing sickness behavior in the French: Validation of the French translation of the sickness questionnaire (SicknessQ) in a non-clinical French population", + "issue": "", + "volume": "34", + "publisher": "Elsevier BV", + "published": "2023-12-02", + "author": [ + "Andreasson A.", + "Tognetti A.", + "Jones M.", + "Lekander M.", + "Lasselin J." + ] + }, + { + "doi": "10.1136/bmjopen-2022-064240", + "available_items": [ + { + "type": "data", + "repo_name": "Zenodo", + "accession_number": "", + "description": "A collection of serology data created by WHO Unity Studies Global SARS-CoV2 Seroepidemiological Investigations. Includes both data published in studies and other data not used in publications.", + "data_type": ["Serology data"], + "data_url": "https://zenodo.org/communities/unity-sero-2021?q=&l=list&p=1&s=20&sort=newest" + } + ], + "title": "Systematic review of seroprevalence of SARS-CoV-2 antibodies and appraisal of evidence, prior to the widespread introduction of vaccine programmes in the WHO European Region, January–December 2020", + "issue": "11", + "volume": "13", + "publisher": "BMJ", + "published": "2023-11-06", + "author": [ + "Vaughan A.", + "Duffell E.", + "Freidl G. S.", + "Lemos D. S.", + "Nardone A." + ] + }, + { + "doi": "10.1186/s13613-023-01201-1", + "available_items": [ + { + "type": "code", + "repo_name": "Zenodo", + "accession_number": "", + "description": "Data curation pipeline for patient data extracted for medical records up to 60th day of ICU stay (written in R, Version v3.0.1 used).", + "data_type": ["Other data", "Public health data"], + "data_url": "https://zenodo.org/records/6063905" + }, + { + "type": "data", + "repo_name": "Zenodo", + "accession_number": "", + "description": "Data dictionaries associated with data curation pipeline used.", + "data_type": ["Other data", "Public health data"], + "data_url": "https://zenodo.org/records/6063905" + } + ], + "title": "Early mobilisation in critically ill COVID-19 patients: a subanalysis of the ESICM-initiated UNITE-COVID observational study", + "issue": "1", + "volume": "13", + "publisher": "Springer Science and Business Media LLC", + "published": "2023-11-14", + "author": [ + "Kloss P.", + "Lindholz M.", + "Milnik A.", + "Azoulay E.", + "Cecconi M." + ] + }, + { + "doi": "10.1016/j.xcrm.2023.101267", + "available_items": [ + { + "type": "data", + "repo_name": "Sequence Read Archive", + "accession_number": "PRJNA1014462", + "description": "Raw sequence reads related to SARS-CoV-2 antibodies from children exhibiting broad neutralisation.", + "data_type": ["Biochemistry data", "Health data", "Serology data"], + "data_url": "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA1014462/" + }, + { + "type": "data", + "repo_name": "Electron Microscopy Databank", + "accession_number": "EMD-41075", + "description": "SARS-CoV-2 spike in complex with Fab 71281-33.", + "data_type": ["Biochemistry data", "Health data", "Serology data"], + "data_url": "https://www.ebi.ac.uk/emdb/EMD-41075" + }, + { + "type": "data", + "repo_name": "Electron Microscopy Databank", + "accession_number": "EMD-41076", + "description": "SARS-CoV-2 spike in complex with Fab 71281-33 (2).", + "data_type": ["Biochemistry data", "Health data", "Serology data"], + "data_url": "https://www.ebi.ac.uk/emdb/EMD-41075" + } + ], + "title": "SARS-CoV-2 antibodies from children exhibit broad neutralization and belong to adult public clonotypes", + "issue": "11", + "volume": "4", + "publisher": "Elsevier BV", + "published": "2023-12-02", + "author": [ + "Wall S. C.", + "Suryadevara N.", + "Kim C.", + "Shiakolas A. R.", + "Holt C. M." + ] + }, + { + "doi": "10.2807/1560-7917.es.2023.28.46.2300595", + "available_items": [ + { + "type": "data", + "repo_name": "GISAID", + "accession_number": "", + "description": "Whole genome sequence data from individuals for all Swedish BA.2.86 cases is available on GISAID. The accession numbers are avilable in the supplementary materials (linked here).", + "data_type": ["Other data", "Genomics & transcriptomics data"], + "data_url": "https://www.eurosurveillance.org/docserver/fulltext/eurosurveillance/28/46/23-00595_MOVERT_Supplement.pdf?expires=1702970040&id=id&accname=guest&checksum=39802568B41757067FA9C2CC9B13E7F2" + }, + { + "type": "data", + "repo_name": "GISAID", + "accession_number": "", + "description": "The findings of the BA.2.86 marker specificity assessment are based on metadata associated with 13,513 sequences available on GISAID from 1 July to 19 October 2023.", + "data_type": ["Other data", "Genomics & transcriptomics data"], + "data_url": "https://www.epicov.org/epi3/epi_set/EPI_SET_231113ve?main=true" + }, + { + "type": "data", + "repo_name": "ENA", + "accession_number": "PRJEB67638", + "description": "Wastewater raw reads from Uppsala, Örebro, Umeå, and Kalmar.", + "data_type": ["Other data", "Genomics & transcriptomics data"], + "data_url": "https://www.ebi.ac.uk/ena/browser/view/PRJEB67638" + } + ], + "title": "Early detection of the emerging SARS-CoV-2 BA.2.86 lineage through integrated genomic surveillance of wastewater and COVID-19 cases in Sweden, weeks 31 to 38 2023", + "issue": "46", + "volume": "28", + "publisher": "European Centre for Disease Control and Prevention (ECDC)", + "published": "2023-11-16", + "author": [ + "Espinosa-Gongora C.", + "Berg C.", + "Rehn M.", + "Varg J. E.", + "Dillner L." + ] + }, + { + "doi": "10.1038/s41586-023-06717-x", + "available_items": [ + { + "type": "data", + "repo_name": "NCBI database", + "accession_number": "PRJNA989123", + "description": "Raw RNA sequence reads produced when patient whole blood samples were analysed by RNA sequencing in order to monitor global changes in transcript abundance levels post-interferon treatment.", + "data_type": [ + "Biochemistry data", + "Genomics & transcriptomics data", + "Health data" + ], + "data_url": "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA989123" + } + ], + "title": "Autoantibodies against type I IFNs in humans with alternative NF-κB pathway deficiency", + "issue": "7988", + "volume": "623", + "publisher": "Springer Science and Business Media LLC", + "published": "2023-11-08", + "author": [ + "Le Voyer T.", + "Parent A. V.", + "Liu X.", + "Cederholm A.", + "Gervais A." + ] + }, + { + "doi": "10.1186/s13059-023-03080-y", + "available_items": [ + { + "type": "data", + "repo_name": "European Genome-Phenome Archive (EGA)", + "accession_number": "EGAS00001006186", + "description": "Raw sequence data are available under contrlled ccess due to the sensitive nature of the data.", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://ega-archive.org/studies/EGAS00001006186" + }, + { + "type": "data", + "repo_name": "European Genome-Phenome Archive (EGA)", + "accession_number": "EGAC00001002635", + "description": "Raw sequence data are available under contrlled ccess due to the sensitive nature of the data.", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://ega-archive.org/dacs/EGAC00001002635" + }, + { + "type": "data", + "repo_name": "Mendeley Dataset", + "accession_number": "", + "description": "Processed gene count matrices, related metadata, corresponding ST tissue microscopy images, and RNAScope images used in the Validation analysis.", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://data.mendeley.com/datasets/xb2w7xvs2b/1" + }, + { + "type": "data", + "repo_name": "Mendeley Dataset", + "accession_number": "", + "description": "ISS images for SARS-CoV-2 S and E genes.", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://data.mendeley.com/datasets/gwjk2cxsf4/1" + }, + { + "type": "data", + "repo_name": "FigShare", + "accession_number": "", + "description": "RNAscope images for the SARS-CoV-2 S gene for sample 1C.", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://figshare.com/articles/figure/RNAscope_images_for_SARS-CoV-2_S_gene_from_Sample_1/19333442" + }, + { + "type": "data", + "repo_name": "FigShare", + "accession_number": "", + "description": "RNAscope images for the SARS-CoV-2 S gene for sample 2C.", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://figshare.com/articles/figure/RNAscope_image_for_SARS-CoV-2_S_gene_from_Sample_2/19351781" + }, + { + "type": "data", + "repo_name": "FigShare", + "accession_number": "", + "description": "RNAscope images for the SARS-CoV-2 S gene for sample 3C.", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://figshare.com/articles/figure/RNAscope_image_for_SARS-CoV-2_S_gene_from_Sample_3/19351784" + }, + { + "type": "data", + "repo_name": "FigShare", + "accession_number": "", + "description": "RNAscope images for the SARS-CoV-2 S gene for sample 4nC.", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://figshare.com/articles/figure/RNAscope_image_for_SARS-CoV-2_S_gene_from_Sample_4/19351787" + }, + { + "type": "data", + "repo_name": "FigShare", + "accession_number": "", + "description": "RNAscope images for the SARS-CoV-2 S gene for sample 5nC.", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://figshare.com/articles/figure/RNAscope_image_for_SARS-CoV-2_S_gene_from_Sample_5/19351796" + }, + { + "type": "data", + "repo_name": "FigShare", + "accession_number": "", + "description": "Deconvolution results as an R object", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://figshare.com/articles/dataset/Analysed_R_object_with_deconvolution_results/22436074" + }, + { + "type": "data", + "repo_name": "Zenodo", + "accession_number": "", + "description": "All RNAScope images for the SARS-CoV-2 S gene probe, positive control probe, and negative control probe.", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://zenodo.org/records/8039011" + }, + { + "type": "code", + "repo_name": "Github", + "accession_number": "", + "description": "Scripts to generate the count matrices and all related R scripts used in the clustering, differential expression, colocalization analysis, and the program for the computational validation.", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://github.com/giacomellolab/DualST_Study" + }, + { + "type": "code", + "repo_name": "Zenodo", + "accession_number": "", + "description": "Scripts to generate the count matrices and all related R scripts used in the clustering, differential expression, colocalization analysis, and the program for the computational validation.", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://zenodo.org/records/8314652" + } + ], + "title": "Dual spatially resolved transcriptomics for human host–pathogen colocalization studies in FFPE tissue sections", + "issue": "1", + "volume": "24", + "publisher": "Springer Science and Business Media LLC", + "published": "2023-10-19", + "author": [ + "Sounart H.", + "Lázár E.", + "Masarapu Y.", + "Wu J.", + "Várkonyi T." + ] + }, + { + "doi": "10.1038/s41467-023-42200-x", + "available_items": [ + { + "type": "data", + "repo_name": "Electron Microscopy Data Bank", + "accession_number": "EMD-15475", + "description": "Structure of the Ancestral Scaffold Antigen-5 of Coronavirus Spike protein (map).", + "data_type": ["Biochemistry data", "Protein data"], + "data_url": "https://www.ebi.ac.uk/emdb/EMD-15475" + }, + { + "type": "data", + "repo_name": "Electron Microscopy Data Bank", + "accession_number": "EMD-15482", + "description": "Structure of the Ancestral Scaffold Antigen-6 of Coronavirus Spike protein (map).", + "data_type": ["Biochemistry data", "Protein data"], + "data_url": "https://www.ebi.ac.uk/emdb/EMD-15482" + }, + { + "type": "data", + "repo_name": "Protein Data Bank", + "accession_number": "8AJA", + "description": "Structure of the Ancestral Scaffold Antigen-5 of Coronavirus Spike protein (atomic coordinates).", + "data_type": ["Biochemistry data", "Protein data"], + "data_url": "https://www.rcsb.org/structure/8AJA" + }, + { + "type": "data", + "repo_name": "Protein Data Bank", + "accession_number": "8AJL", + "description": "Structure of the Ancestral Scaffold Antigen-6 of Coronavirus Spike protein (atomic coordinates).", + "data_type": ["Biochemistry data", "Protein data"], + "data_url": "https://www.rcsb.org/structure/8AJL" + } + ], + "title": "Design, structure and plasma binding of ancestral β-CoV scaffold antigens", + "issue": "1", + "volume": "14", + "publisher": "Springer Science and Business Media LLC", + "published": "2023-10-16", + "author": [ + "Hueting D.", + "Schriever K.", + "Sun R.", + "Vlachiotis S.", + "Zuo F." + ] + }, + { + "doi": "10.1093/biomethods/bpad021", + "available_items": [ + { + "type": "data", + "repo_name": "Protein Model Database", + "accession_number": "PM0084589", + "description": "The designed vaccine structure for Vacdeltm.", + "data_type": ["Protein data"], + "data_url": "http://srv00.recas.ba.infn.it/PMDB/zip_model.php?target=9367" + }, + { + "type": "data", + "repo_name": "Protein Model Database", + "accession_number": "PM0084590", + "description": "The designed vaccine structure for VacFL.", + "data_type": ["Protein data"], + "data_url": "http://srv00.recas.ba.infn.it/PMDB/zip_model.php?target=9368" + } + ], + "title": "De novo design of anti-variant COVID-19 vaccine", + "issue": "1", + "volume": "8", + "publisher": "Oxford University Press (OUP)", + "published": "2023-09-23", + "author": ["Goswami A.", "Kumar M.", "Ullah S.", "Gore M. M."] + }, + { + "doi": "10.1101/2023.07.05.23292245", + "available_items": [ + { + "type": "data", + "repo_name": "GitHub", + "accession_number": "", + "description": "Data used in modelling, including location and population size.", + "data_type": ["Biochemistry data", "Serology data", "Health data"], + "data_url": "https://github.com/covid19-forecast-hub-europe/aggregation-info-loss/tree/main/data" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Data processing code in R is available on Github", + "data_type": ["Biochemistry data", "Serology data", "Health data"], + "data_url": "https://github.com/covid19-forecast-hub-europe/aggregation-info-loss/tree/main/code" + } + ], + "title": "Characterising information loss due to aggregating epidemic model outputs", + "issue": "", + "volume": "", + "publisher": "Cold Spring Harbor Laboratory", + "published": "2023-07-07", + "author": [ + "Sherratt K.", + "Srivastava A.", + "Ainslie K.", + "Singh D. E.", + "Cublier A." + ] + }, + { + "doi": "10.1016/j.lanepe.2023.100646", + "available_items": [ + { + "type": "data", + "repo_name": "GitHub", + "accession_number": "", + "description": "Data processing code in R is available on Github", + "data_type": [ + "Health data", + "Serology data", + "Public health data", + "Biochemistry data" + ], + "data_url": "https://github.com/johanssonresearch/Correlate-of-vaccine-protection-against-fatal-COVID-19" + } + ], + "title": "Vaccine-induced correlate of protection against fatal COVID-19 in older and frail adults during waves of neutralization-resistant variants of concern: an observational study", + "issue": "", + "volume": "30", + "publisher": "Elsevier BV", + "published": "2023-07-03", + "author": [ + "Vikström L.", + "Fjällström P.", + "Gwon Y.", + "Sheward D. J.", + "Wigren-Byström J." + ] + }, + { + "doi": "10.1101/2023.06.14.23290814", + "available_items": [ + { + "type": "data", + "repo_name": "Figshare", + "accession_number": "", + "description": "Clinical data and biobanks samples from 250 critically ill COVID-19 patients. Appropriate permits are required for access.", + "data_type": [ + "Genomics & transcriptomics data", + "Biochemistry data", + "Serology data", + "Health data" + ], + "data_url": "https://doi.org/10.17044/scilifelab.14229410.v1" + }, + { + "type": "data", + "repo_name": "BQC-19", + "accession_number": "", + "description": "Data from the BQC-19 repository is available after appropriate permissions and data access agreements", + "data_type": [ + "Genomics & transcriptomics data", + "Biochemistry data", + "Serology data", + "Health data" + ], + "data_url": "https://en.quebeccovidbiobank.ca/" + } + ], + "title": "Sustained IFN signaling is associated with delayed development of SARS-CoV-2-specific immunity", + "issue": "", + "volume": "", + "publisher": "Cold Spring Harbor Laboratory", + "published": "2023-06-20", + "author": [ + "Brunet-Ratnasingham E.", + "Morin S.", + "Randolph H. E.", + "Labrecque M.", + "Bélair J." + ] + }, + { + "doi": "10.3389/fpsyg.2023.1124627", + "available_items": [ + { + "type": "data", + "repo_name": "OSF", + "accession_number": "d99ed5ce0ed641ca80965e54c11afc81", + "description": "Data used in analysis assessing personality traits", + "data_type": [ + "Health data", + "Public health data", + "Social science and humanities data" + ], + "data_url": "https://osf.io/f7ucb/?view_only=d99ed5ce0ed641ca80965e54c11afc81" + }, + { + "type": "code", + "repo_name": "OSF", + "accession_number": "d99ed5ce0ed641ca80965e54c11afc81", + "description": "Script for data re-analysis of traits", + "data_type": [ + "Health data", + "Public health data", + "Social science and humanities data" + ], + "data_url": "https://osf.io/f7ucb/?view_only=d99ed5ce0ed641ca80965e54c11afc81" + } + ], + "title": "Regional differences in personalities account for substantial heterogeneity of loneliness change from before to during the COVID-19", + "issue": "", + "volume": "14", + "publisher": "Frontiers Media SA", + "published": "2023-05-05", + "author": ["Xiao S.", "Dang J."] + }, + { + "doi": "10.1007/s41669-023-00418-x", + "available_items": [ + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "POETIC-COVID CEA PROJECT - R code that supports the findings of the study", + "data_type": ["Other data", "Public health data"], + "data_url": "https://github.com/EECCnetwork/POETIC_CEA" + } + ], + "title": "Cost Effectiveness of Strategies for Caring for Critically Ill Patients with COVID-19 in Tanzania", + "issue": "", + "volume": "", + "publisher": "Springer Science and Business Media LLC", + "published": "2023-05-13", + "author": [ + "Shah H. A.", + "Baker T.", + "Schell C. O.", + "Kuwawenaruwa A.", + "Awadh K." + ] + }, + { + "doi": "10.1038/s41467-023-38020-8", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Data cannot be shared publicly, but applications can be made for access.", + "data_type": ["Serology data", "Health data"], + "data_url": "mailto:\"geldmacher@lrz.uni-muenchen.de\"" + } + ], + "title": "Nucleocapsid-specific T cell responses associate with control of SARS-CoV-2 in the upper airways before seroconversion", + "issue": "1", + "volume": "14", + "publisher": "Springer Science and Business Media LLC", + "published": "2023-05-24", + "author": [ + "Eser T. M.", + "Baranov O.", + "Huth M.", + "Ahmed M. I. M.", + "Deák F." + ] + }, + { + "doi": "10.1016/j.lanepe.2023.100646", + "available_items": [ + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Data processing code is available on GitHub", + "data_type": ["Serology data", "Health data"], + "data_url": "https://github.com/johanssonresearch/Correlate-of-vaccine-protection-against-fatal-COVID-19" + } + ], + "title": "Vaccine-induced correlate of protection against fatal COVID-19 in older and frail adults during waves of neutralization-resistant variants of concern: an observational study", + "issue": "", + "volume": "", + "publisher": "Elsevier BV", + "published": "2023-05-15", + "author": [ + "Vikström L.", + "Fjällström P.", + "Gwon Y.", + "Sheward D. J.", + "Wigren-Byström J." + ] + }, + { + "doi": "10.1128/jvi.01992-22", + "available_items": [ + { + "type": "data", + "repo_name": "zenodo", + "accession_number": "7826331", + "description": "Movies and data to accompany the study", + "data_type": [ + "Imaging data", + "Biochemistry data", + "Genomics & transcriptomics data", + "Health data" + ], + "data_url": "https://zenodo.org/record/7826331" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Image and time series analysis code written in MATLAB is available on GitHub", + "data_type": [ + "Imaging data", + "Biochemistry data", + "Genomics & transcriptomics data", + "Health data" + ], + "data_url": "https://github.com/kassonlab/micrograph-spot-analysis" + } + ], + "title": "Single-Virus Fusion Measurements Reveal Multiple Mechanistically Equivalent Pathways for SARS-CoV-2 Entry", + "issue": "5", + "volume": "97", + "publisher": "American Society for Microbiology", + "published": "2023-05-31", + "author": [ + "Sengar A.", + "Cervantes M.", + "Bondalapati S. T.", + "Hess T.", + "Kasson P. M." + ] + }, + { + "doi": "10.1038/s41598-023-33168-1", + "available_items": [ + { + "type": "data", + "repo_name": "GenBank", + "accession_number": "", + "description": "Nucleotide sequence are available as assembled FASTA consensus sequences at GenBank. Accession-ID: OP585690-OP585783", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://www.ncbi.nlm.nih.gov/nuccore/?term=OP585690:OP585783[pacc]" + } + ], + "title": "Comparison of SARS-CoV-2 whole genome sequencing using tiled amplicon enrichment and bait hybridization", + "issue": "1", + "volume": "13", + "publisher": "Springer Science and Business Media LLC", + "published": "2023-04-20", + "author": [ + "Koskela von Sydow A.", + "Lindqvist C. M.", + "Asghar N.", + "Johansson M.", + "Sundqvist M." + ] + }, + { + "doi": "10.3389/fviro.2023.1128253", + "available_items": [ + { + "type": "data", + "repo_name": "GenBank", + "accession_number": "ON086926", + "description": "The HC sequences of CAB-F52 anti-SARS-CoV-2 immunoglobulin heavy chain variable region mRNA", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://www.ncbi.nlm.nih.gov/nuccore/ON086926" + }, + { + "type": "data", + "repo_name": "GenBank", + "accession_number": "ON086941", + "description": "The LC sequences of CAB-F52 anti-SARS-CoV-2 immunoglobulin heavy chain variable region mRNA", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://www.ncbi.nlm.nih.gov/nuccore/ON086941.1/" + }, + { + "type": "data", + "repo_name": "ProteomeXchange", + "accession_number": "PXD031945", + "description": "The hydrogen–deuterium exchange mass spectrometry data", + "data_type": ["Protein data"], + "data_url": "https://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD031945" + } + ], + "title": "Frequent use of IGHV3-30-3 in SARS-CoV-2 neutralizing antibody responses", + "issue": "", + "volume": "3", + "publisher": "Frontiers Media SA", + "published": "2023-03-01", + "author": [ + "Pushparaj P.", + "Nicoletto A.", + "Castro Dopico X.", + "Sheward D. J.", + "Kim S." + ] + }, + { + "doi": "10.1038/s41380-023-02062-7", + "available_items": [ + { + "type": "data", + "repo_name": "OSF", + "accession_number": "", + "description": "Anonymised databases with the individual participant data and the metadata for Bayesian analyses, along with a data dictionary", + "data_type": ["Other data"], + "data_url": "https://osf.io/m5cvj/" + }, + { + "type": "protocol", + "repo_name": "OSF", + "accession_number": "", + "description": "The Study Protocol and Bayesian Statistical Analysis Plan", + "data_type": ["Other data"], + "data_url": "https://osf.io/2xn5m/" + } + ], + "title": "Treating intrusive memories after trauma in healthcare workers: a Bayesian adaptive randomised trial developing an imagery-competing task intervention", + "issue": "", + "volume": "", + "publisher": "Springer Science and Business Media LLC", + "published": "2023-04-26", + "author": [ + "Ramineni V.", + "Millroth P.", + "Iyadurai L.", + "Jaki T.", + "Kingslake J." + ] + }, + { + "doi": "10.1016/j.tbench.2023.100088", + "available_items": [ + { + "type": "data", + "repo_name": "Mendeley Data", + "accession_number": "", + "description": "COVID19, Pneumonia, and Normal Chest X-ray Posteroanterior Dataset", + "data_type": ["Health data"], + "data_url": "https://data.mendeley.com/datasets/mxc6vb7svm" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Scripts used in this project to analyse the datasets", + "data_type": ["Health data"], + "data_url": "https://github.com/Asraf047/COVID19-CNN-RNN" + } + ], + "title": "Diagnosis of COVID-19 from X-rays using combined CNN-RNN architecture with transfer learning", + "issue": "4", + "volume": "2", + "publisher": "Elsevier BV", + "published": "2023-03-27", + "author": [ + "Islam M. M.", + "Islam M. Z.", + "Asraf A.", + "Al-Rakhami M. S.", + "Ding W." + ] + }, + { + "doi": "10.1371/journal.pgph.0001110", + "available_items": [ + { + "type": "data", + "repo_name": "FigShare", + "accession_number": "", + "description": "Fully anonymised data from two cross-sectional surveys", + "data_type": ["Public health data", "Other data"], + "data_url": "https://figshare.com/articles/dataset/Community_survey_data_from_the_DClare_Project_Faridpur_District_Bangladesh/19337831/1" + } + ], + "title": "Changes in non-communicable diseases, diet and exercise in a rural Bangladesh setting before and after the first wave of COVID-19", + "issue": "9", + "volume": "2", + "publisher": "Public Library of Science (PLoS)", + "published": "2022-09-30", + "author": [ + "King C.", + "Shaha S. K.", + "Morrison J.", + "Ahmed N.", + "Kuddus A." + ] + }, + { + "doi": "10.1371/journal.pgph.0001204", + "available_items": [ + { + "type": "data", + "repo_name": "Zenodo", + "accession_number": "", + "description": "Municipal-level vaccination data compiled from several publicly available data sources", + "data_type": ["Public health data"], + "data_url": "https://zenodo.org/record/6983689#YvVPOHZBw2z" + } + ], + "title": "Variations in vaccination uptake: COVID-19 vaccination rates in Swedish municipalities", + "issue": "10", + "volume": "2", + "publisher": "Public Library of Science (PLoS)", + "published": "2022-10-20", + "author": ["Larsson E. C.", "Wittberg E.", "Lundåsen S. W."] + }, + { + "doi": "10.3390/ijerph20043642", + "available_items": [ + { + "type": "data", + "repo_name": "Figshare", + "accession_number": "", + "description": "Questionaire data on levels of physical activity and sedentary behaviour", + "data_type": ["Social science and humanities data", "Health data"], + "data_url": "https://doi.org/10.6084/m9.figshare.21802941.v1" + } + ], + "title": "How Have Physical Activity and Sedentary Behavior, Changed during the COVID-19 Pandemic? A Swedish Repeated Cross-Sectional Design Study", + "issue": "4", + "volume": "20", + "publisher": "MDPI AG", + "published": "2023-02-18", + "author": [ + "Lindberg D.", + "Elvén M.", + "Nilsson K. W.", + "Von Heideken Wågert P.", + "Stier J." + ] + }, + { + "doi": "10.3390/ijerph20043559", + "available_items": [ + { + "type": "code", + "repo_name": "Figshare", + "accession_number": "", + "description": "Codes for analysis", + "data_type": ["Social science and humanities data"], + "data_url": "https://figshare.com/articles/software/Nature_visits_and_covid19/22056869/1" + } + ], + "title": "Visiting Urban Green Space and Orientation to Nature Is Associated with Better Wellbeing during COVID-19", + "issue": "4", + "volume": "20", + "publisher": "MDPI AG", + "published": "2023-02-17", + "author": [ + "Lin B. B.", + "Chang C.", + "Andersson E.", + "Astell-Burt T.", + "Gardner J." + ] + }, + { + "doi": "10.12688/wellcomeopenres.17403.3", + "available_items": [ + { + "type": "data", + "repo_name": "Zenodo", + "accession_number": "", + "description": "Characteristics and outcomes of COVID-19 patients with COPD", + "data_type": ["Health data"], + "data_url": "https://doi.org/10.5281/zenodo.5729423" + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Aggregate data from COVID-19 patients with COPD", + "data_type": ["Health data"], + "data_url": "https://data.ohdsi.org/Covid19CharacterizationCharybdis/" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Code used for analysis", + "data_type": ["Health data"], + "data_url": "https://github.com/ohdsi-studies/Covid19CharacterizationCharybdis" + }, + { + "type": "code", + "repo_name": "Zenodo", + "accession_number": "", + "description": "Archived code used for analysis", + "data_type": ["Health data"], + "data_url": "https://doi.org/10.5281/zenodo.5779264" + } + ], + "title": "Characteristics and outcomes of COVID-19 patients with COPD from the United States, South Korea, and Europe", + "issue": "", + "volume": "7", + "publisher": "F1000 Research Ltd", + "published": "2023-02-24", + "author": [ + "Moreno-Martos D.", + "Verhamme K.", + "Ostropolets A.", + "Kostka K.", + "Duarte-Sales T." + ] + }, + { + "doi": "10.1038/s42255-023-00742-w", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Summary statistics related to body mass index (BMI)", + "data_type": [ + "Health data", + "Genomics & transcriptomics data", + "Protein data" + ], + "data_url": "https://portals.broadinstitute.org/collaboration/giant/" + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Summary statistics on plasma proteome from the deCODE study", + "data_type": [ + "Health data", + "Genomics & transcriptomics data", + "Protein data" + ], + "data_url": "https://www.decode.com/summarydata/" + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Summary statistics related to COVID-19 outcomes", + "data_type": [ + "Health data", + "Genomics & transcriptomics data", + "Protein data" + ], + "data_url": "https://www.covid19hg.org/results/r7/" + }, + { + "type": "data", + "repo_name": "GTEx", + "accession_number": "phs000424.v9", + "description": "Long Read RNASeq data", + "data_type": [ + "Health data", + "Genomics & transcriptomics data", + "Protein data" + ], + "data_url": "https://gtexportal.org/home/datasets/" + }, + { + "type": "data", + "repo_name": "OpenGWAS", + "accession_number": "ukb-b-8909", + "description": "Body fat percentage data", + "data_type": [ + "Health data", + "Genomics & transcriptomics data", + "Protein data" + ], + "data_url": "https://gwas.mrcieu.ac.uk/datasets/ukb-b-8909/" + }, + { + "type": "data", + "repo_name": "OpenGWAS", + "accession_number": "ukb-b-19393", + "description": "Whole body fat mass data", + "data_type": [ + "Health data", + "Genomics & transcriptomics data", + "Protein data" + ], + "data_url": "https://gwas.mrcieu.ac.uk/datasets/ukb-b-19393/" + }, + { + "type": "data", + "repo_name": "OpenGWAS", + "accession_number": "ukb-b-13354", + "description": "Whole body fat-free mass data", + "data_type": [ + "Health data", + "Genomics & transcriptomics data", + "Protein data" + ], + "data_url": "https://gwas.mrcieu.ac.uk/datasets/ukb-b-13354/" + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "scRNA-seq data of COVID-19 lung autopsy samples", + "data_type": [ + "Health data", + "Genomics & transcriptomics data", + "Protein data" + ], + "data_url": "https://singlecell.broadinstitute.org/single_cell/study/SCP1052/covid-19-lung-autopsy-samples" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Custom analysis codes", + "data_type": [ + "Health data", + "Genomics & transcriptomics data", + "Protein data" + ], + "data_url": "https://github.com/satoshi-yoshiji/TwostepMR_obesity_COVID/" + } + ], + "title": "Proteome-wide Mendelian randomization implicates nephronectin as an actionable mediator of the effect of obesity on COVID-19 severity", + "issue": "2", + "volume": "5", + "publisher": "Springer Science and Business Media LLC", + "published": "2023-02-20", + "author": [ + "Yoshiji S.", + "Butler-Laporte G.", + "Lu T.", + "Willett J. D. S.", + "Su C." + ] + }, + { + "doi": "10.3389/fphar.2023.1090717", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Supplementary material including information on proteomics, mutations, T-cell epitope prediction, and much more, including accession numbers for other open data sources", + "data_type": ["Genomics & transcriptomics data", "Protein data"], + "data_url": "https://www.frontiersin.org/articles/10.3389/fphar.2023.1090717/full#supplementary-material" + } + ], + "title": "Variant-specific deleterious mutations in the SARS-CoV-2 genome reveal immune responses and potentials for prophylactic vaccine development", + "issue": "", + "volume": "14", + "publisher": "Frontiers Media SA", + "published": "2023-02-07", + "author": [ + "Islam M. A.", + "Shahi S.", + "Marzan A. A.", + "Amin M. R.", + "Hasan M. N." + ] + }, + { + "doi": "10.3390/ijerph20043040", + "available_items": [ + { + "type": "data", + "repo_name": "GitHub", + "accession_number": "", + "description": "Data related to development of a statistical methodology for predicting true daily quantities and their uncertainty, estimated using historical reporting delays", + "data_type": ["Other data"], + "data_url": "https://github.com/adamaltmejd/covid_reporting_delay_prediction" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "R code related to development of a statistical methodology for predicting true daily quantities and their uncertainty, estimated using historical reporting delays", + "data_type": ["Other data"], + "data_url": "https://github.com/adamaltmejd/covid_reporting_delay_prediction" + } + ], + "title": "Nowcasting COVID-19 Statistics Reported with Delay: A Case-Study of Sweden and the UK", + "issue": "4", + "volume": "20", + "publisher": "MDPI AG", + "published": "2023-02-09", + "author": ["Altmejd A.", "Rocklöv J.", "Wallin J."] + }, + { + "doi": "10.3389/fpubh.2023.1052946", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Information on open data sources used e.g. for socioeconomic factors, environment, biodiveristy, health, among others.", + "data_type": ["Other data", "Health data", "Public health data"], + "data_url": "https://www.frontiersin.org/articles/10.3389/fpubh.2023.1052946/full#h12" + } + ], + "title": "Monkeypox outbreaks in the context of the COVID-19 pandemic: Network and clustering analyses of global risks and modified SEIR prediction of epidemic trends", + "issue": "", + "volume": "11", + "publisher": "Frontiers Media SA", + "published": "2023-01-24", + "author": ["Gao J.", "Zhou C.", "Liang H.", "Jiao R.", "Wheelock Å. M."] + }, + { + "doi": "10.1016/j.xgen.2021.100065", + "available_items": [ + { + "type": "data", + "repo_name": "Gene Expression Omnibus", + "accession_number": "GSE185715", + "description": "Genome-wide Spatial Expression Profiling in Formalin-fixed Tissues", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE185715" + }, + { + "type": "data", + "repo_name": "Mendeley", + "accession_number": "", + "description": "Processed genome-wide spatial expression profiling data", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://data.mendeley.com/datasets/xjtv62ncwr/1" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "FFPE mouse brain spatial transcriptomics data explorer app", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://github.com/ludvigla/FFPE_mouse_brain_explorer" + }, + { + "type": "code", + "repo_name": "Mendeley", + "accession_number": "", + "description": "Original analysis code", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://data.mendeley.com/datasets/xjtv62ncwr/1" + } + ], + "title": "Genome-wide spatial expression profiling in formalin-fixed tissues", + "issue": "3", + "volume": "1", + "publisher": "Elsevier BV", + "published": "2022-08-05", + "author": [ + "Gracia Villacampa E.", + "Larsson L.", + "Mirzazadeh R.", + "Kvastad L.", + "Andersson A." + ] + }, + { + "doi": "10.1371/journal.pdig.0000007", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Protein quantities table along with the associated metadata", + "data_type": ["Protein data"], + "data_url": "https://europepmc.org/article/MED/36812516#sec011" + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Input proteomics data for training machine learning models", + "data_type": ["Protein data"], + "data_url": "https://europepmc.org/articles/PMC9931303/bin/pdig.0000007.s005.zip" + }, + { + "type": "code", + "repo_name": "", + "accession_number": "", + "description": "Scripts training machine learning models", + "data_type": ["Protein data"], + "data_url": "https://europepmc.org/articles/PMC9931303/bin/pdig.0000007.s005.zip" + }, + { + "type": "data", + "repo_name": "ProteomeXchange Consortium", + "accession_number": "PXD029009", + "description": "Mass spectrometry proteomics data used for survival analysis", + "data_type": ["Protein data"], + "data_url": "http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD029009" + } + ], + "title": "A proteomic survival predictor for COVID-19 patients in intensive care", + "issue": "1", + "volume": "1", + "publisher": "Public Library of Science (PLoS)", + "published": "2022-01-18", + "author": [ + "Demichev V.", + "Tober-Lau P.", + "Nazarenko T.", + "Lemke O.", + "Kaur Aulakh S." + ] + }, + { + "doi": "10.1038/s41597-022-01811-7", + "available_items": [ + { + "type": "data", + "repo_name": "Open Science Framework", + "accession_number": "", + "description": "Data used in the Shiny app for The Psychological Science Accelerator's COVID-19 Rapid-Response Project", + "data_type": ["Social science and humanities data"], + "data_url": "https://osf.io/gvw56/" + }, + { + "type": "code", + "repo_name": "Open Science Framework", + "accession_number": "", + "description": "Code for the Shiny app for The Psychological Science Accelerator's COVID-19 Rapid-Response Project", + "data_type": ["Social science and humanities data"], + "data_url": "https://osf.io/gvw56/" + } + ], + "title": "The Psychological Science Accelerator’s COVID-19 rapid-response dataset", + "issue": "1", + "volume": "10", + "publisher": "Springer Science and Business Media LLC", + "published": "2023-02-11", + "author": [ + "Buchanan E. M.", + "Lewis S. C.", + "Paris B.", + "Forscher P. S.", + "Pavlacic J. M." + ] + }, + { + "doi": "10.1016/j.concog.2023.103464", + "available_items": [ + { + "type": "data", + "repo_name": "OSF", + "accession_number": "", + "description": "Students survey data on COVID-19 status", + "data_type": ["Social science and humanities data"], + "data_url": "https://osf.io/9stbm/" + } + ], + "title": "COVID-19 infection does not seem to affect cognition in college students", + "issue": "", + "volume": "108", + "publisher": "Elsevier BV", + "published": "2023-01-30", + "author": ["Francis G.", "Thunell E."] + }, + { + "doi": "10.1038/s41597-022-01880-8", + "available_items": [ + { + "type": "data", + "repo_name": "OSF", + "accession_number": "", + "description": "Familydemic survey data related to the work and family nexus", + "data_type": ["Social science and humanities data"], + "data_url": "https://osf.io/mjfz3/" + } + ], + "title": "Familydemic Cross Country and Gender Dataset on work and family outcomes during COVID-19 pandemic", + "issue": "1", + "volume": "10", + "publisher": "Springer Science and Business Media LLC", + "published": "2023-01-03", + "author": [ + "Kurowska A.", + "Barardehi I. H.", + "Fuller S.", + "Petts R. J.", + "Kaufman G." + ] + }, + { + "doi": "10.1038/s41586-022-05512-4", + "available_items": [ + { + "type": "data", + "repo_name": "Zenodo", + "accession_number": "", + "description": "Randomised controlled trial data from Sweden and United States for COVID-19 first dose vaccination", + "data_type": ["Social science and humanities data", "Other data"], + "data_url": "https://zenodo.org/record/7214856#.Y9obkezMKX0" + }, + { + "type": "code", + "repo_name": "Zenodo", + "accession_number": "", + "description": "Analyses were conducted using STATA 16, the code to replicate the analysis is in the article", + "data_type": ["Social science and humanities data", "Other data"], + "data_url": "https://zenodo.org/record/7214856#.Y9obkezMKX0" + } + ], + "title": "Financial incentives for vaccination do not have negative unintended consequences", + "issue": "7944", + "volume": "613", + "publisher": "Springer Science and Business Media LLC", + "published": "2023-01-11", + "author": [ + "Schneider F. H.", + "Campos-Mercade P.", + "Meier S.", + "Pope D.", + "Wengström E." + ] + }, + { + "doi": "10.1371/journal.pone.0280355", + "available_items": [ + { + "type": "data", + "repo_name": "Github", + "accession_number": "", + "description": "Aggregated data of COVID-19 mortality and long-term air pollution concentrations", + "data_type": ["Public health data", "Other data"], + "data_url": "https://github.com/LopezFeldman/Airpollution_Covid19" + }, + { + "type": "code", + "repo_name": "Github", + "accession_number": "", + "description": "Stata scripts used to compile the statitics", + "data_type": ["Public health data", "Other data"], + "data_url": "https://github.com/LopezFeldman/Airpollution_Covid19" + } + ], + "title": "Association between long-term air pollution exposure and COVID-19 mortality in Latin America", + "issue": "1", + "volume": "18", + "publisher": "Public Library of Science (PLoS)", + "published": "2023-01-17", + "author": [ + "Bonilla J. A.", + "Lopez-Feldman A.", + "Pereda P. C.", + "Rivera N. M.", + "Ruiz-Tagle J. C." + ] + }, + { + "doi": "10.3389/fimmu.2022.1079995", + "available_items": [ + { + "type": "data", + "repo_name": "NCBI", + "accession_number": "PRJNA900274", + "description": "All genomic datasets from this project are available as part of an NCBI BioProject", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://www.ncbi.nlm.nih.gov/biosample?LinkName=bioproject_biosample_all&from_uid=900274" + } + ], + "title": "Persistence of salivary antibody responses after COVID-19 vaccination is associated with oral microbiome variation in both healthy and people living with HIV", + "issue": "", + "volume": "13", + "publisher": "Frontiers Media SA", + "published": "2023-01-10", + "author": [ + "Ghorbani M.", + "Al-Manei K.", + "Naud S.", + "Healy K.", + "Gabarrini G." + ] + }, + { + "doi": "10.1007/s44155-022-00027-9", + "available_items": [ + { + "type": "data", + "repo_name": "FigShare", + "accession_number": "", + "description": "Results of a Qualatrics questionnaire related to perceived risk of viral infection with different social distances.", + "data_type": ["Social science and humanities data"], + "data_url": "https://su.figshare.com/articles/dataset/On_Interpersonal_Distance_Time_of_a_Conversation_and_Perceived_Virus_Exposure/20472165/1" + } + ], + "title": "Perceived Corona virus exposure as a function of interpersonal distance and time of a conversation", + "issue": "1", + "volume": "2", + "publisher": "Springer Science and Business Media LLC", + "published": "2022-12-05", + "author": ["Svenson O."] + }, + { + "doi": "10.1101/2022.11.25.22282676", + "available_items": [ + { + "type": "data", + "repo_name": "Zenodo", + "accession_number": "", + "description": "Results of a multi-country longitudinal social contact survey exploring the influence of COVID-19 vaccination status and risk perceptions related to SARS-CoV-2 on social contact.", + "data_type": ["Social science and humanities data"], + "data_url": "http://www.socialcontactdata.org/data/" + } + ], + "title": "The influence of COVID-19 risk perception and vaccination status on the number of social contacts across Europe: insights from the CoMix study", + "issue": "", + "volume": "", + "publisher": "Cold Spring Harbor Laboratory", + "published": "2022-11-29", + "author": [ + "Wambua J.", + "Loedy N.", + "Jarvis C. I.", + "Wong K. L.", + "Faes C." + ] + }, + { + "doi": "10.1038/s41467-022-35641-3", + "available_items": [ + { + "type": "data", + "repo_name": "Zenodo", + "accession_number": "", + "description": "Models of SARS-CoV-2 virus spike protein bound to 1-3 of ACE2 receptors embedded in lipid nanodisks.", + "data_type": ["Protein data"], + "data_url": "https://zenodo.org/record/7401939#.Y8AFIy8w2u4" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Code for simulation of high speed AFM imaging.", + "data_type": ["Protein data"], + "data_url": "https://github.com/matsikora/AFM_emulator" + } + ], + "title": "Force-tuned avidity of spike variant-ACE2 interactions viewed on the single-molecule level", + "issue": "1", + "volume": "13", + "publisher": "Springer Science and Business Media LLC", + "published": "2022-12-24", + "author": [ + "Zhu R.", + "Canena D.", + "Sikora M.", + "Klausberger M.", + "Seferovic H." + ] + }, + { + "doi": "10.1186/s12982-022-00119-6", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Sensitivity analysis and mortality rate data available in the paper.", + "data_type": ["Public health data", "Health data"], + "data_url": "https://europepmc.org/article/MED/36550573#id605303" + }, + { + "type": "data", + "repo_name": "Zenodo", + "accession_number": "", + "description": "Mortality rate data.", + "data_type": ["Public health data", "Health data"], + "data_url": "http://doi.org/10.5281/zenodo.5136641" + }, + { + "type": "code", + "repo_name": "Zenodo", + "accession_number": "", + "description": "Analysis code", + "data_type": ["Public health data", "Health data"], + "data_url": "http://doi.org/10.5281/zenodo.5136641" + } + ], + "title": "Dynamics of COVID-19 progression and the long-term influences of measures on pandemic outcomes", + "issue": "1", + "volume": "19", + "publisher": "Springer Science and Business Media LLC", + "published": "2022-12-22", + "author": ["Lan Y.", "Yin L.", "Wang X."] + }, + { + "doi": "10.1186/s13148-022-01398-1", + "available_items": [ + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Analysis and visualisation scripts", + "data_type": [ + "Health data", + "Genomics & transcriptomics data", + "Other data" + ], + "data_url": "https://github.com/Lerm-Lab/PACS" + } + ], + "title": "Defining post-acute COVID-19 syndrome (PACS) by an epigenetic biosignature in peripheral blood mononuclear cells", + "issue": "1", + "volume": "14", + "publisher": "Springer Science and Business Media LLC", + "published": "2022-12-14", + "author": [ + "Nikesjö F.", + "Sayyab S.", + "Karlsson L.", + "Apostolou E.", + "Rosén A." + ] + }, + { + "doi": "10.1371/journal.pcbi.1010767", + "available_items": [ + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Analysis scripts R", + "data_type": ["Public health data"], + "data_url": "https://github.com/fannybergstrom/nowcasting_covid19" + }, + { + "type": "data", + "repo_name": "GitHub", + "accession_number": "", + "description": "COVID-19 surveillance data", + "data_type": ["Public health data"], + "data_url": "https://github.com/fannybergstrom/nowcasting_covid19" + } + ], + "title": "Bayesian nowcasting with leading indicators applied to COVID-19 fatalities in Sweden", + "issue": "12", + "volume": "18", + "publisher": "Public Library of Science (PLoS)", + "published": "2022-12-07", + "author": ["Bergström F.", "Günther F.", "Höhle M.", "Britton T."] + }, + { + "doi": "10.1371/journal.pcbi.1010078", + "available_items": [ + { + "type": "data", + "repo_name": "GitHub", + "accession_number": "", + "description": "Incidence data on which the model is based.", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://github.com/yunPKU/infer_heterogeneity_from_incidence" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Code for instant-individual heterogeneity model to estimate real-time transmission heterogeneity from incidence data.", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://github.com/yunPKU/infer_heterogeneity_from_incidence" + } + ], + "title": "Monitoring real-time transmission heterogeneity from incidence data", + "issue": "12", + "volume": "18", + "publisher": "Public Library of Science (PLoS)", + "published": "2022-12-01", + "author": ["Zhang Y.", "Britton T.", "Zhou X."] + }, + { + "doi": "10.1016/j.immuni.2022.12.005", + "available_items": [ + { + "type": "data", + "repo_name": "Figshare", + "accession_number": "", + "description": "Individualised IGHV Genotype Sequences of 14 SARS-CoV-2 Convalescent Donors", + "data_type": ["Genomics & transcriptomics data", "Protein data"], + "data_url": "http://doi.org/10.17044/scilifelab.19317512" + }, + { + "type": "data", + "repo_name": "ProteomeXchange", + "accession_number": "", + "description": "Mass spectrometry raw files and HDX analysis", + "data_type": ["Genomics & transcriptomics data", "Protein data"], + "data_url": "http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD031945" + }, + { + "type": "data", + "repo_name": "PDB", + "accession_number": "8A99", + "description": "SARS Cov2 Spike in 1-up conformation complex with Fab47", + "data_type": ["Genomics & transcriptomics data", "Protein data"], + "data_url": "https://www.rcsb.org/structure/unreleased/8A99" + }, + { + "type": "data", + "repo_name": "PDB", + "accession_number": "8A94", + "description": "SARS CoV2 Spike in the 2-up state in complex with Fab47", + "data_type": ["Genomics & transcriptomics data", "Protein data"], + "data_url": "https://www.rcsb.org/structure/unreleased/8A94" + }, + { + "type": "data", + "repo_name": "PDB", + "accession_number": "8A96", + "description": "SARS Cov2 Spike RBD in complex with Fab47", + "data_type": ["Genomics & transcriptomics data", "Protein data"], + "data_url": "https://www.rcsb.org/structure/unreleased/8A96" + }, + { + "type": "data", + "repo_name": "Electron Microscopy Data Bank", + "accession_number": "EMD-15273", + "description": "SARS Cov2 Spike in 1-up conformation complex with Fab47", + "data_type": ["Genomics & transcriptomics data", "Protein data"], + "data_url": "https://www.ebi.ac.uk/emdb/search/EMD-15273" + }, + { + "type": "data", + "repo_name": "Electron Microscopy Data Bank", + "accession_number": "EMD-15269", + "description": "SARS CoV2 Spike in the 2-up state in complex with Fab47", + "data_type": ["Genomics & transcriptomics data", "Protein data"], + "data_url": "https://www.ebi.ac.uk/emdb/search/EMD-15269" + }, + { + "type": "data", + "repo_name": "Electron Microscopy Data Bank", + "accession_number": "EMD-15271", + "description": "SARS Cov2 Spike RBD in complex with Fab47", + "data_type": ["Genomics & transcriptomics data", "Protein data"], + "data_url": "https://www.ebi.ac.uk/emdb/search/EMD-15271" + }, + { + "type": "data", + "repo_name": "Mendeley", + "accession_number": "", + "description": "Supplemental data, including Cryo-EM models", + "data_type": ["Genomics & transcriptomics data", "Protein data"], + "data_url": "https://data.mendeley.com/datasets/mg7p5msrfs/1" + } + ], + "title": "Immunoglobulin germline gene polymorphisms influence the function of SARS-CoV-2 neutralizing antibodies", + "issue": "1", + "volume": "56", + "publisher": "Elsevier BV", + "published": "2023-01-10", + "author": [ + "Pushparaj P.", + "Nicoletto A.", + "Sheward D. J.", + "Das H.", + "Castro Dopico X." + ] + }, + { + "doi": "10.1186/s13049-022-01056-8", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Literature review data realted to disaster training programs for medical first responders.", + "data_type": ["Social science and humanities data"], + "data_url": "https://europepmc.org/article/MED/36566227#id696386" + } + ], + "title": "Preparing medical first responders for crises: a systematic literature review of disaster training programs and their effectiveness", + "issue": "1", + "volume": "30", + "publisher": "Springer Science and Business Media LLC", + "published": "2022-12-24", + "author": [ + "Baetzner A. S.", + "Wespi R.", + "Hill Y.", + "Gyllencreutz L.", + "Sauter T. C." + ] + }, + { + "doi": "10.1371/journal.pgen.1010367", + "available_items": [ + { + "type": "data", + "repo_name": "GWAS Catalog", + "accession_number": "GCST90132193", + "description": "Single variant association studies summary statistics", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://www.ebi.ac.uk/gwas/studies/GCST90132193" + }, + { + "type": "data", + "repo_name": "GWAS Catalog", + "accession_number": "GCST90132194", + "description": "Single variant association studies summary statistics", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://www.ebi.ac.uk/gwas/studies/GCST90132194" + }, + { + "type": "data", + "repo_name": "GWAS Catalog", + "accession_number": "GCST90132195", + "description": "Single variant association studies summary statistics", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://www.ebi.ac.uk/gwas/studies/GCST90132195" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Analysis scripts", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://github.com/DrGBL/WES.WGS" + } + ], + "title": "Exome-wide association study to identify rare variants influencing COVID-19 outcomes: Results from the Host Genetics Initiative", + "issue": "11", + "volume": "18", + "publisher": "Public Library of Science (PLoS)", + "published": "2022-11-03", + "author": [ + "Butler-Laporte G.", + "Povysil G.", + "Kosmicki J. A.", + "Cirulli E. T.", + "Drivas T." + ] + }, + { + "doi": "10.1371/journal.ppat.1010931", + "available_items": [ + { + "type": "data", + "repo_name": "Gene Expression Omnibus", + "accession_number": "GSE196472", + "description": "Raw sequencing data", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE196472" + }, + { + "type": "data", + "repo_name": "Gene Expression Omnibus", + "accession_number": "GSE196473", + "description": "Processed sequencing data", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE196473" + } + ], + "title": "Cross-protection against African swine fever virus upon intranasal vaccination is associated with an adaptive-innate immune crosstalk", + "issue": "11", + "volume": "18", + "publisher": "Public Library of Science (PLoS)", + "published": "2022-11-09", + "author": [ + "Bosch-Camós L.", + "Alonso U.", + "Esteve-Codina A.", + "Chang C.", + "Martín-Mur B." + ] + }, + { + "doi": "10.1038/s41598-022-23415-2", + "available_items": [ + { + "type": "data", + "repo_name": "Open Science Framework", + "accession_number": "", + "description": "All survey data and study material used in this project", + "data_type": ["Social science and humanities data"], + "data_url": "https://osf.io/c8zhn/" + }, + { + "type": "code", + "repo_name": "Open Science Framework", + "accession_number": "Code used for analysis", + "description": "", + "data_type": ["Social science and humanities data"], + "data_url": "https://osf.io/c8zhn/" + } + ], + "title": "Acute anxiety during the COVID-19 pandemic was associated with higher levels of everyday altruism", + "issue": "1", + "volume": "12", + "publisher": "Springer Science and Business Media LLC", + "published": "2022-11-03", + "author": [ + "Vieira J. B.", + "Pierzchajlo S.", + "Jangard S.", + "Marsh A. A.", + "Olsson A." + ] + }, + { + "doi": "10.1371/journal.pone.0277470", + "available_items": [ + { + "type": "data", + "repo_name": "Open Science Framework", + "accession_number": "", + "description": "Survey data from 321 early career dementia researchers, including relevant socialdemographic characteristics", + "data_type": ["Social science and humanities data"], + "data_url": "https://osf.io/fr8j2/" + } + ], + "title": "Impact of the COVID-19 pandemic on early career dementia researchers: A global online survey", + "issue": "11", + "volume": "17", + "publisher": "Public Library of Science (PLoS)", + "published": "2022-11-09", + "author": [ + "Bartels S. L.", + "Shaaban C. E.", + "Brum W. S.", + "Welikovitch L. A.", + "Folarin R." + ] + }, + { + "doi": "10.3389/fpubh.2022.996036", + "available_items": [ + { + "type": "data", + "repo_name": "OSF", + "accession_number": "", + "description": "Data for collectivism and mobility", + "data_type": ["Social science and humanities data"], + "data_url": "https://osf.io/xt5qs/?view_only=e7da6b6f69f24bc7b3a9656d00cebb10" + } + ], + "title": "Collectivism reduces objective mobility trends to public areas during the COVID-19 pandemic", + "issue": "", + "volume": "10", + "publisher": "Frontiers Media SA", + "published": "2022-09-28", + "author": ["Dang J.", "Xiao S."] + }, + { + "doi": "10.1038/s41380-022-01786-2", + "available_items": [ + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Source code to reproduce the findings", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://github.com/SellgrenLab/organoid-Covid19" + } + ], + "title": "SARS-CoV-2 promotes microglial synapse elimination in human brain organoids", + "issue": "", + "volume": "", + "publisher": "Springer Science and Business Media LLC", + "published": "2022-10-05", + "author": [ + "Samudyata S.", + "Oliveira A. O.", + "Malwade S.", + "Rufino de Sousa N.", + "Goparaju S. K." + ] + }, + { + "doi": "10.1371/journal.pone.0275380", + "available_items": [ + { + "type": "protocol", + "repo_name": "OSF", + "accession_number": "", + "description": "The protocol for this study", + "data_type": ["Other data"], + "data_url": "https://osf.io/jgwvk/" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Data used to evaluate publications and model types, and the code used for analysis.", + "data_type": ["Other data"], + "data_url": "https://github.com/zavalis/transparency-indicators-inf-dis-models" + } + ], + "title": "A meta-epidemiological assessment of transparency indicators of infectious disease models", + "issue": "10", + "volume": "17", + "publisher": "Public Library of Science (PLoS)", + "published": "2022-10-07", + "author": ["Zavalis E. A.", "Ioannidis J. P. A."] + }, + { + "doi": "10.1038/s41598-022-17303-y", + "available_items": [ + { + "type": "data", + "repo_name": "OSF", + "accession_number": "", + "description": "Processed and anonymised demographic and health data.", + "data_type": ["Social science and humanities data", "Other data"], + "data_url": "https://osf.io/vr6p4/?view_only=070d364b489b43fca34bfcfd811ed22b" + } + ], + "title": "Development and cross-national investigation of a model explaining participation in WHO-recommended and placebo behaviours to prevent COVID-19 infection", + "issue": "1", + "volume": "12", + "publisher": "Springer Science and Business Media LLC", + "published": "2022-10-21", + "author": [ + "Kłosowska J.", + "Bajcar E. A.", + "Bieniek H.", + "Brączyk J.", + "Joshanloo M." + ] + }, + { + "doi": "10.1016/j.evolhumbehav.2022.09.003", + "available_items": [ + { + "type": "data", + "repo_name": "OSF", + "accession_number": "", + "description": "Data related to social motivation", + "data_type": ["Social science and humanities data", "Other data"], + "data_url": "https://osf.io/p9z2a/" + } + ], + "title": "Family still matters: Human social motivation across 42 countries during a global pandemic", + "issue": "6", + "volume": "43", + "publisher": "Elsevier BV", + "published": "2022-11-02", + "author": [ + "Pick C. M.", + "Ko A.", + "Wormley A. S.", + "Wiezel A.", + "Kenrick D. T." + ] + }, + { + "doi": "10.1038/s41598-022-22711-1", + "available_items": [ + { + "type": "data", + "repo_name": "MR-base", + "accession_number": "ebi-a-GCST005536", + "description": "Exposure dataset for type 1 diabetes mellitus", + "data_type": ["Genomics & transcriptomics data", "Other data"], + "data_url": "https://gwas.mrcieu.ac.uk/datasets/ebi-a-GCST005536" + }, + { + "type": "data", + "repo_name": "MR-base", + "accession_number": "ebi-a-GCST003156", + "description": "Exposure dataset for systemic lupus erythematosus", + "data_type": ["Genomics & transcriptomics data", "Other data"], + "data_url": "https://gwas.mrcieu.ac.uk/datasets/ebi-a-GCST003156" + }, + { + "type": "data", + "repo_name": "MR-base", + "accession_number": "ebi-a-GCST005527", + "description": "Exposure dataset for psoriasis", + "data_type": ["Genomics & transcriptomics data", "Other data"], + "data_url": "https://gwas.mrcieu.ac.uk/datasets/ebi-a-GCST005527" + }, + { + "type": "data", + "repo_name": "MR-base", + "accession_number": "ieu-b-18", + "description": "Exposure dataset for multiple sclerosis", + "data_type": ["Genomics & transcriptomics data", "Other data"], + "data_url": "https://gwas.mrcieu.ac.uk/datasets/ieu-b-18" + }, + { + "type": "data", + "repo_name": "MR-base", + "accession_number": "ieu-a-1112", + "description": "Exposure dataset for primary sclerosing cholangitis", + "data_type": ["Genomics & transcriptomics data", "Other data"], + "data_url": "https://gwas.mrcieu.ac.uk/datasets/ieu-a-1112" + }, + { + "type": "data", + "repo_name": "MR-base", + "accession_number": "ebi-a-GCST005581", + "description": "Exposure dataset for primary biliary cirrhosis", + "data_type": ["Genomics & transcriptomics data", "Other data"], + "data_url": "https://gwas.mrcieu.ac.uk/datasets/ebi-a-GCST005581" + }, + { + "type": "data", + "repo_name": "COVID19-hg GWAS", + "accession_number": "", + "description": "Outcome datasets generated in the current study.", + "data_type": ["Genomics & transcriptomics data", "Other data"], + "data_url": "https://www.covid19hg.org/results/r6/" + } + ], + "title": "A Mendelian randomization study of genetic predisposition to autoimmune diseases and COVID-19", + "issue": "1", + "volume": "12", + "publisher": "Springer Science and Business Media LLC", + "published": "2022-10-21", + "author": ["Li S.", "Yuan S.", "Schooling C. M.", "Larsson S. C."] + }, + { + "doi": "10.1101/2022.10.06.22280777", + "available_items": [ + { + "type": "data", + "repo_name": "OSF", + "accession_number": "", + "description": "Anonymised databases with the individual participant data and the metadata for Bayesian analyses.", + "data_type": ["Social science and humanities data", "Other data"], + "data_url": "https://osf.io/2xn5m/" + }, + { + "type": "code", + "repo_name": "OSF", + "accession_number": "", + "description": "Code used for data analysis.", + "data_type": ["Social science and humanities data", "Other data"], + "data_url": "https://osf.io/2xn5m/" + } + ], + "title": "Treating intrusive memories after trauma in healthcare workers: a Bayesian adaptive randomised trial developing an imagery-competing task intervention", + "issue": "", + "volume": "", + "publisher": "Cold Spring Harbor Laboratory", + "published": "2022-10-07", + "author": [ + "Ramineni V.", + "Millroth P.", + "Iyadurai L.", + "Jaki T.", + "Kingslake J." + ] + }, + { + "doi": "10.15252/emmm.202215821", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Raw time series data related to vaccine efficacy, blood testing, and histology. ", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://ki.se/en/research/opencorona" + } + ], + "title": "A universal SARS‐CoV DNA vaccine inducing highly cross‐reactive neutralizing antibodies and T cells", + "issue": "", + "volume": "", + "publisher": "EMBO", + "published": "2022-09-02", + "author": [ + "Appelberg S.", + "Ahlén G.", + "Yan J.", + "Nikouyan N.", + "Weber S." + ] + }, + { + "doi": "10.12688/hrbopenres.13516.1", + "available_items": [ + { + "type": "data", + "repo_name": "FigShare", + "accession_number": "", + "description": "Long COVID Survey Data", + "data_type": ["Social science and humanities data"], + "data_url": "https://doi.org/10.6084/m9.figshare.19364828.v1" + }, + { + "type": "data", + "repo_name": "FigShare", + "accession_number": "", + "description": "Long COVID Survey questionnaire", + "data_type": ["Social science and humanities data"], + "data_url": "https://figshare.com/articles/online_resource/Long_COVID_Survey/19447919" + } + ], + "title": "Impact of Long COVID on health and quality of life", + "issue": "", + "volume": "5", + "publisher": "F1000 Research Ltd", + "published": "2022-04-22", + "author": [ + "O’ Mahony L.", + "Buwalda T.", + "Blair M.", + "Forde B.", + "Lunjani N." + ] + }, + { + "doi": "10.1038/s41598-022-19155-y", + "available_items": [ + { + "type": "data", + "repo_name": "GitHub", + "accession_number": "", + "description": "Data on direct and indirect indicators of transmission e.g. mobility data, number of calls to the national healthcare advice line and vaccination coverage.", + "data_type": ["Public health data"], + "data_url": "https://github.com/MolEpicUU/spatiotemporal_predictions_COVID19" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Code used to produce models.", + "data_type": ["Public health data"], + "data_url": "https://github.com/MolEpicUU/spatiotemporal_predictions_COVID19" + } + ], + "title": "Spatio-temporal predictions of COVID-19 test positivity in Uppsala County, Sweden: a comparative approach", + "issue": "1", + "volume": "12", + "publisher": "Springer Science and Business Media LLC", + "published": "2022-09-07", + "author": [ + "van Zoest V.", + "Varotsis G.", + "Menzel U.", + "Wigren A.", + "Kennedy B." + ] + }, + { + "doi": "10.1098/rsos.220440", + "available_items": [ + { + "type": "data", + "repo_name": "dryad", + "accession_number": "", + "description": "Survey responses collected through Qualtrix", + "data_type": ["Other data"], + "data_url": "https://datadryad.org/stash/dataset/doi:10.5061/dryad.rfj6q57d0" + }, + { + "type": "code", + "repo_name": "dryad", + "accession_number": "", + "description": "Code used for analysis (in R)", + "data_type": ["Other data"], + "data_url": "https://datadryad.org/stash/dataset/doi:10.5061/dryad.rfj6q57d0" + } + ], + "title": "Forecasting the publication and citation outcomes of COVID-19 preprints", + "issue": "9", + "volume": "9", + "publisher": "The Royal Society", + "published": "2022-09-28", + "author": [ + "Gordon M.", + "Bishop M.", + "Chen Y.", + "Dreber A.", + "Goldfedder B." + ] + }, + { + "doi": "10.1016/j.cels.2022.06.006", + "available_items": [ + { + "type": "data", + "repo_name": "FigShare", + "accession_number": "", + "description": "Metabolomics data", + "data_type": ["Health data", "Other data"], + "data_url": "https://dx.doi.org/10.6084/m9.figshare.13336862" + }, + { + "type": "code", + "repo_name": "Zenodo", + "accession_number": "", + "description": "Analysis code", + "data_type": ["Health data", "Other data"], + "data_url": "https://dx.doi.org/10.5281/zenodo.6706499" + } + ], + "title": "Multi-omics personalized network analyses highlight progressive disruption of central metabolism associated with COVID-19 severity", + "issue": "8", + "volume": "13", + "publisher": "Elsevier BV", + "published": "2022-08-20", + "author": [ + "Ambikan A. T.", + "Yang H.", + "Krishnan S.", + "Svensson Akusjärvi S.", + "Gupta S." + ] + }, + { + "doi": "10.1016/j.medj.2022.07.007", + "available_items": [ + { + "type": "data", + "repo_name": "GISAID", + "accession_number": "EPI_ISL_11414777-11415389 and EPI_ISL_11450500-11450677", + "description": "Assembled SARS-CoV-2 genomes", + "data_type": [ + "Biochemistry data", + "Health data", + "Genomics & transcriptomics data" + ], + "data_url": "https://gisaid.org/" + }, + { + "type": "data", + "repo_name": "ArrayExpress", + "accession_number": "E-MTAB-11650", + "description": "Raw sequencing data", + "data_type": [ + "Biochemistry data", + "Health data", + "Genomics & transcriptomics data" + ], + "data_url": "https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-11650/" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Computational code", + "data_type": [ + "Biochemistry data", + "Health data", + "Genomics & transcriptomics data" + ], + "data_url": "https://github.com/reiniuslab/OmicronWaves/" + } + ], + "title": "Monitoring of the SARS-CoV-2 Omicron BA.1/BA.2 lineage transition in the Swedish population reveals increased viral RNA levels in BA.2 cases", + "issue": "9", + "volume": "3", + "publisher": "Elsevier BV", + "published": "2022-09-11", + "author": ["Lentini A.", "Pereira A.", "Winqvist O.", "Reinius B."] + }, + { + "doi": "10.1038/s41558-022-01426-1", + "available_items": [ + { + "type": "data", + "repo_name": "GitHub", + "accession_number": "", + "description": "All data collected as part of the literature search (list of considered diseases, and references for empirical cases.", + "data_type": ["Other data"], + "data_url": "https://github.com/Camilo-Mora/Diseases" + } + ], + "title": "Over half of known human pathogenic diseases can be aggravated by climate change", + "issue": "9", + "volume": "12", + "publisher": "Springer Science and Business Media LLC", + "published": "2022-08-08", + "author": [ + "Mora C.", + "McKenzie T.", + "Gaw I. M.", + "Dean J. M.", + "von Hammerstein H." + ] + }, + { + "doi": "10.1038/s41467-022-32357-2", + "available_items": [ + { + "type": "data", + "repo_name": "EGA", + "accession_number": "EGAS00001005304", + "description": "Genotype data generated (SPGRX cohort)", + "data_type": ["Biochemistry data", "Genomics & transcriptomics data"], + "data_url": "https://ega-archive.org/studies/EGAS00001005304" + }, + { + "type": "data", + "repo_name": "Gene Expression Omnibus", + "accession_number": "GSE179325", + "description": "Methylation data", + "data_type": ["Biochemistry data", "Genomics & transcriptomics data"], + "data_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE179325" + } + ], + "title": "Whole blood DNA methylation analysis reveals respiratory environmental traits involved in COVID-19 severity following SARS-CoV-2 infection", + "issue": "1", + "volume": "13", + "publisher": "Springer Science and Business Media LLC", + "published": "2022-08-06", + "author": [ + "Barturen G.", + "Carnero-Montoro E.", + "Martínez-Bueno M.", + "Rojo-Rello S.", + "Sobrino B." + ] + }, + { + "doi": "10.1016/j.immuni.2022.07.005", + "available_items": [ + { + "type": "data", + "repo_name": "ArrayExpress", + "accession_number": "E-MTAB-11845", + "description": "Processed scRNA-seq data", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-11845/" + } + ], + "title": "Immunodeficiency syndromes differentially impact the functional profile of SARS-CoV-2-specific T cells elicited by mRNA vaccination", + "issue": "9", + "volume": "55", + "publisher": "Elsevier BV", + "published": "2022-09-14", + "author": [ + "Gao Y.", + "Cai C.", + "Wullimann D.", + "Niessl J.", + "Rivera-Ballesteros O." + ] + }, + { + "doi": "10.3389/fimmu.2022.932388", + "available_items": [ + { + "type": "data", + "repo_name": "Gene Expression Omnibus", + "accession_number": "GSE201551", + "description": "Expression profiling by high throughput sequencing", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE201551" + } + ], + "title": "Type I Interferons Promote Germinal Centers Through B Cell Intrinsic Signaling and Dendritic Cell Dependent Th1 and Tfh Cell Lineages", + "issue": "", + "volume": "13", + "publisher": "Frontiers Media SA", + "published": "2022-07-13", + "author": [ + "Dahlgren M. W.", + "Plumb A. W.", + "Niss K.", + "Lahl K.", + "Brunak S." + ] + }, + { + "doi": "10.3389/fimmu.2022.924244", + "available_items": [ + { + "type": "data", + "repo_name": "Gene Expression Omnibus", + "accession_number": "GSE201772", + "description": "Expression profiling by high throughput sequencing", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE201772" + } + ], + "title": "Dynamically upregulated mast cell CPA3 patterns in chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis", + "issue": "", + "volume": "13", + "publisher": "Frontiers Media SA", + "published": "2022-08-02", + "author": [ + "Siddhuraj P.", + "Jönsson J.", + "Alyamani M.", + "Prabhala P.", + "Magnusson M." + ] + }, + { + "doi": "10.1057/s41599-022-01257-7", + "available_items": [ + { + "type": "data", + "repo_name": "Open Science Framework", + "accession_number": "", + "description": "Data related to herd immunity, willingness to get vaccinated, and demographic factors.", + "data_type": ["Social science and humanities data", "Other data"], + "data_url": "https://osf.io/7nbzr/?view_only=1b1483f5ce494d809f08eaa529bed982" + } + ], + "title": "The effect of herd immunity thresholds on willingness to vaccinate", + "issue": "1", + "volume": "9", + "publisher": "Springer Science and Business Media LLC", + "published": "2022-07-18", + "author": ["Andersson P. A.", "Tinghög G.", "Västfjäll D."] + }, + { + "doi": "10.1007/s10664-022-10176-9", + "available_items": [ + { + "type": "code", + "repo_name": "Zenodo", + "accession_number": "", + "description": "R code for Bayesian analysis", + "data_type": ["Social science and humanities data", "Other data"], + "data_url": "https://zenodo.org/record/5115661#.YymQIOxByX0" + } + ], + "title": "Agile software development one year into the COVID-19 pandemic", + "issue": "6", + "volume": "27", + "publisher": "Springer Science and Business Media LLC", + "published": "2022-06-22", + "author": ["Ågren P.", "Knoph E.", "Berntsson Svensson R."] + }, + { + "doi": "10.1038/s41598-022-13218-w", + "available_items": [ + { + "type": "data", + "repo_name": "Zenodo", + "accession_number": "", + "description": "A comparative dataset on public perceptions of multiple risks during the COVID-19 pandemic in Italy and Sweden.", + "data_type": ["Social science and humanities data", "Other data"], + "data_url": "https://zenodo.org/record/5653322#.YymOvexByX2" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Code for processing and visualisations", + "data_type": ["Social science and humanities data", "Other data"], + "data_url": "https://github.com/eleraf/epidemics-risk-perception" + } + ], + "title": "Epidemic risk perceptions in Italy and Sweden driven by authority responses to COVID-19", + "issue": "1", + "volume": "12", + "publisher": "Springer Science and Business Media LLC", + "published": "2022-06-03", + "author": ["Raffetti E.", "Mondino E.", "Di Baldassarre G."] + }, + { + "doi": "10.1590/1678-4685-gmb-2022-0034", + "available_items": [ + { + "type": "data", + "repo_name": "BioProject", + "accession_number": "PRJNA736341", + "description": "Beaudette genome sequencing and assembly", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://www.ebi.ac.uk/ena/browser/view/PRJNA736341?show=reads" + }, + { + "type": "data", + "repo_name": "ENA", + "accession_number": "MZ368698", + "description": "Avian coronavirus strain Beaudette, complete genome.", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://www.ebi.ac.uk/ena/browser/view/MZ368698" + } + ], + "title": "The order of events on Avian coronavirus life cycle shapes the order of quasispecies evolution during host switches", + "issue": "2", + "volume": "45", + "publisher": "FapUNIFESP (SciELO)", + "published": "2022-07-26", + "author": [ + "Brandão P. E.", + "Berg M.", + "Leite B. A.", + "Silva S. O.", + "Taniwaki S. A." + ] + }, + { + "doi": "10.1080/19490976.2022.2073131", + "available_items": [ + { + "type": "data", + "repo_name": "ENA", + "accession_number": "PRJEB50040", + "description": "Sequence data", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://www.ebi.ac.uk/ena/browser/view/PRJEB50040" + }, + { + "type": "data", + "repo_name": "FigShare", + "accession_number": "", + "description": "Metabolite data", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://figshare.com/articles/dataset/Metabolomics_Data_xlsx/18046400" + } + ], + "title": "A high-risk gut microbiota configuration associates with fatal hyperinflammatory immune and metabolic responses to SARS-CoV-2", + "issue": "1", + "volume": "14", + "publisher": "Informa UK Limited", + "published": "2022-05-15", + "author": [ + "Albrich W. C.", + "Ghosh T. S.", + "Ahearn-Ford S.", + "Mikaeloff F.", + "Lunjani N." + ] + }, + { + "doi": "10.1038/s41467-022-30340-5", + "available_items": [ + { + "type": "data", + "repo_name": "Zenodo", + "accession_number": "", + "description": "Data on the effect of an mRNA vaccine booster on immunogenicity in individuals vaccinated with two doses of inactivated vaccine.", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://zenodo.org/record/6305550#.Yyl_tuxByX1" + } + ], + "title": "Heterologous immunisation with inactivated vaccine followed by mRNA-booster elicits strong immunity against SARS-CoV-2 Omicron variant", + "issue": "1", + "volume": "13", + "publisher": "Springer Science and Business Media LLC", + "published": "2022-05-13", + "author": [ + "Zuo F.", + "Abolhassani H.", + "Du L.", + "Piralla A.", + "Bertoglio F." + ] + }, + { + "doi": "10.1128/mbio.00892-22", + "available_items": [ + { + "type": "data", + "repo_name": "ArrayExpress", + "accession_number": "E-MTAB-10687", + "description": "Bulk and single-cell RNA-Seq gene counts", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-10687" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "R and Python code used for analysis", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://github.com/henriksson-lab/covidali_r.git" + } + ], + "title": "Serine Protease Inhibitors Restrict Host Susceptibility to SARS-CoV-2 Infections", + "issue": "3", + "volume": "13", + "publisher": "American Society for Microbiology", + "published": "2022-06-28", + "author": [ + "Rosendal E.", + "Mihai I. S.", + "Becker M.", + "Das D.", + "Frängsmyr L." + ] + }, + { + "doi": "10.1371/journal.pmed.1003987", + "available_items": [ + { + "type": "data", + "repo_name": "GitHub", + "accession_number": "", + "description": "Data from the systematic review on asymptomatic and presymptomatic SARS-CoV-2 infection", + "data_type": ["Other data"], + "data_url": "https://github.com/leonieheron/LSR_Asymp_v5" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Code used to display and synthesise the results", + "data_type": ["Other data"], + "data_url": "https://github.com/leonieheron/LSR_Asymp_v5" + } + ], + "title": "Occurrence and transmission potential of asymptomatic and presymptomatic SARS-CoV-2 infections: Update of a living systematic review and meta-analysis", + "issue": "5", + "volume": "19", + "publisher": "Public Library of Science (PLoS)", + "published": "2022-05-26", + "author": [ + "Buitrago-Garcia D.", + "Ipekci A. M.", + "Heron L.", + "Imeri H.", + "Araujo-Chaveron L." + ] + }, + { + "doi": "10.1016/s2666-5247(21)00304-9", + "available_items": [ + { + "type": "data", + "repo_name": "BioProject", + "accession_number": "PRJNA748764", + "description": "Deidentified individual patient data and raw fastq microbial sequencing alignments", + "data_type": ["Health data", "Genomics & transcriptomics data"], + "data_url": "https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA748764" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Background correction algorithm", + "data_type": ["Health data", "Genomics & transcriptomics data"], + "data_url": "https://github.com/czbiohub/idseqr" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Rules-based model", + "data_type": ["Health data", "Genomics & transcriptomics data"], + "data_url": "https://github.com/alexandra-t/rules_based_model" + } + ], + "title": "Lower respiratory tract infections in children requiring mechanical ventilation: a multicentre prospective surveillance study incorporating airway metagenomics", + "issue": "4", + "volume": "3", + "publisher": "Elsevier BV", + "published": "2022-03-30", + "author": [ + "Tsitsiklis A.", + "Osborne C. M.", + "Kamm J.", + "Williamson K.", + "Kalantar K." + ] + }, + { + "doi": "10.15252/embr.202154499", + "available_items": [ + { + "type": "data", + "repo_name": "ArrayExpress", + "accession_number": "E‐MTAB‐10679", + "description": "RNA-seq results", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-10679/" + } + ], + "title": "Myeloid cell‐specific topoisomerase 1 inhibition using DNA origami mitigates neuroinflammation", + "issue": "7", + "volume": "23", + "publisher": "EMBO", + "published": "2022-05-20", + "author": ["Zhu K.", "Wang Y.", "Sarlus H.", "Geng K.", "Nutma E."] + }, + { + "doi": "10.3390/biomedicines10050982", + "available_items": [ + { + "type": "data", + "repo_name": "BioProject", + "accession_number": "PRJNA781460", + "description": "Raw shotgun metagenome sequencing data", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA781460" + } + ], + "title": "Characterization of the Upper Respiratory Bacterial Microbiome in Critically Ill COVID-19 Patients", + "issue": "5", + "volume": "10", + "publisher": "MDPI AG", + "published": "2022-04-23", + "author": [ + "Bai X.", + "Narayanan A.", + "Skagerberg M.", + "Ceña-Diez R.", + "Giske C. G." + ] + }, + { + "doi": "10.1371/journal.pcbi.1009973", + "available_items": [ + { + "type": "data", + "repo_name": "Zenodo", + "accession_number": "", + "description": "Data time series of metereological factors, regional measures and mobility", + "data_type": ["Social science and humanities data", "Other data"], + "data_url": "https://zenodo.org/record/6120655#.YyqzGexByX0" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Scripts for the model", + "data_type": ["Social science and humanities data", "Other data"], + "data_url": "https://github.com/katharinaledebur/regional_differences_covid" + } + ], + "title": "Meteorological factors and non-pharmaceutical interventions explain local differences in the spread of SARS-CoV-2 in Austria", + "issue": "4", + "volume": "18", + "publisher": "Public Library of Science (PLoS)", + "published": "2022-04-04", + "author": [ + "Ledebur K.", + "Kaleta M.", + "Chen J.", + "Lindner S. D.", + "Matzhold C." + ] + }, + { + "doi": "10.1039/d0sc05064d", + "available_items": [ + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Structural ensembles of camostat, GBPA, and nafamostat", + "data_type": ["Protein data", "Drug discovery data"], + "data_url": "https://github.com/noegroup/tmprss2_structures" + } + ], + "title": "Molecular mechanism of inhibiting the SARS-CoV-2 cell entry facilitator TMPRSS2 with camostat and nafamostat", + "issue": "3", + "volume": "12", + "publisher": "Royal Society of Chemistry (RSC)", + "published": "2022-02-24", + "author": [ + "Hempel T.", + "Raich L.", + "Olsson S.", + "Azouz N. P.", + "Klingler A. M." + ] + }, + { + "doi": "10.1038/s42003-022-03187-1 ", + "available_items": [ + { + "type": "data", + "repo_name": "PDB", + "accession_number": "6XN3", + "description": "Structure of the lactococcus lactis csm ctr_4:3 crispr-cas complex", + "data_type": ["Protein data"], + "data_url": "http://dx.doi.org/10.2210/pdb6xn3/pdb" + }, + { + "type": "data", + "repo_name": "PDB", + "accession_number": "6XN5", + "description": "Structure of the lactococcus lactis csm apo- crispr-cas complex", + "data_type": ["Protein data"], + "data_url": "https://dx.doi.org/10.2210/pdb6xn5/pdb" + }, + { + "type": "data", + "repo_name": "PDB", + "accession_number": "6XN4", + "description": "Structure of the lactococcus lactis csm ctr_3:2 crispr-cas complex", + "data_type": ["Protein data"], + "data_url": "https://dx.doi.org/10.2210/pdb6xn4/pdb" + }, + { + "type": "data", + "repo_name": "PDB", + "accession_number": "6XN7", + "description": "structure of the lactococcus lactis csm ntr crispr-cas complex", + "data_type": ["Protein data"], + "data_url": "https://dx.doi.org/10.2210/pdb6xn7/pdb" + } + ], + "title": "Structural and biochemical characterization of in vivo assembled Lactococcus lactis CRISPR-Csm complex", + "issue": "1", + "volume": "5", + "publisher": "Springer Science and Business Media LLC", + "published": "2022-03-29", + "author": ["Sridhara S.", "Rai J.", "Whyms C.", "Goswami H.", "He H."] + }, + { + "doi": "10.1161/CIRCULATIONAHA.121.056663", + "available_items": [ + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Code used in the main analysis", + "data_type": ["Health data"], + "data_url": "https://github.com/alhenry/cvd1-hf" + } + ], + "title": "Therapeutic Targets for Heart Failure Identified Using Proteomics and Mendelian Randomization", + "issue": "16", + "volume": "145", + "publisher": "Ovid Technologies (Wolters Kluwer Health)", + "published": "2022-04-19", + "author": [ + "Henry A.", + "Gordillo-Marañón M.", + "Finan C.", + "Schmidt A. F.", + "Ferreira J. P." + ] + }, + { + "doi": "10.1002/sim.9365", + "available_items": [ + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Code and simulated data", + "data_type": ["Social science and humanities data", "Other data"], + "data_url": "https://github.com/jsheen/NPI" + } + ], + "title": "The required size of cluster randomized trials of nonpharmaceutical interventions in epidemic settings", + "issue": "13", + "volume": "41", + "publisher": "Wiley", + "published": "2022-03-07", + "author": [ + "Sheen J. K.", + "Haushofer J.", + "Metcalf C. J. E.", + "Kennedy‐Shaffer L." + ] + }, + { + "doi": "10.3389/fgene.2022.792090", + "available_items": [ + { + "type": "code", + "repo_name": "BitBucket", + "accession_number": "", + "description": "Dataset used to to assess cross-talk based approaches for drug repurposing", + "data_type": ["Drug discovery data"], + "data_url": "https://bitbucket.org/sonnhammergroup/drugrepurposingbench/src/master/" + }, + { + "type": "data", + "repo_name": "BitBucket", + "accession_number": "", + "description": "Code used for analysis", + "data_type": ["Drug discovery data"], + "data_url": "https://bitbucket.org/sonnhammergroup/drugrepurposingbench/src/master/" + } + ], + "title": "Network Crosstalk as a Basis for Drug Repurposing", + "issue": "", + "volume": "13", + "publisher": "Frontiers Media SA", + "published": "2022-03-08", + "author": ["Guala D.", "Sonnhammer E. L. L."] + }, + { + "doi": "10.1126/sciadv.abm0220", + "available_items": [ + { + "type": "data", + "repo_name": "BioProject", + "accession_number": "PRJNA814713", + "description": "NGS data", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA814713/" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Implementation of the seqUMAP algorithm", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://github.com/MurrellGroup/SeqUMAP.jl" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Codes for processing NGS nanobody", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://github.com/MurrellGroup/FuNGS" + } + ], + "title": "Multivariate mining of an alpaca immune repertoire identifies potent cross-neutralizing SARS-CoV-2 nanobodies", + "issue": "12", + "volume": "8", + "publisher": "American Association for the Advancement of Science (AAAS)", + "published": "2022-03-25", + "author": [ + "Hanke L.", + "Sheward D. J.", + "Pankow A.", + "Vidakovics L. P.", + "Karl V." + ] + }, + { + "doi": "10.1038/s41467-022-28865-w", + "available_items": [ + { + "type": "data", + "repo_name": "FigShare", + "accession_number": "16866202.v1", + "description": "Raw data and predicted PDB files", + "data_type": ["Genomics & transcriptomics data", "Protein data"], + "data_url": "https://scilifelab.figshare.com/articles/dataset/Data_and_most_relevant_results_for_the_FoldDock_project/16866202/1" + } + ], + "title": "Improved prediction of protein-protein interactions using AlphaFold2", + "issue": "1", + "volume": "13", + "publisher": "Springer Science and Business Media LLC", + "published": "2022-03-10", + "author": ["Bryant P.", "Pozzati G.", "Elofsson A."] + }, + { + "doi": "10.3390/ijerph19052558", + "available_items": [ + { + "type": "data", + "repo_name": "FigShare", + "accession_number": "", + "description": "Dataset including variables of physical activity and sedentary behavior during the COVID-19 pandemic", + "data_type": ["Social science and humanities data"], + "data_url": "https://doi.org/10.6084/m9.figshare.19208538" + } + ], + "title": "Changes in Physical Activity and Sedentary Behavior before and during the COVID-19 Pandemic: A Swedish Population Study", + "issue": "5", + "volume": "19", + "publisher": "MDPI AG", + "published": "2022-02-23", + "author": [ + "Elvén M.", + "Kerstis B.", + "Stier J.", + "Hellström C.", + "von Heideken Wågert P." + ] + }, + { + "doi": "10.7554/elife.64709", + "available_items": [ + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "SiteLocalization software for binding site localisation on non-homogeneous cell surfaces using topological image averaging", + "data_type": ["Imaging data"], + "data_url": "https://github.com/nordenfeltLab/SiteLocalization" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "FluoroDist.jl - software for simulated fluorescence images with accurate surface distances", + "data_type": ["Imaging data"], + "data_url": "https://github.com/nordenfeltLab/FluoroDist.jl" + }, + { + "type": "data", + "repo_name": "Dryad", + "accession_number": "", + "description": "Site localisation measurements data", + "data_type": ["Imaging data"], + "data_url": "https://doi.org/10.5061/dryad.h18931znn" + } + ], + "title": "Nanoscale binding site localization by molecular distance estimation on native cell surfaces using topological image averaging", + "issue": "", + "volume": "11", + "publisher": "eLife Sciences Publications, Ltd", + "published": "2022-02-24", + "author": [ + "Kumra Ahnlide V.", + "Kumra Ahnlide J.", + "Wrighton S.", + "Beech J. P.", + "Nordenfelt P." + ] + }, + { + "doi": "10.1038/s41598-022-05597-x", + "available_items": [ + { + "type": "data", + "repo_name": "Gene Expression Omnibus", + "accession_number": "GSE63229", + "description": "Expression profiling by array", + "data_type": [ + "Drug discovery data", + "Genomics & transcriptomics data" + ], + "data_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE63229" + }, + { + "type": "data", + "repo_name": "Gene Expression Omnibus", + "accession_number": "GSE123574", + "description": "Genome binding/occupancy profiling by high throughput sequencing", + "data_type": [ + "Drug discovery data", + "Genomics & transcriptomics data" + ], + "data_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE123574" + } + ], + "title": "An in silico analysis identifies drugs potentially modulating the cytokine storm triggered by SARS-CoV-2 infection", + "issue": "1", + "volume": "12", + "publisher": "Springer Science and Business Media LLC", + "published": "2022-01-31", + "author": [ + "Sanchez-Burgos L.", + "Gómez-López G.", + "Al-Shahrour F.", + "Fernandez-Capetillo O." + ] + }, + { + "doi": "10.1073/pnas.2116435119", + "available_items": [ + { + "type": "data", + "repo_name": "dbSNP", + "accession_number": "RS17713054", + "description": "Reference single nucleotide polymorphism report", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://www.ncbi.nlm.nih.gov/snp/rs17713054" + }, + { + "type": "data", + "repo_name": "dbSNP", + "accession_number": "RS17764980", + "description": "Reference single nucleotide polymorphism report", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://www.ncbi.nlm.nih.gov/snp/rs17764980" + }, + { + "type": "data", + "repo_name": "dbSNP", + "accession_number": "RS17714101", + "description": "Reference single nucleotide polymorphism report", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://www.ncbi.nlm.nih.gov/snp/rs17714101" + }, + { + "type": "data", + "repo_name": "dbSNP", + "accession_number": "RS17714228", + "description": "Reference single nucleotide polymorphism report", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://www.ncbi.nlm.nih.gov/snp/rs17714228" + }, + { + "type": "data", + "repo_name": "dbSNP", + "accession_number": "RS71325092", + "description": "Reference single nucleotide polymorphism report", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://www.ncbi.nlm.nih.gov/snp/rs71325092" + } + ], + "title": "The major genetic risk factor for severe COVID-19 is associated with protection against HIV", + "issue": "9", + "volume": "119", + "publisher": "Proceedings of the National Academy of Sciences", + "published": "2022-02-22", + "author": ["Zeberg H."] + }, + { + "doi": "10.1186/s12915-021-01086-1", + "available_items": [ + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Data analysis code.", + "data_type": ["Drug discovery data"], + "data_url": "https://github.com/pharmbio/antiviral-phenomics" + }, + { + "type": "data", + "repo_name": "Figshare", + "accession_number": "", + "description": "Images, analysis pipelines, and feature data.", + "data_type": ["Drug discovery data"], + "data_url": "https://doi.org/10.17044/scilifelab.14188403.v1" + } + ], + "title": "A phenomics approach for antiviral drug discovery", + "issue": "1", + "volume": "19", + "publisher": "Springer Science and Business Media LLC", + "published": "2021-08-02", + "author": [ + "Rietdijk J.", + "Tampere M.", + "Pettke A.", + "Georgiev P.", + "Lapins M." + ] + }, + { + "doi": "10.1371/journal.pone.0255270", + "available_items": [ + { + "type": "data", + "repo_name": "GitHub", + "accession_number": "", + "description": "Information on interactions between proteins & human cells, potential drug targets, genes related to potential targets.", + "data_type": ["Drug discovery data"], + "data_url": "https://github.com/MahnazHabibi/Drug-repurposing" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Matlab analysis code required to process data.", + "data_type": ["Drug discovery data"], + "data_url": "https://github.com/MahnazHabibi/Drug-repurposing" + } + ], + "title": "Topological network based drug repurposing for coronavirus 2019", + "issue": "7", + "volume": "16", + "publisher": "Public Library of Science (PLoS)", + "published": "2021-07-29", + "author": ["Habibi M.", "Taheri G."] + }, + { + "doi": "10.3390/md19070391", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "All data are included in the article or supplementary material (Sarcophyton cembranoid diterpenes metabolites).", + "data_type": ["Drug discovery data", "Protein data"], + "data_url": "https://www.mdpi.com/1660-3397/19/7/391/htm" + } + ], + "title": "Blue Biotechnology: Computational Screening of Sarcophyton Cembranoid Diterpenes for SARS-CoV-2 Main Protease Inhibition", + "issue": "7", + "volume": "19", + "publisher": "MDPI AG", + "published": "2021-07-13", + "author": [ + "Ibrahim M. A. A.", + "Abdelrahman A. H. M.", + "Atia M. A. M.", + "Mohamed T. A.", + "Moustafa M. F." + ] + }, + { + "doi": "10.1038/s41586-021-03767-x", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Summary statistics by COVID-19 HGI.", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://www.covid19hg.org/results/r5/" + }, + { + "type": "data", + "repo_name": "GWAS", + "accession_number": "GCST011074", + "description": "GWAS catalog study.", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://www.ebi.ac.uk/gwas/studies/GCST011074" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Code for summary statistics, PCA pipeline with precomputed loadings and meta-analyses.", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://github.com/covid19-hg/" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Code for Mendelian randomization and genetic correlation pipeline.", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://github.com/marcoralab/MRcovid" + } + ], + "title": "Mapping the human genetic architecture of COVID-19", + "issue": "7889", + "volume": "600", + "publisher": "Springer Science and Business Media LLC", + "published": "2021-07-08", + "author": [ + "Niemi M. E. K.", + "Karjalainen J.", + "Liao R. G.", + "Neale B. M.", + "Daly M." + ] + }, + { + "doi": "10.1172/jci152386", + "available_items": [ + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Code for data management and analysis (commit 183ddb7).", + "data_type": ["Genomics & transcriptomics data", "Health data"], + "data_url": "https://github.com/tomoconaka/COVID19-chr3" + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Data are held in multiple international repositories. Details about gaining access are contained in the paper.", + "data_type": ["Genomics & transcriptomics data", "Health data"], + "data_url": "https://www.jci.org/articles/view/152386" + } + ], + "title": "Age-dependent impact of the major common genetic risk factor for COVID-19 on severity and mortality", + "issue": "23", + "volume": "131", + "publisher": "American Society for Clinical Investigation", + "published": "2021-12-01", + "author": [ + "Nakanishi T.", + "Pigazzini S.", + "Degenhardt F.", + "Cordioli M.", + "Butler-Laporte G." + ] + }, + { + "doi": "10.1038/s41588-021-00996-8", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "COVID-19 summary statistics for individuals of African ancestry.", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://www.covid19hg.org/results/r6/" + }, + { + "type": "data", + "repo_name": "Combined Annotation Dependent Depletion", + "accession_number": "", + "description": "CADD-scores v.1.6.", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://cadd.gs.washington.edu/score" + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Genomes from the 1000 Genomes Project.", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://www.internationalgenome.org/data" + }, + { + "type": "data", + "repo_name": "Zenodo", + "accession_number": "", + "description": "Fine-mapping association summary statistics produced in this study.", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://doi.org/10.5281/zenodo.5708333" + }, + { + "type": "code", + "repo_name": "Zenodo", + "accession_number": "", + "description": "Code used for the fine-mapping analysis.", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://doi.org/10.5281/zenodo.5708333" + } + ], + "title": "Multi-ancestry fine mapping implicates OAS1 splicing in risk of severe COVID-19", + "issue": "2", + "volume": "54", + "publisher": "Springer Science and Business Media LLC", + "published": "2022-01-13", + "author": [ + "Huffman J. E.", + "Butler-Laporte G.", + "Khan A.", + "Pairo-Castineira E.", + "Drivas T. G." + ] + }, + { + "doi": "10.1093/heapol/czab113", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "All data are available in the article, or in sources therein (e.g. information on healthcare and political systems).", + "data_type": [ + "Public health data", + "Social science and humanities data" + ], + "data_url": "https://academic.oup.com/heapol/article/37/3/297/6373138#341608669" + } + ], + "title": "Priority setting and equity in COVID-19 pandemic plans: a comparative analysis of 18 African countries", + "issue": "3", + "volume": "37", + "publisher": "Oxford University Press (OUP)", + "published": "2021-10-07", + "author": [ + "Kapiriri L.", + "Kiwanuka S.", + "Biemba G.", + "Velez C.", + "Razavi S. D." + ] + }, + { + "doi": "10.3390/jcm10194411", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Data on influenza/pneumonia deaths & hospitalisations due to sepsis, subdivided by mental health condition, physical comorbidities, and demographic features.", + "data_type": [ + "Health data", + "Public health data", + "Social science and humanities data" + ], + "data_url": "https://www.mdpi.com/2077-0383/10/19/4411/s1?version=1632654678" + } + ], + "title": "Increased Risks of Death and Hospitalization in Influenza/Pneumonia and Sepsis for Individuals Affected by Psychotic Disorders, Bipolar Disorders, and Single Manic Episodes: A Retrospective Cross-Sectional Study", + "issue": "19", + "volume": "10", + "publisher": "MDPI AG", + "published": "2021-09-26", + "author": [ + "Nilsson N.", + "Bendix M.", + "Öhlund L.", + "Widerström M.", + "Werneke U." + ] + }, + { + "doi": "10.3389/fpsyg.2021.736499", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Descriptive data on subjects included in the study, particularly focussed on the reasons behind limitations in ability to train.", + "data_type": ["Health data", "Social science and humanities data"], + "data_url": "https://www.frontiersin.org/articles/10.3389/fpsyg.2021.736499/full#supplementary-material" + } + ], + "title": "Effects of the COVID-19 Health Crisis on Sports Practice, Life Quality, and Emotional Status in Spanish High-Performance Athletes", + "issue": "", + "volume": "12", + "publisher": "Frontiers Media SA", + "published": "2021-09-27", + "author": [ + "Conde E.", + "Martínez-Aranda L. M.", + "Sanz G.", + "López de Subijana C.", + "Sánchez-Pato A." + ] + }, + { + "doi": "10.1136/bmjopen-2021-052777", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Data related to literature requests available in the paper and supplementary materials.", + "data_type": ["Health data", "Public health data"], + "data_url": "https://bmjopen.bmj.com/content/bmjopen/11/10/e049267/DC1/embed/inline-supplementary-material-1.pdf?download=true" + } + ], + "title": "Diabetes, hypertension, body mass index, smoking and COVID-19-related mortality: a systematic review and meta-analysis of observational studies", + "issue": "10", + "volume": "11", + "publisher": "BMJ", + "published": "2021-10-25", + "author": [ + "Mahamat-Saleh Y.", + "Fiolet T.", + "Rebeaud M. E.", + "Mulot M.", + "Guihur A." + ] + }, + { + "doi": "10.3390/ijerph182010680", + "available_items": [ + { + "type": "data", + "repo_name": "Open Science Framework", + "accession_number": "", + "description": "Raw data on physical activity and psychological well-being.", + "data_type": [ + "Health data", + "Public health data", + "Social science and humanities data" + ], + "data_url": "https://osf.io/w4gfe/" + } + ], + "title": "Changes in Physical Activity Are Associated with Corresponding Changes in Psychological Well-Being: A Pandemic Case Study", + "issue": "20", + "volume": "18", + "publisher": "MDPI AG", + "published": "2021-10-12", + "author": [ + "Dahlen M.", + "Thorbjørnsen H.", + "Sjåstad H.", + "von Heideken Wågert P.", + "Hellström C." + ] + }, + { + "doi": "10.3389/fpsyg.2021.708037", + "available_items": [ + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "R-code used for data analyses.", + "data_type": [ + "Public health data", + "Social science and humanities data" + ], + "data_url": "http://github.com/hakanwall/covid_study" + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Data cannot be made publicly available, but access can be requested for data with some personal details removed.", + "data_type": [ + "Public health data", + "Social science and humanities data" + ], + "data_url": "https://www.frontiersin.org/articles/10.3389/fpsyg.2021.708037/full#h7" + } + ], + "title": "A Longitudinal Study of Gambling Behaviors During the COVID-19 Pandemic in Sweden", + "issue": "", + "volume": "12", + "publisher": "Frontiers Media SA", + "published": "2021-10-14", + "author": [ + "Månsson V.", + "Wall H.", + "Berman A. H.", + "Jayaram-Lindström N.", + "Rosendahl I." + ] + }, + { + "doi": "10.1093/eurpub/ckab138", + "available_items": [ + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "The code of the individual-based epidemiological model.", + "data_type": [ + "Public health data", + "Social science and humanities data" + ], + "data_url": "https://github.com/ImperialCollegeLondon/covid19model" + }, + { + "type": "data", + "repo_name": "GitHub", + "accession_number": "", + "description": "The raw data from the Quarterly Labour Force Survey October to December 2019 used for the labour force model.", + "data_type": [ + "Public health data", + "Social science and humanities data" + ], + "data_url": "https://www.ukdataservice.ac.uk/" + } + ], + "title": "The impact of a COVID-19 lockdown on work productivity under good and poor compliance", + "issue": "5", + "volume": "31", + "publisher": "Oxford University Press (OUP)", + "published": "2021-08-06", + "author": [ + "Ohrnberger J.", + "Segal A. B.", + "Forchini G.", + "Miraldo M.", + "Skarp J." + ] + }, + { + "doi": "10.1021/jacs.1c08402", + "available_items": [ + { + "type": "data", + "repo_name": "Figshare", + "accession_number": "", + "description": "Information on methods, data on chemical structures and assay data", + "data_type": ["Drug discovery data"], + "data_url": "https://doi.org/10.1021/jacs.1c08402" + } + ], + "title": "Ultralarge Virtual Screening Identifies SARS-CoV-2 Main Protease Inhibitors with Broad-Spectrum Activity against Coronaviruses", + "issue": "7", + "volume": "144", + "publisher": "American Chemical Society (ACS)", + "published": "2022-02-10", + "author": [ + "Luttens A.", + "Gullberg H.", + "Abdurakhmanov E.", + "Vo D. D.", + "Akaberi D." + ] + }, + { + "doi": "10.1016/j.dib.2021.107698", + "available_items": [ + { + "type": "protocol", + "repo_name": "Zenodo", + "accession_number": "", + "description": "Chronological data on Swedish Governmental COVID-19 policy/actions", + "data_type": [ + "Public health data", + "Social science and humanities data", + "Other data" + ], + "data_url": "https://doi.org/10.5281/zenodo.5718432" + } + ], + "title": "Dataset: COVID-19 epidemic policy and events timeline (Sweden)", + "issue": "", + "volume": "40", + "publisher": "Elsevier BV", + "published": "2022-06-04", + "author": ["Olofsson T.", "Vilhelmsson A."] + }, + { + "doi": "10.1371/journal.pone.0262169", + "available_items": [ + { + "type": "data", + "repo_name": "Figshare", + "accession_number": "", + "description": "Metadata record for dataset", + "data_type": ["Public health data", "Serology data"], + "data_url": "https://doi.org/10.17044/scilifelab.13567355.v3" + } + ], + "title": "SARS-CoV-2 induces a durable and antigen specific humoral immunity after asymptomatic to mild COVID-19 infection", + "issue": "1", + "volume": "17", + "publisher": "Public Library of Science (PLoS)", + "published": "2022-01-12", + "author": [ + "Havervall S.", + "Jernbom Falk A.", + "Klingström J.", + "Ng H.", + "Greilert-Norin N." + ] + }, + { + "doi": "10.1038/s41588-021-00996-8", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "COVID-19 summary statistics for individuals of African ancestry", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://www.covid19hg.org/results/r6/" + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "CADD-scores v.1.6.", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://cadd.gs.washington.edu/score" + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Genomes from 1000 Genomes project", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://www.internationalgenome.org/data" + }, + { + "type": "data", + "repo_name": "Zenodo", + "accession_number": "", + "description": "Summary data for OAS1/2/3 multi-ancestry fine mapping", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://zenodo.org/record/5708333#.YnOVnS8Rqu4" + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Source data for LD in OAS1/2/3 region", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "10.1038/s41588-021-00996-8#Sec17" + }, + { + "type": "code", + "repo_name": "", + "accession_number": "", + "description": "Code for fine mapping", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://doi.org/10.5281/zenodo.5708333" + } + ], + "title": "Multi-ancestry fine mapping implicates OAS1 splicing in risk of severe COVID-19", + "issue": "2", + "volume": "54", + "publisher": "Springer Science and Business Media LLC", + "published": "2022-01-13", + "author": [ + "Huffman J. E.", + "Butler-Laporte G.", + "Khan A.", + "Pairo-Castineira E.", + "Drivas T. G." + ] + }, + { + "doi": "10.1038/s41467-021-27610-z", + "available_items": [ + { + "type": "data", + "repo_name": "Electron Microscopy Data Bank", + "accession_number": "EMD-12561", + "description": "cryo-EM density maps", + "data_type": ["Biochemistry data", "Protein data"], + "data_url": "https://www.ebi.ac.uk/emdb/EMD-12561" + }, + { + "type": "data", + "repo_name": "Electron Microscopy Data Bank", + "accession_number": "EMD-12465", + "description": "cryo-EM density maps", + "data_type": ["Biochemistry data", "Protein data"], + "data_url": "https://www.ebi.ac.uk/emdb/search/EMD-12465" + }, + { + "type": "data", + "repo_name": "Protein Data Bank", + "accession_number": "7NS6", + "description": "Atomic coordinates", + "data_type": ["Biochemistry data", "Protein data"], + "data_url": "https://www.rcsb.org/structure/unreleased/7NS6" + }, + { + "type": "data", + "repo_name": "Protein Data Bank", + "accession_number": "7NLL", + "description": "Atomic coordinates", + "data_type": ["Biochemistry data", "Protein data"], + "data_url": "https://www.rcsb.org/structure/unreleased/7NLL" + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Source Data for Study", + "data_type": ["Biochemistry data", "Protein data"], + "data_url": "https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-021-27610-z/MediaObjects/41467_2021_27610_MOESM3_ESM.xlsx" + } + ], + "title": "A bispecific monomeric nanobody induces spike trimer dimers and neutralizes SARS-CoV-2 in vivo", + "issue": "1", + "volume": "13", + "publisher": "Springer Science and Business Media LLC", + "published": "2022-01-10", + "author": [ + "Hanke L.", + "Das H.", + "Sheward D. J.", + "Perez Vidakovics L.", + "Urgard E." + ] + }, + { + "doi": "10.1039/D1CB00135C", + "available_items": [ + { + "type": "data", + "repo_name": "Protein Data Bank", + "accession_number": "7ORW", + "description": "Protein model", + "data_type": ["Protein data", "Public health data"], + "data_url": "https://www.rcsb.org/structure/7ORW" + }, + { + "type": "data", + "repo_name": "Protein Data Bank", + "accession_number": "7ORV", + "description": "Protein model", + "data_type": ["Protein data", "Public health data"], + "data_url": "https://www.rcsb.org/structure/7ORV" + }, + { + "type": "data", + "repo_name": "Protein Data Bank", + "accession_number": "7ORU", + "description": "Protein model", + "data_type": ["Protein data", "Public health data"], + "data_url": "https://www.rcsb.org/structure/7ORU" + }, + { + "type": "data", + "repo_name": "Protein Data Bank", + "accession_number": "7ORR", + "description": "Protein model", + "data_type": ["Protein data", "Public health data"], + "data_url": "http://xlink.rsc.org/?pdb=7ORR" + }, + { + "type": "data", + "repo_name": "Zenodo", + "accession_number": "", + "description": "Crystallographic fragment screen", + "data_type": ["Protein data", "Public health data"], + "data_url": "https://zenodo.org/record/5234009#.YnOdVS8RphE" + } + ], + "title": "Identification of fragments binding to SARS-CoV-2 nsp10 reveals ligand-binding sites in conserved interfaces between nsp10 and nsp14/nsp16", + "issue": "1", + "volume": "3", + "publisher": "Royal Society of Chemistry (RSC)", + "published": "2022-01-05", + "author": [ + "Kozielski F.", + "Sele C.", + "Talibov V. O.", + "Lou J.", + "Dong D." + ] + }, + { + "doi": "10.1098/rsif.2021.0819", + "available_items": [ + { + "type": "data", + "repo_name": "Figshare", + "accession_number": "", + "description": "Data related to respiratory events", + "data_type": ["Public health data"], + "data_url": "https://figshare.com/articles/dataset/An_Effective_Model_for_Evaluating_The_Direct_Infection_Risk_Associated_to_Respiratory_Events/16826374" + }, + { + "type": "code", + "repo_name": "Figshare", + "accession_number": "", + "description": "Code used to generate visualisations (Python)", + "data_type": ["Public health data"], + "data_url": "https://figshare.com/articles/dataset/An_Effective_Model_for_Evaluating_The_Direct_Infection_Risk_Associated_to_Respiratory_Events/16826374" + } + ], + "title": "Modelling the direct virus exposure risk associated with respiratory events", + "issue": "186", + "volume": "19", + "publisher": "The Royal Society", + "published": "2022-01-12", + "author": [ + "Wang J.", + "Dalla Barba F.", + "Roccon A.", + "Sardina G.", + "Soldati A." + ] + }, + { + "doi": "10.1016/j.celrep.2021.110242", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Patient VDJ data, raw FASTQ files", + "data_type": ["Public health data"], + "data_url": "http://www.ncbi.nlm.nih.gov/bioproject/782883" + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Enriched hybridoma NGS, raw FASTQ files", + "data_type": ["Public health data"], + "data_url": "http://www.ncbi.nlm.nih.gov/bioproject/782992" + }, + { + "type": "code", + "repo_name": "Github", + "accession_number": "", + "description": "Code for analysis", + "data_type": ["Public health data"], + "data_url": "https://github.com/LSSI-ETH" + } + ], + "title": "SARS-CoV-2 reactive and neutralizing antibodies discovered by single-cell sequencing of plasma cells and mammalian display", + "issue": "3", + "volume": "38", + "publisher": "Elsevier BV", + "published": "2022-01-25", + "author": [ + "Ehling R. A.", + "Weber C. R.", + "Mason D. M.", + "Friedensohn S.", + "Wagner B." + ] + }, + { + "doi": "10.7554/eLife.73641", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Molecular models and simulation trajectories", + "data_type": ["Drug discovery data"], + "data_url": "https://covid.bioexcel.eu/simulations/" + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Drug targeting modalities for COVID-19 drug discovery", + "data_type": ["Drug discovery data"], + "data_url": "https://covid.molssi.org//targets/#blocking-sars-cov-2-spike-protein-binding-to-human-ace2-receptor" + } + ], + "title": "Structure-guided glyco-engineering of ACE2 for improved potency as soluble SARS-CoV-2 decoy receptor", + "issue": "", + "volume": "10", + "publisher": "eLife Sciences Publications, Ltd", + "published": "2021-12-20", + "author": [ + "Capraz T.", + "Kienzl N. F.", + "Laurent E.", + "Perthold J. W.", + "Föderl-Höbenreich E." + ] + }, + { + "doi": "10.1371/journal.pone.0260453", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Pseudonymised, individual-level data", + "data_type": ["Public health data"], + "data_url": "https://b2share.eudat.eu" + }, + { + "type": "data", + "repo_name": "Figshare", + "accession_number": "", + "description": "Individual health care workers cohort data from KI Hospital", + "data_type": ["Public health data"], + "data_url": "https://doi.org/10.6084/m9.figshare.17114138" + }, + { + "type": "data", + "repo_name": "Figshare", + "accession_number": "", + "description": "Additional data from South Hospital in Stockholm", + "data_type": ["Public health data"], + "data_url": "https://doi.org/10.6084/m9.figshare.17117093" + } + ], + "title": "Potential SARS-CoV-2 infectiousness among asymptomatic healthcare workers", + "issue": "12", + "volume": "16", + "publisher": "Public Library of Science (PLoS)", + "published": "2021-12-17", + "author": [ + "Pimenoff V. N.", + "Elfström M.", + "Conneryd Lundgren K.", + "Klevebro S.", + "Melen E." + ] + }, + { + "doi": "10.3390/v13122537", + "available_items": [ + { + "type": "data", + "repo_name": "Gene Expression Omnibus", + "accession_number": "GSE185657", + "description": "Expression profiling by high throughput sequencing", + "data_type": ["Protein data"], + "data_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE185657" + } + ], + "title": "Differential Effect of SARS-CoV-2 Spike Glycoprotein 1 on Human Bronchial and Alveolar Lung Mucosa Models: Implications for Pathogenicity", + "issue": "12", + "volume": "13", + "publisher": "MDPI AG", + "published": "2021-12-17", + "author": [ + "Rahman M.", + "Irmler M.", + "Keshavan S.", + "Introna M.", + "Beckers J." + ] + }, + { + "doi": "10.1371/journal.pone.0261315#sec018", + "available_items": [ + { + "type": "data", + "repo_name": "Figshare", + "accession_number": "", + "description": "Data is sensitive and cannot be shared openly, but data transfer agreement could be established", + "data_type": ["Health data"], + "data_url": "https://scilifelab.figshare.com/articles/dataset/PRONMED_Uppsala_COVID-19_ICU_Biobank/14229410/1" + } + ], + "title": "ECG pathology and its association with death in critically ill COVID-19 patients, a cohort study", + "issue": "12", + "volume": "16", + "publisher": "Public Library of Science (PLoS)", + "published": "2021-12-14", + "author": [ + "Rosén J.", + "Noreland M.", + "Stattin K.", + "Lipcsey M.", + "Frithiof R." + ] + }, + { + "doi": "10.1371/journal.pone.0251834#sec006", + "available_items": [ + { + "type": "data", + "repo_name": "BioMagResBank", + "accession_number": "50915", + "description": "Chemical shifts of full-length SARS-CoV-2", + "data_type": ["Protein data"], + "data_url": "https://bmrb.io/data_library/summary/index.php?bmrbId=50915" + } + ], + "title": "1H, 13C and 15N resonance assignment of the SARS-CoV-2 full-length nsp1 protein and its mutants reveals its unique secondary structure features in solution", + "issue": "12", + "volume": "16", + "publisher": "Public Library of Science (PLoS)", + "published": "2021-12-07", + "author": [ + "Agback T.", + "Dominguez F.", + "Frolov I.", + "Frolova E. I.", + "Agback P." + ] + }, + { + "doi": "10.1038/s41467-021-23893-4", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Source Data (data on antibody titer, among other things)", + "data_type": ["Serology data"], + "data_url": "10.1038/s41467-021-23893-4#Sec25" + }, + { + "type": "code", + "repo_name": "Github", + "accession_number": "", + "description": "Code for analysis (R)", + "data_type": ["Serology data"], + "data_url": "https://github.com/Schwenk-Lab/covid19-serology/tree/v1.0.0" + } + ], + "title": "Multianalyte serology in home-sampled blood enables an unbiased assessment of the immune response against SARS-CoV-2", + "issue": "1", + "volume": "12", + "publisher": "Springer Science and Business Media LLC", + "published": "2021-06-17", + "author": ["Roxhed N.", "Bendes A.", "Dale M.", "Mattsson C.", "Hanke L."] + }, + { + "doi": "10.1038/s41467-021-22446-z", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Source Data (includes mortality data, among other things)", + "data_type": ["Public health data"], + "data_url": "10.1038/s41467-021-22446-z#Sec15" + }, + { + "type": "code", + "repo_name": "Open Science Framework", + "accession_number": "", + "description": "Code for metaanalysis", + "data_type": ["Public health data"], + "data_url": "https://osf.io/qesv4/" + } + ], + "title": "Mortality outcomes with hydroxychloroquine and chloroquine in COVID-19 from an international collaborative meta-analysis of randomized trials", + "issue": "1", + "volume": "12", + "publisher": "Springer Science and Business Media LLC", + "published": "2021-04-15", + "author": [ + "Axfors C.", + "Schmitt A. M.", + "Janiaud P.", + "van’t Hooft J.", + "Abd-Elsalam S." + ] + }, + { + "doi": "10.1002/eji.202149626", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Curated data are available for exploration via the Karolinska KI/K COVID-19 Immune Atlas", + "data_type": ["Health data", "Other data"], + "data_url": "https://covid19cellatlas.com/#/" + } + ], + "title": "COVID‐19‐specific metabolic imprint yields insights into multiorgan system perturbations", + "issue": "3", + "volume": "52", + "publisher": "Wiley", + "published": "2021-12-16", + "author": [ + "Cornillet M.", + "Strunz B.", + "Rooyackers O.", + "Ponzetta A.", + "Chen P." + ] + }, + { + "doi": "10.1038/s41597-021-01071-x", + "available_items": [ + { + "type": "code", + "repo_name": "", + "accession_number": "", + "description": "Code used to generate synthetic evalutation datasets", + "data_type": ["Other data"], + "data_url": "https://github.com/KCL-BMEIS/ExeTeraEval" + }, + { + "type": "code", + "repo_name": "", + "accession_number": "", + "description": "Source code for ExeTera", + "data_type": ["Other data"], + "data_url": "https://github.com/KCL-BMEIS/ExeTera" + } + ], + "title": "Accessible data curation and analytics for international-scale citizen science datasets", + "issue": "1", + "volume": "8", + "publisher": "Springer Science and Business Media LLC", + "published": "2021-11-22", + "author": [ + "Murray B.", + "Kerfoot E.", + "Chen L.", + "Deng J.", + "Graham M. S." + ] + }, + { + "doi": "10.1186/s12879-021-06829-7", + "available_items": [ + { + "type": "data", + "repo_name": "Open Science Framework", + "accession_number": "", + "description": "Data from clinical trial registries used in the study", + "data_type": ["Health data", "Public health data"], + "data_url": "https://osf.io/gr8jt/" + } + ], + "title": "Association between convalescent plasma treatment and mortality in COVID-19: a collaborative systematic review and meta-analysis of randomized clinical trials", + "issue": "1", + "volume": "21", + "publisher": "Springer Science and Business Media LLC", + "published": "2021-11-20", + "author": [ + "Axfors C.", + "Janiaud P.", + "Schmitt A. M.", + "van’t Hooft J.", + "Smith E. R." + ] + }, + { + "doi": "10.1016/j.xcrm.2021.100450", + "available_items": [ + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Data from clinical trial registries used in the study", + "data_type": [ + "Health data", + "Public health data", + "Biochemistry data" + ], + "data_url": "https://github.com/MurrellGroup/VOCfreq" + } + ], + "title": "Beta RBD boost broadens antibody-mediated protection against SARS-CoV-2 variants in animal models", + "issue": "11", + "volume": "2", + "publisher": "Elsevier BV", + "published": "2021-11-16", + "author": [ + "Sheward D. J.", + "Mandolesi M.", + "Urgard E.", + "Kim C.", + "Hanke L." + ] + }, + { + "doi": "10.7554/eLife.70843", + "available_items": [ + { + "type": "data", + "repo_name": "ProteomeXchange", + "accession_number": "PXD026366", + "description": "Proteomics data", + "data_type": ["Protein data"], + "data_url": "http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD026366" + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Mass spectrometry data generated", + "data_type": ["Protein data"], + "data_url": "https://panoramaweb.org/Panorama%20Public/2021/KTH%20Uhlen%20Lab%20-%20SARS-CoV-2%20SISCAPA/project-begin.view?" + } + ], + "title": "Rapid and sensitive detection of SARS-CoV-2 infection using quantitative peptide enrichment LC-MS analysis", + "issue": "", + "volume": "10", + "publisher": "eLife Sciences Publications, Ltd", + "published": "2021-11-08", + "author": [ + "Hober A.", + "Tran-Minh K. H.", + "Foley D.", + "McDonald T.", + "Vissers J. P." + ] + }, + { + "doi": "10.3390/ijms222111622", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Data available in the supplementary material", + "data_type": ["Health data", "Imaging data"], + "data_url": "https://www.mdpi.com/article/10.3390/ijms222111622/s1" + } + ], + "title": "Infection of Brain Pericytes Underlying Neuropathology of COVID-19 Patients", + "issue": "21", + "volume": "22", + "publisher": "MDPI AG", + "published": "2021-10-27", + "author": [ + "Bocci M.", + "Oudenaarden C.", + "Sàenz-Sardà X.", + "Simrén J.", + "Edén A." + ] + }, + { + "doi": "10.1126/scitranslmed.abj7521", + "available_items": [ + { + "type": "data", + "repo_name": "ProteomeXchange", + "accession_number": "PXD025265", + "description": "Proteomics data", + "data_type": [ + "Genomics & transcriptomics data", + "Protein data", + "Health data" + ], + "data_url": "http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD025265" + }, + { + "type": "data", + "repo_name": "Gene Expression Omnibus", + "accession_number": "GSE172114", + "description": "RNA-seq datasets", + "data_type": [ + "Genomics & transcriptomics data", + "Protein data", + "Health data" + ], + "data_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE172114" + }, + { + "type": "code", + "repo_name": "Zenodo", + "accession_number": "", + "description": "Code to perform classification and structural causal modeling", + "data_type": [ + "Genomics & transcriptomics data", + "Protein data", + "Health data" + ], + "data_url": "https://zenodo.org/record/5557611#.YnjTii8Rqu5" + } + ], + "title": "Identification of driver genes for critical forms of COVID-19 in a deeply phenotyped young patient cohort", + "issue": "628", + "volume": "14", + "publisher": "American Association for the Advancement of Science (AAAS)", + "published": "2022-01-19", + "author": ["Carapito R.", "Li R.", "Helms J.", "Carapito C.", "Gujja S."] + }, + { + "doi": "10.1021/acs.jproteome.1c00657", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Union of proteins in both the plasma and blood extracellular vesicle PeptideAtlas builds", + "data_type": ["Health data", "Protein data"], + "data_url": "https://pubs.acs.org/doi/10.1021/acs.jproteome.1c00657" + } + ], + "title": "Advances and Utility of the Human Plasma Proteome", + "issue": "12", + "volume": "20", + "publisher": "American Chemical Society (ACS)", + "published": "2021-10-21", + "author": [ + "Deutsch E. W.", + "Omenn G. S.", + "Sun Z.", + "Maes M.", + "Pernemalm M." + ] + }, + { + "doi": "10.1038/s41598-021-99721-y", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Raw and processed data available in Bitbucket", + "data_type": ["Health data", "Drug discovery data"], + "data_url": "https://bitbucket.org/sonnhammergroup/unadrug" + }, + { + "type": "code", + "repo_name": "", + "accession_number": "", + "description": "Code for data processing and figure reproduction available in Bitbucket", + "data_type": ["Health data", "Drug discovery data"], + "data_url": "https://bitbucket.org/sonnhammergroup/unadrug" + } + ], + "title": "Drug repurposing improves disease targeting 11-fold and can be augmented by network module targeting, applied to COVID-19", + "issue": "1", + "volume": "11", + "publisher": "Springer Science and Business Media LLC", + "published": "2021-10-19", + "author": [ + "Rivero-García I.", + "Castresana-Aguirre M.", + "Guglielmo L.", + "Guala D.", + "Sonnhammer E. L. L." + ] + }, + { + "doi": "10.1016/j.isci.2021.103185", + "available_items": [ + { + "type": "data", + "repo_name": "Mendeley", + "accession_number": "", + "description": "Clinical and raw data related to serological assay", + "data_type": ["Health data", "Serology data"], + "data_url": "https://data.mendeley.com/datasets/69tvkst9ct/1" + } + ], + "title": "SARS-CoV-2 integral membrane proteins shape the serological responses of patients with COVID-19", + "issue": "10", + "volume": "24", + "publisher": "Elsevier BV", + "published": "2022-07-24", + "author": [ + "Martin S.", + "Heslan C.", + "Jégou G.", + "Eriksson L. A.", + "Le Gallo M." + ] + }, + { + "doi": "10.1080/15592294.2021.1969499", + "available_items": [ + { + "type": "code", + "repo_name": "", + "accession_number": "", + "description": "R scripts to analyse Alveolar macrophages (HLA-DR+/CD3-) and lymphocytes (CD3+) specific cell types from DNA methylation analysis.", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://github.com/JD2112/Alveolar-Cell-Type-Deconvolution" + } + ], + "title": "DNA methylome-based validation of induced sputum as an effective protocol to study lung immunity: construction of a classifier of pulmonary cell types", + "issue": "8", + "volume": "17", + "publisher": "Informa UK Limited", + "published": "2021-09-05", + "author": [ + "Das J.", + "Idh N.", + "Sikkeland L. I. B.", + "Paues J.", + "Lerm M." + ] + }, + { + "doi": "10.1016/j.cell.2021.09.003", + "available_items": [ + { + "type": "data", + "repo_name": "Zenodo", + "accession_number": "", + "description": "Initial release of SARS-CoV2 variation data", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://zenodo.org/record/5149112#.YnjZ_S8Rqu4" + }, + { + "type": "data, code", + "repo_name": "", + "accession_number": "", + "description": "Visualising selection analysis results for evolution of the B.1.351 clade", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://observablehq.com/@spond/n501y-clades@3752" + }, + { + "type": "data, code", + "repo_name": "", + "accession_number": "", + "description": "Frequency trends and selection detection of subsets of sites in SARS-CoV-2 genes", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://observablehq.com/@spond/sc2-selection-trends" + }, + { + "type": "data, code", + "repo_name": "", + "accession_number": "", + "description": "Temporal evolution of selective pressures on SARS-CoV-2 genes", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://observablehq.com/@spond/sc2-temporal-selection-trends" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Collection of result files and underlying sequence alignments processed by the RASCL SARS-CoV-2 clade analysis pipeline", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://github.com/spond/SARS-CoV-2-clade-analysis" + } + ], + "title": "The emergence and ongoing convergent evolution of the SARS-CoV-2 N501Y lineages", + "issue": "20", + "volume": "184", + "publisher": "Elsevier BV", + "published": "2022-05-19", + "author": [ + "Martin D. P.", + "Weaver S.", + "Tegally H.", + "San J. E.", + "Shank S. D." + ] + }, + { + "doi": "10.1016/j.invent.2021.100402", + "available_items": [ + { + "type": "data", + "repo_name": "Figshare", + "accession_number": "", + "description": "Data and metadata from a randomised clinical trial, and the demographic questionaire ", + "data_type": ["Health data"], + "data_url": "https://figshare.com/articles/dataset/Efficacy_of_Internet-based_cognitive_behavioral_therapy_and_applied_relaxation_for_tinnitus_distress_in_the_United_States_ICBT_vs_IAR_study_A_Randomized_Clinical_Trial/13679179" + } + ], + "title": "Dismantling internet-based cognitive behavioral therapy for tinnitus. The contribution of applied relaxation: A randomized controlled trial", + "issue": "", + "volume": "25", + "publisher": "Elsevier BV", + "published": "2021-09-16", + "author": [ + "Beukes E. W.", + "Andersson G.", + "Fagelson M. A.", + "Manchaiah V." + ] + }, + { + "doi": "10.1002/cti2.1340", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "COVID-19 patients’ repertoire data: AIRR-seq data (iReceptor Study ID IR-Binder-000001)", + "data_type": ["Genomics & transcriptomics data", "Health data"], + "data_url": "https://gateway.ireceptor.org/login" + }, + { + "type": "data", + "repo_name": "European Nucleotide Archive", + "accession_number": "PRJEB38339", + "description": "Raw FASTQ sequencing files are deposited in the European Nucleotide Archive", + "data_type": ["Genomics & transcriptomics data", "Health data"], + "data_url": "https://www.ebi.ac.uk/ena/browser/view/PRJEB38339" + } + ], + "title": "Landscape of T‐cell repertoires with public COVID‐19‐associated T‐cell receptors in pre‐pandemic risk cohorts", + "issue": "9", + "volume": "10", + "publisher": "Wiley", + "published": "2021-09-27", + "author": [ + "Simnica D.", + "Schultheiß C.", + "Mohme M.", + "Paschold L.", + "Willscher E." + ] + }, + { + "doi": "10.1002/mpr.1892", + "available_items": [ + { + "type": "data", + "repo_name": "Figshare", + "accession_number": "", + "description": "Database with codebook for the European Alcohol Use and COVID-19 Survey", + "data_type": [ + "Public health data", + "Health data", + "Social science and humanities data" + ], + "data_url": "https://figshare.com/articles/dataset/ESAC_database/13580693/1" + } + ], + "title": "Measuring changes in alcohol use in Finland and Norway during the COVID‐19 pandemic: Comparison between data sources", + "issue": "4", + "volume": "30", + "publisher": "Wiley", + "published": "2021-08-27", + "author": [ + "Mäkelä P.", + "Rossow I.", + "Moan I. S.", + "Bye E. K.", + "Kilian C." + ] + }, + { + "doi": "10.1136/bmjopen-2020-048025", + "available_items": [ + { + "type": "data, code", + "repo_name": "Open Science Framework", + "accession_number": "", + "description": "Data on vaccine acceptance and code for analysis", + "data_type": [ + "Public health data", + "Social science and humanities data" + ], + "data_url": "https://osf.io/vgez2/" + }, + { + "type": "data", + "repo_name": "Figshare", + "accession_number": "", + "description": "Image data, the image analysis pipelines, and extracted features", + "data_type": [ + "Public health data", + "Social science and humanities data" + ], + "data_url": "https://scilifelab.figshare.com/articles/dataset/A_phenomics_approach_for_antiviral_drug_discovery_-_Images_analysis_pipelines_and_feature_data/14188403/1" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Code for analysis", + "data_type": [ + "Public health data", + "Social science and humanities data" + ], + "data_url": "https://github.com/pharmbio/antiviral-phenomics" + } + ], + "title": "Correlates of intended COVID-19 vaccine acceptance across time and countries: results from a series of cross-sectional surveys", + "issue": "8", + "volume": "11", + "publisher": "BMJ", + "published": "2021-08-02", + "author": [ + "Kerr J. R.", + "Schneider C. R.", + "Recchia G.", + "Dryhurst S.", + "Sahlin U." + ] + }, + { + "doi": "10.1038/s41562-021-01173-x", + "available_items": [ + { + "type": "data, code", + "repo_name": "Open Science Framework", + "accession_number": "", + "description": "Data (raw and processed) and analysis code related to emotion-regulation strategy testing", + "data_type": [ + "Public health data", + "Social science and humanities data" + ], + "data_url": "https://osf.io/jeu73/" + } + ], + "title": "A multi-country test of brief reappraisal interventions on emotions during the COVID-19 pandemic", + "issue": "8", + "volume": "5", + "publisher": "Springer Science and Business Media LLC", + "published": "2021-08-02", + "author": [ + "Wang K.", + "Goldenberg A.", + "Dorison C. A.", + "Miller J. K.", + "Uusberg A." + ] + }, + { + "doi": "https://doi.org/10.1038/s41467-021-24832-z", + "available_items": [ + { + "type": "data, code", + "repo_name": "Figshare", + "accession_number": "", + "description": "Data from different provinces and analysis code", + "data_type": [ + "Public health data", + "Social science and humanities data", + "Other data" + ], + "data_url": "https://figshare.com/articles/software/NatComm/14153351/1" + } + ], + "title": "Impact of tiered restrictions on human activities and the epidemiology of the second wave of COVID-19 in Italy", + "issue": "", + "volume": "12", + "publisher": "Nature Communications", + "published": "2021-07-27", + "author": [ + "Manica M.", + "Guzzetta G.", + "Riccardo F.", + "Valenti A.", + "Poletti P." + ] + }, + { + "doi": "10.1080/23744235.2021.1957143", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Data on subjects from first and second infection", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://www.tandfonline.com/doi/figure/10.1080/23744235.2021.1957143?scroll=top&needAccess=true" + } + ], + "title": "Recurrent and persistent infection with SARS-CoV-2 – epidemiological data and case reports from Western Sweden, 2020", + "issue": "12", + "volume": "53", + "publisher": "Informa UK Limited", + "published": "2021-07-24", + "author": [ + "Ringlander J.", + "Olausson J.", + "Nyström K.", + "Härnqvist T.", + "Jakobsson H. E." + ] + }, + { + "doi": "10.1098/rstb.2020.0267", + "available_items": [ + { + "type": "data, code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Data and code related to household-contact-tracing", + "data_type": [ + "Public health data", + "Social science and humanities data" + ], + "data_url": "https://github.com/martyn1fyles/HouseholdContactTracing" + } + ], + "title": "Using a household-structured branching process to analyse contact tracing in the SARS-CoV-2 pandemic", + "issue": "1829", + "volume": "376", + "publisher": "The Royal Society", + "published": "2021-05-31", + "author": [ + "Fyles M.", + "Fearon E.", + "Overton C.", + "Wingfield T.", + "Medley G. F." + ] + }, + { + "doi": "10.1038/s41591-021-01454-y", + "available_items": [ + { + "type": "data, code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Deidentified participant data, analysis code and replication files", + "data_type": [ + "Public health data", + "Social science and humanities data" + ], + "data_url": "https://github.com/wzb-ipi/covid_vaccines_nmed" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Analysis code and replication exercise", + "data_type": [ + "Public health data", + "Social science and humanities data" + ], + "data_url": "https://wzb-ipi.github.io/covid_vaccines_nmed/" + } + ], + "title": "COVID-19 vaccine acceptance and hesitancy in low- and middle-income countries", + "issue": "8", + "volume": "27", + "publisher": "Springer Science and Business Media LLC", + "published": "2021-07-16", + "author": [ + "Solís Arce J. S.", + "Warren S. S.", + "Meriggi N. F.", + "Scacco A.", + "McMurry N." + ] + }, + { + "doi": "10.1038/s41366-021-00893-4", + "available_items": [ + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Analysis code used by the CHARYBDIS study", + "data_type": ["Public health data"], + "data_url": "https://github.com/ohdsi-studies/Covid19CharacterizationCharybdis" + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Data produced and used by the CHARYBDIS study", + "data_type": ["Public health data"], + "data_url": "https://data.ohdsi.org/Covid19CharacterizationCharybdis/" + } + ], + "title": "Characteristics and outcomes of 627 044 COVID-19 patients living with and without obesity in the United States, Spain, and the United Kingdom", + "issue": "11", + "volume": "45", + "publisher": "Springer Science and Business Media LLC", + "published": "2021-07-15", + "author": [ + "Recalde M.", + "Roel E.", + "Pistillo A.", + "Sena A. G.", + "Prats-Uribe A." + ] + }, + { + "doi": "10.1016/j.janxdis.2021.102454", + "available_items": [ + { + "type": "data", + "repo_name": "Open Science Framework", + "accession_number": "", + "description": "Methods used and survey results on factors related to mental health issues related to COVID-19", + "data_type": [ + "Public health data", + "Social science and humanities data" + ], + "data_url": "https://osf.io/jcnf3/" + } + ], + "title": "Fear and anxiety in the face of COVID-19: Negative dispositions towards risk and uncertainty as vulnerability factors", + "issue": "", + "volume": "83", + "publisher": "Elsevier BV", + "published": "2021-09-09", + "author": ["Millroth P.", "Frey R."] + }, + { + "doi": "10.1136/bmjopen-2021-049302", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Numbers of deaths by influenza and suicide and total population for 1910-1978", + "data_type": [ + "Public health data", + "Social science and humanities data" + ], + "data_url": "https://osf.io/jcnf3/" + } + ], + "title": "Swedish nationwide time series analysis of influenza and suicide deaths from 1910 to 1978", + "issue": "7", + "volume": "11", + "publisher": "BMJ", + "published": "2022-01-13", + "author": [ + "Rück C.", + "Mataix-Cols D.", + "Malki K.", + "Adler M.", + "Flygare O." + ] + }, + { + "doi": "10.1038/s41598-021-93390-7", + "available_items": [ + { + "type": "data", + "repo_name": "Zenodo", + "accession_number": "", + "description": "Proteomics dataset based on plasma samples from 1,388 subjects.", + "data_type": [ + "Public health data", + "Protein data", + "Genomics & transcriptomics data" + ], + "data_url": "https://zenodo.org/record/4280776#.YnkeOy8RpTZ" + } + ], + "title": "An artificial neural network approach integrating plasma proteomics and genetic data identifies PLXNA4 as a new susceptibility locus for pulmonary embolism", + "issue": "1", + "volume": "11", + "publisher": "Springer Science and Business Media LLC", + "published": "2021-07-07", + "author": [ + "Razzaq M.", + "Iglesias M. J.", + "Ibrahim-Kosta M.", + "Goumidi L.", + "Soukarieh O." + ] + }, + { + "doi": "10.1177/14034948211023633", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Perceived changes in capability during the COVID-19 pandemic (includes data on socioeconomic position, place of birth and regional residence)", + "data_type": [ + "Public health data", + "Health data", + "Social science and humanities data" + ], + "data_url": "https://snd.gu.se/sv/catalogue/study/2020-206/1/1#dataset" + } + ], + "title": "Perceived changes in capability during the COVID-19 pandemic: A Swedish cross-sectional study from June 2020", + "issue": "1", + "volume": "50", + "publisher": "SAGE Publications", + "published": "2021-07-02", + "author": ["Meili K. W.", "Jonsson H.", "Lindholm L.", "Månsdotter A."] + }, + { + "doi": "10.1098/rsos.210386", + "available_items": [ + { + "type": "data", + "repo_name": "Figshare", + "accession_number": "", + "description": "Information on Matlab files, summary statistics, R0 values, and data visualisations", + "data_type": ["Public health data"], + "data_url": "https://rs.figshare.com/collections/Supplementary_material_from_The_risk_for_a_new_COVID-19_wave_and_how_it_depends_on_i_R_i_sub_0_sub_the_current_immunity_level_and_current_restrictions_/5526951" + } + ], + "title": "The risk for a new COVID-19 wave and how it depends on\n R\n 0\n , the current immunity level and current restrictions", + "issue": "7", + "volume": "8", + "publisher": "The Royal Society", + "published": "2021-07-28", + "author": ["Britton T.", "Trapman P.", "Ball F."] + }, + { + "doi": "10.1002/advs.202101222", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Raw, patient-level characteristics and data available in Supporting Information", + "data_type": ["Public health data", "Health data"], + "data_url": "10.1002/advs.202101222" + } + ], + "title": "Combined Metabolic Activators Accelerates Recovery in Mild‐to‐Moderate COVID‐19", + "issue": "17", + "volume": "8", + "publisher": "Wiley", + "published": "2021-06-28", + "author": ["Altay O.", "Arif M.", "Li X.", "Yang H.", "Aydın M."] + }, + { + "doi": "10.1136/bmjopen-2020-048172", + "available_items": [ + { + "type": "data", + "repo_name": "Open Science Framework", + "accession_number": "", + "description": "Vaccine acceptance in Denmark, France, Germany, Hungary, Sweden, Italy, UK and USA; September 2020 to February 2021.", + "data_type": [ + "Public health data", + "Social science and humanities data" + ], + "data_url": "10.1002/advs.202101222" + } + ], + "title": "Public acceptance of COVID-19 vaccines: cross-national evidence on levels and individual-level predictors using observational data", + "issue": "6", + "volume": "11", + "publisher": "BMJ", + "published": "2021-06-15", + "author": ["Lindholt M. F.", "Jørgensen F.", "Bor A.", "Petersen M. B."] + }, + { + "doi": "10.12688/wellcomeopenres.16661.2", + "available_items": [ + { + "type": "data", + "repo_name": "Zenodo", + "accession_number": "", + "description": "Data underlying cov-lineages.org website.", + "data_type": [ + "Public health data", + "Genomics & transcriptomics data" + ], + "data_url": "https://zenodo.org/record/4640140#.YntNOi8Rqu4" + }, + { + "type": "data", + "repo_name": "Zenodo", + "accession_number": "", + "description": "Accession IDs included in publication tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2.", + "data_type": [ + "Public health data", + "Genomics & transcriptomics data" + ], + "data_url": "https://zenodo.org/record/4642401#.YntNGC8Rqu4" + }, + { + "type": "data", + "repo_name": "Zenodo", + "accession_number": "", + "description": "Supplementary materials with group affiliations for tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2.", + "data_type": [ + "Public health data", + "Genomics & transcriptomics data" + ], + "data_url": "https://zenodo.org/record/4704471#.YntODS8Rqu4" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Current source code for grinch (global report investigating novel coronavirus haplotypes) software.", + "data_type": [ + "Public health data", + "Genomics & transcriptomics data" + ], + "data_url": "https://github.com/cov-lineages/grinch" + }, + { + "type": "data", + "repo_name": "GitHub", + "accession_number": "", + "description": "Data on global lineage reports (on variants of concern), lineages, and software tools.", + "data_type": [ + "Public health data", + "Genomics & transcriptomics data" + ], + "data_url": "https://cov-lineages.org/index.html#global_reports" + } + ], + "title": "Tracking the international spread of SARS-CoV-2 lineages B.1.1.7 and B.1.351/501Y-V2 with grinch", + "issue": "", + "volume": "6", + "publisher": "F1000 Research Ltd", + "published": "2021-09-17", + "author": [ + "O'Toole Á.", + "Hill V.", + "Pybus O. G.", + "Watts A.", + "Bogoch I. I." + ] + }, + { + "doi": "10.1186/s12985-021-01556-6", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Summary swab results, and Ct values and RT-qPCR validation results for samples all included with the article", + "data_type": ["Public health data"], + "data_url": "https://virologyj.biomedcentral.com/articles/10.1186/s12985-021-01556-6" + } + ], + "title": "SARS-CoV-2 in hospital indoor environments is predominantly non-infectious", + "issue": "1", + "volume": "18", + "publisher": "Springer Science and Business Media LLC", + "published": "2021-06-02", + "author": [ + "Krambrich J.", + "Akaberi D.", + "Ling J.", + "Hoffman T.", + "Svensson L." + ] + }, + { + "doi": "10.1186/s12959-021-00272-z", + "available_items": [ + { + "type": "data", + "repo_name": "Figshare", + "accession_number": "", + "description": "Metadata record for PRONMED Uppsala COVID-19 ICU Biobank (facilitates data access requests)", + "data_type": ["Health data", "Genomics & transcriptomics data"], + "data_url": "https://scilifelab.figshare.com/articles/dataset/PRONMED_Uppsala_COVID-19_ICU_Biobank/14229410/1" + } + ], + "title": "Point of care ultrasound screening for deep vein thrombosis in critically ill COVID-19 patients, an observational study", + "issue": "1", + "volume": "19", + "publisher": "Springer Science and Business Media LLC", + "published": "2021-06-02", + "author": [ + "Galien S.", + "Hultström M.", + "Lipcsey M.", + "Stattin K.", + "Frithiof R." + ] + }, + { + "doi": "10.1136/bmjnph-2021-000250", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "ZOE COVID Study website (providing information on raw data and data visualisations).", + "data_type": ["Health data", "Public health data"], + "data_url": "https://covid.joinzoe.com" + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Supplementary Information (includes information on relevant survey questions, summary statistics and flowcharts about the study).", + "data_type": ["Health data", "Public health data"], + "data_url": "https://nutrition.bmj.com/content/4/1/149#supplementary-materials" + } + ], + "title": "Modest effects of dietary supplements during the COVID-19 pandemic: insights from 445 850 users of the COVID-19 Symptom Study app", + "issue": "1", + "volume": "4", + "publisher": "BMJ", + "published": "2021-04-19", + "author": [ + "Louca P.", + "Murray B.", + "Klaser K.", + "Graham M. S.", + "Mazidi M." + ] + }, + { + "doi": "10.1016/S2589-7500(21)00077-7", + "available_items": [ + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Code for data processing, visualisation, and analysis.", + "data_type": ["Health data"], + "data_url": "https://github.com/brueggemann-lab/iris-ldh-2020" + } + ], + "title": "Changes in the incidence of invasive disease due to Streptococcus pneumoniae, Haemophilus influenzae, and Neisseria meningitidis during the COVID-19 pandemic in 26 countries and territories in the Invasive Respiratory Infection Surveillance Initiative: a prospective analysis of surveillance data", + "issue": "6", + "volume": "3", + "publisher": "Elsevier BV", + "published": "2022-07-24", + "author": [ + "Brueggemann A. B.", + "Jansen van Rensburg M. J.", + "Shaw D.", + "McCarthy N. D.", + "Jolley K. A." + ] + }, + { + "doi": "10.1016/j.jmb.2021.167118", + "available_items": [ + { + "type": "data", + "repo_name": "Protein Data Bank", + "accession_number": "7KFI", + "description": "7KFI SARS-CoV-2 Main protease immature form - apo structure", + "data_type": ["Genomics & transcriptomics data", "Protein data"], + "data_url": "https://www.rcsb.org/structure/7KFI" + }, + { + "type": "data", + "repo_name": "Protein Data Bank", + "accession_number": "7MBG", + "description": "7MBG SARS-CoV-2 Main protease in orthorhombic space group", + "data_type": ["Genomics & transcriptomics data", "Protein data"], + "data_url": "https://www.rcsb.org/structure/7MBG" + }, + { + "type": "data", + "repo_name": "Protein Data Bank", + "accession_number": "7KPH", + "description": "7KPH SARS-CoV-2 Main Protease in mature form", + "data_type": ["Genomics & transcriptomics data", "Protein data"], + "data_url": "https://www.rcsb.org/structure/7KPH" + }, + { + "type": "data", + "repo_name": "Protein Data Bank", + "accession_number": "7N6N", + "description": "7N6N SARS-CoV-2 Main protease C145S mutant in complex with N and C-terminal residues", + "data_type": ["Genomics & transcriptomics data", "Protein data"], + "data_url": "https://www.rcsb.org/structure/7N6N" + }, + { + "type": "data", + "repo_name": "Protein Data Bank", + "accession_number": "7LFE", + "description": "7LFE SARS-CoV-2 Main protease immature form - F2X Entry Library E03 fragment", + "data_type": ["Genomics & transcriptomics data", "Protein data"], + "data_url": "https://www.rcsb.org/structure/7LFE" + }, + { + "type": "data", + "repo_name": "Protein Data Bank", + "accession_number": "7LDX", + "description": "7LDX SARS-CoV-2 Main protease immature form - F2X Entry Library E06 fragment", + "data_type": ["Genomics & transcriptomics data", "Protein data"], + "data_url": "https://www.rcsb.org/structure/7LDX" + }, + { + "type": "data", + "repo_name": "Protein Data Bank", + "accession_number": "7LFP", + "description": "7LFP SARS-CoV-2 Main protease immature form - F2X Entry Library G05 fragment", + "data_type": ["Genomics & transcriptomics data", "Protein data"], + "data_url": "https://www.rcsb.org/structure/7LFP" + }, + { + "type": "data", + "repo_name": "Protein Data Bank", + "accession_number": "7KVL", + "description": "7KVL SARS-CoV-2 Main protease immature form - FMAX Library E01 fragment", + "data_type": ["Genomics & transcriptomics data", "Protein data"], + "data_url": "https://www.rcsb.org/structure/7KVL" + }, + { + "type": "data", + "repo_name": "Protein Data Bank", + "accession_number": "7N5Z", + "description": "7N5Z SARS-CoV-2 Main protease C145S mutant", + "data_type": ["Genomics & transcriptomics data", "Protein data"], + "data_url": "https://www.rcsb.org/structure/7N5Z" + }, + { + "type": "data", + "repo_name": "Protein Data Bank", + "accession_number": "7KVR", + "description": "7KVR SARS-CoV-2 Main protease immature form - FMAX Library E09 fragment", + "data_type": ["Genomics & transcriptomics data", "Protein data"], + "data_url": "https://www.rcsb.org/structure/7KVR" + } + ], + "title": "A Crystallographic Snapshot of SARS-CoV-2 Main Protease Maturation Process", + "issue": "18", + "volume": "433", + "publisher": "Elsevier BV", + "published": "2022-06-23", + "author": [ + "Noske G.", + "Nakamura A.", + "Gawriljuk V.", + "Fernandes R.", + "Lima G." + ] + }, + { + "doi": "10.1101/2021.05.28.446179", + "available_items": [ + { + "type": "data", + "repo_name": "Zenodo", + "accession_number": "", + "description": "Biophysical characterisation of the SARS-CoV-2 E protein.", + "data_type": ["Protein data"], + "data_url": "https://zenodo.org/record/4818292#.YntbbC8RpTY" + } + ], + "title": "Probing effects of the SARS-CoV-2 E protein on membrane curvature and intracellular calcium", + "issue": "", + "volume": "", + "publisher": "Cold Spring Harbor Laboratory", + "published": "2021-05-28", + "author": [ + "Mehregan A.", + "Pérez-Conesa S.", + "Zhuang Y.", + "Elbahnsi A.", + "Pasini D." + ] + }, + { + "doi": "10.1038/s41467-021-22664-5", + "available_items": [ + { + "type": "data", + "repo_name": "Gene Expression Omnibus", + "accession_number": "GSE163688", + "description": "Sequencing data for all experiments.", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE163688" + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Primer sequences are in Supplementary Data 2.", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-021-22664-5/MediaObjects/41467_2021_22664_MOESM5_ESM.xlsx" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "code to analyse Next-Generation Sequencing (NGS) data.", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://github.com/alex-stark-imp/SARSeq" + } + ], + "title": "Multiplexed detection of SARS-CoV-2 and other respiratory infections in high throughput by SARSeq", + "issue": "1", + "volume": "12", + "publisher": "Springer Science and Business Media LLC", + "published": "2021-05-25", + "author": [ + "Yelagandula R.", + "Bykov A.", + "Vogt A.", + "Heinen R.", + "Özkan E." + ] + }, + { + "doi": "10.1038/s41420-021-00487-z", + "available_items": [ + { + "type": "data", + "repo_name": "ProteomeXchange", + "accession_number": "PXD023450", + "description": "Raw mass spectromic data.", + "data_type": ["Protein data"], + "data_url": "http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD023450" + }, + { + "type": "data", + "repo_name": "GitHub", + "accession_number": "", + "description": "bioinformatic analysis codes.", + "data_type": ["Protein data"], + "data_url": "https://github.com/neogilab/COVID_IFN" + } + ], + "title": "Type-I interferon signatures in SARS-CoV-2 infected Huh7 cells", + "issue": "1", + "volume": "7", + "publisher": "Springer Science and Business Media LLC", + "published": "2021-05-18", + "author": [ + "Chen X.", + "Saccon E.", + "Appelberg K. S.", + "Mikaeloff F.", + "Rodriguez J. E." + ] + }, + { + "doi": "10.1371/journal.pone.0251151", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Dataset on the COVID-19 pandemic and serious psychological consequences in Bangladesh: a population-based nationwide study.", + "data_type": ["Social science and humanities data", "Health data"], + "data_url": "https://dataverse.harvard.edu/dataset.xhtml?persistentId=doi:10.7910/DVN/YKH9C1" + } + ], + "title": "Knowledge and preventive behaviors regarding COVID-19 in Bangladesh: A nationwide distribution", + "issue": "5", + "volume": "16", + "publisher": "Public Library of Science (PLoS)", + "published": "2021-05-03", + "author": [ + "Hosen I.", + "Pakpour A. H.", + "Sakib N.", + "Hussain N.", + "al Mamun F." + ] + }, + { + "doi": "10.1038/s41598-021-88481-4", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "OxCOVID19 Database to download", + "data_type": ["Public health data"], + "data_url": "https://covid19.eng.ox.ac.uk/" + }, + { + "type": "data", + "repo_name": "GitHub", + "accession_number": "", + "description": "CSV extracts from the OxCOVID19 Database", + "data_type": ["Public health data"], + "data_url": "https://github.com/covid19db/data" + }, + { + "type": "data", + "repo_name": "Figshare", + "accession_number": "", + "description": "Complete OxCOVID19 Database in CSV format as of 2020-07-31", + "data_type": ["Public health data"], + "data_url": "https://doi.org/10.6084/m9.figshare.12746150" + } + ], + "title": "OxCOVID19 Database, a multimodal data repository for better understanding the global impact of COVID-19", + "issue": "1", + "volume": "11", + "publisher": "Springer Science and Business Media LLC", + "published": "2021-04-29", + "author": ["Mahdi A.", "Błaszczyk P.", "Dłotko P.", "Salvi D.", "Chan T."] + }, + { + "doi": "10.1186/s12889-021-10897-4", + "available_items": [ + { + "type": "data", + "repo_name": "Figshare", + "accession_number": "", + "description": "Individual-level demographic, occupational, COVID-19 data", + "data_type": ["Social science and humanities data", "Health data"], + "data_url": "https://figshare.com/articles/dataset/QUAN_Strand_Dataset_-_Occupational_Burnout_and_Job_Satisfaction_Among_Physicians_in_Times_of_COVID-19_Crisis_A_Convergent_Parallel_Mixed-Method_Study/14058185/1" + } + ], + "title": "Occupational burnout and job satisfaction among physicians in times of COVID-19 crisis: a convergent parallel mixed-method study", + "issue": "1", + "volume": "21", + "publisher": "Springer Science and Business Media LLC", + "published": "2021-04-28", + "author": [ + "Alrawashdeh H. M.", + "Al-Tammemi A. B.", + "Alzawahreh M. K.", + "Al-Tamimi A.", + "Elkholy M." + ] + }, + { + "doi": "10.1038/s41598-021-85877-0", + "available_items": [ + { + "type": "data", + "repo_name": "BioStudies", + "accession_number": "S-BSST416", + "description": "Proteomic data", + "data_type": ["Protein data"], + "data_url": "https://www.ebi.ac.uk/biostudies/studies/S-BSST416?query=S-BSST416" + }, + { + "type": "code", + "repo_name": "Zenodo", + "accession_number": "", + "description": "Application related to proteomic data analysis", + "data_type": ["Protein data"], + "data_url": "https://zenodo.org/record/3895886#.Yo3E_S8RpTY" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Code behind application related to proteomic data analysis", + "data_type": ["Protein data"], + "data_url": "https://github.com/hamelpatel/COVID19_proteomic/blob/v1.0" + } + ], + "title": "Proteomic blood profiling in mild, severe and critical COVID-19 patients", + "issue": "1", + "volume": "11", + "publisher": "Springer Science and Business Media LLC", + "published": "2021-03-18", + "author": [ + "Patel H.", + "Ashton N. J.", + "Dobson R. J. B.", + "Andersson L.", + "Yilmaz A." + ] + }, + { + "doi": "10.1007/s40279-021-01438-5", + "available_items": [ + { + "type": "data", + "repo_name": "Open Science Framework", + "accession_number": "", + "description": "Raw data, plots, surveys", + "data_type": ["Health data", "Social science and humanities data"], + "data_url": "https://osf.io/xhryf/" + } + ], + "title": "The Impact of Coronavirus (COVID-19) Related Public-Health Measures on Training Behaviours of Individuals Previously Participating in Resistance Training: A Cross-Sectional Survey Study", + "issue": "7", + "volume": "51", + "publisher": "Springer Science and Business Media LLC", + "published": "2021-04-19", + "author": [ + "Steele J.", + "Androulakis-Korakakis P.", + "Carlson L.", + "Williams D.", + "Phillips S." + ] + }, + { + "doi": "10.21203/rs.3.rs-419853/v1", + "available_items": [ + { + "type": "data", + "repo_name": "Figshare", + "accession_number": "", + "description": "Metadata record detailing data access requirements", + "data_type": ["Health data"], + "data_url": "https://scilifelab.figshare.com/articles/dataset/PRONMED_Uppsala_COVID-19_ICU_Biobank/14229410/1" + } + ], + "title": "ECG with Prior Myocardial Infarction Pattern or acute ST-T Pathology is Associated with Death in Critically Ill COVID-19 Patients", + "issue": "", + "volume": "", + "publisher": "Research Square Platform LLC", + "published": "2021-04-19", + "author": [ + "Rosen J.", + "Noreland M.", + "Stattin K.", + "Lipcsey M.", + "Frithiof R." + ] + }, + { + "doi": "10.1101/2021.04.03.438330", + "available_items": [ + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Code to acquire and analyse data", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://github.com/MurrellGroup/VOCfreq" + } + ], + "title": "Driving potent neutralization of a SARS-CoV-2 Variant of Concern with a heterotypic boost", + "issue": "", + "volume": "", + "publisher": "Cold Spring Harbor Laboratory", + "published": "2021-04-05", + "author": [ + "Sheward D. J.", + "Mandolesi M.", + "Urgard E.", + "Kim C.", + "Hanke L." + ] + }, + { + "doi": "10.2807/1560-7917.ES.2021.26.16.2100348", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Data in supplementary materials/appendices - data on genetic data divided by demogaphic factors", + "data_type": ["Genomics & transcriptomics data", "Other data"], + "data_url": "https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2021.26.16.2100348" + } + ], + "title": "Characteristics of SARS-CoV-2 variants of concern B.1.1.7, B.1.351 or P.1: data from seven EU/EEA countries, weeks 38/2020 to 10/2021", + "issue": "16", + "volume": "26", + "publisher": "European Centre for Disease Control and Prevention (ECDC)", + "published": "2021-04-22", + "author": [ + "Funk T.", + "Pharris A.", + "Spiteri G.", + "Bundle N.", + "Melidou A." + ] + }, + { + "doi": "10.1038/s41587-021-00860-4", + "available_items": [ + { + "type": "data", + "repo_name": "ProteomeXchange", + "accession_number": "PXD023613", + "description": "The data generated for the benchmarks and the drug response screen in yeast", + "data_type": ["Protein data"], + "data_url": "http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD023613" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Open-source algorithms made available through the DIA–NN software suite", + "data_type": ["Protein data"], + "data_url": "https://github.com/vdemichev/diann" + } + ], + "title": "Ultra-fast proteomics with Scanning SWATH", + "issue": "7", + "volume": "39", + "publisher": "Springer Science and Business Media LLC", + "published": "2021-03-25", + "author": [ + "Messner C. B.", + "Demichev V.", + "Bloomfield N.", + "Yu J. S. L.", + "White M." + ] + }, + { + "doi": "10.1017/S0950268821000649", + "available_items": [ + { + "type": "data", + "repo_name": "Zenodo", + "accession_number": "", + "description": "Datasets of the original ECDC data and the curve fits", + "data_type": ["Public health data"], + "data_url": "https://zenodo.org/record/4454173#.Yo3Rby8RpTY" + } + ], + "title": "A simple model for the total number of SARS-CoV-2 infections on a national level", + "issue": "", + "volume": "149", + "publisher": "Cambridge University Press (CUP)", + "published": "2021-04-06", + "author": [ + "Blanco N.", + "Stafford K. A.", + "Lavoie M. C.", + "Brandenburg A.", + "Górna M. W." + ] + }, + { + "doi": "10.1136/bmjopen-2021-058422", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Data are from the SNAC-K Project, a population-based study on ageing and dementia. Need approval for access.", + "data_type": [ + "Public health data", + "Other data", + "Social science and humanities data" + ], + "data_url": "https://www.snac-k.se" + } + ], + "title": "COVID-19 collateral damage—psychological burden and behavioural changes among older adults during the first outbreak in Stockholm, Sweden: a cross-sectional study", + "issue": "1", + "volume": "12", + "publisher": "BMJ", + "published": "2022-01-07", + "author": [ + "Beridze G.", + "Triolo F.", + "Grande G.", + "Fratiglioni L.", + "Calderón-Larrañaga A." + ] + }, + { + "doi": "10.1016/j.celrep.2021.108852", + "available_items": [ + { + "type": "data", + "repo_name": "Mendeley", + "accession_number": "", + "description": "Data required to produce the figures, includes data on proteomics and immunology", + "data_type": ["Serology data", "Protein data"], + "data_url": "https://data.mendeley.com/datasets/stxwzbyfsc/1?__hstc=25856994.201473a88516d23766c33b93f465990b.1653472457683.1653472457683.1653472457683.1&__hssc=25856994.1.1653472457683&__hsfp=1159211105" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "R code for multi-omics factor analyses, correlations, and plots", + "data_type": ["Serology data", "Protein data"], + "data_url": "https://github.com/GRP92/PRNT_manuscript" + } + ], + "title": "Virological and immunological features of SARS-CoV-2-infected children who develop neutralizing antibodies", + "issue": "11", + "volume": "34", + "publisher": "Elsevier BV", + "published": "2021-06-24", + "author": [ + "Cotugno N.", + "Ruggiero A.", + "Bonfante F.", + "Petrara M. R.", + "Zicari S." + ] + }, + { + "doi": "10.1101/2021.03.10.21252820", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Summary statistics generated by COVID-19 HGI", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://www.covid19hg.org/results/r5/" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Code for Mendelian randomization and genetic correlation pipeline", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://github.com/marcoralab/MRcovid" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Code for summary statistics liftover and meta-analysis and PCA pipeline", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://github.com/covid19-hg/" + } + ], + "title": "Mapping the human genetic architecture of COVID-19 by worldwide meta-analysis", + "issue": "", + "volume": "", + "publisher": "Cold Spring Harbor Laboratory", + "published": "2021-03-12", + "author": ["Ganna A."] + }, + { + "doi": "10.1136/bmjopen-2020-042387", + "available_items": [ + { + "type": "code", + "repo_name": "GitLab", + "accession_number": "", + "description": "R and Stata code related to COVID-19 mortality assessment", + "data_type": [ + "Health data", + "Social science and humanities data", + "Other data" + ], + "data_url": "https://gitlab.switch.ch/torsten.hothorn/relative_covid-19_mortality" + } + ], + "title": "Assessing relative COVID-19 mortality: a Swiss population-based study", + "issue": "3", + "volume": "11", + "publisher": "BMJ", + "published": "2021-03-08", + "author": [ + "Hothorn T.", + "Bopp M.", + "Günthard H.", + "Keiser O.", + "Roelens M." + ] + }, + { + "doi": "10.1038/s41598-021-84356-w", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Pseudonymised, individual-level data that allow full replication of the results in this article are freely available from joakim.dillner@sll.se or from the Karolinska University Hospital data analysis department: tableau.karolinska@sll.se.", + "data_type": ["Public health data", "Serology data"], + "data_url": "https://www.nature.com/articles/s41598-021-84356-w" + } + ], + "title": "Antibodies to SARS-CoV-2 and risk of past or future sick leave", + "issue": "1", + "volume": "11", + "publisher": "Springer Science and Business Media LLC", + "published": "2021-03-04", + "author": [ + "Dillner J.", + "Elfström K. M.", + "Blomqvist J.", + "Eklund C.", + "Lagheden C." + ] + }, + { + "doi": "10.1073/pnas.2020834118", + "available_items": [ + { + "type": "code", + "repo_name": "Open Science Framework", + "accession_number": "", + "description": "Analysis code", + "data_type": [ + "Health data", + "Other data", + "Social science and humanities data" + ], + "data_url": "https://osf.io/4zegu/" + } + ], + "title": "The effects of school closures on SARS-CoV-2 among parents and teachers", + "issue": "9", + "volume": "118", + "publisher": "Proceedings of the National Academy of Sciences", + "published": "2021-02-11", + "author": ["Vlachos J.", "Hertegård E.", "B. Svaleryd H."] + }, + { + "doi": "10.1017/S0950268821000510", + "available_items": [ + { + "type": "code", + "repo_name": "", + "accession_number": "", + "description": "Analysis code (R)", + "data_type": ["Health data", "Other data"], + "data_url": "https://static.cambridge.org/content/id/urn:cambridge.org:id:article:S0950268821000510/resource/name/S0950268821000510sup001.zip" + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Data related to incubation period and patient.", + "data_type": ["Health data", "Other data"], + "data_url": "https://static.cambridge.org/content/id/urn:cambridge.org:id:article:S0950268821000510/resource/name/S0950268821000510sup001.zip" + } + ], + "title": "Epidemiology and transmission characteristics of early COVID-19 cases, 20 January–19 March 2020, in Bavaria, Germany", + "issue": "", + "volume": "149", + "publisher": "Cambridge University Press (CUP)", + "published": "2021-03-15", + "author": [ + "Böhm S.", + "Woudenberg T.", + "Chen D.", + "Marosevic D. V.", + "Böhmer M. M." + ] + }, + { + "doi": "10.1016/j.ebiom.2021.103259", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Possible to apply for access to deidentified patient data and samples", + "data_type": ["Serology data"], + "data_url": "https://covid-consortium.com/application-for-samples/" + } + ], + "title": "Time series analysis and mechanistic modelling of heterogeneity and sero-reversion in antibody responses to mild SARS‑CoV-2 infection", + "issue": "", + "volume": "65", + "publisher": "Elsevier BV", + "published": "2021-05-29", + "author": [ + "Manisty C.", + "Treibel T. A.", + "Jensen M.", + "Semper A.", + "Joy G." + ] + }, + { + "doi": "10.3390/jcm10050896", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Patient characteristics, medical treatment regiments, symptoms, laboratory findings, ophthalmic findings, systemic symtoms for each patient", + "data_type": ["Other data"], + "data_url": "https://www.mdpi.com/2077-0383/10/5/896/s1" + } + ], + "title": "Ophthalmic Screening in Patients with Coronavirus Disease 2019: A Prospective Cohort Study", + "issue": "5", + "volume": "10", + "publisher": "MDPI AG", + "published": "2021-02-24", + "author": [ + "Papazoglou A.", + "Conen A.", + "Haubitz S.", + "Tschopp M.", + "Guignard V. J." + ] + }, + { + "doi": "10.1101/2021.02.18.21251422", + "available_items": [ + { + "type": "data", + "repo_name": "Gitlab", + "accession_number": "", + "description": "Data related to olfaction tests", + "data_type": ["Public health data", "Other data"], + "data_url": "https://gitlab.com/snitz/smelltracker_article" + }, + { + "type": "code", + "repo_name": "Gitlab", + "accession_number": "", + "description": "Analysis code (Matlab)", + "data_type": ["Public health data", "Other data"], + "data_url": "https://gitlab.com/snitz/smelltracker_article" + } + ], + "title": "A Novel Olfactory Self-Test Effectively Screens for COVID-19", + "issue": "", + "volume": "", + "publisher": "Cold Spring Harbor Laboratory", + "published": "2021-02-23", + "author": [ + "Snitz K.", + "Honigstein D.", + "Weissgross R.", + "Ravia A.", + "Mishor E." + ] + }, + { + "doi": "10.3389/fpubh.2021.579948", + "available_items": [ + { + "type": "data", + "repo_name": "GitHub", + "accession_number": "", + "description": "Data held on daily death counts for Sweden from 1860 to 31.08.2020; the total population of Sweden for the years 1860 to 2019 (from Statistics Sweden).", + "data_type": ["Public health data"], + "data_url": "https://github.com/aledberg/outbreaks" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Code to do analysis and produce figures.", + "data_type": ["Public health data"], + "data_url": "https://github.com/aledberg/outbreaks" + } + ], + "title": "Mortality of the COVID-19 Outbreak in Sweden in Relation to Previous Severe Disease Outbreaks", + "issue": "", + "volume": "9", + "publisher": "Frontiers Media SA", + "published": "2021-02-18", + "author": ["Ledberg A."] + }, + { + "doi": "10.1371/journal.pone.0244924", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Knowledge, attitudes, and practices (KAP) survey results.", + "data_type": [ + "Public health data", + "Other data", + "Social science and humanities data" + ], + "data_url": "https://reshare.ukdataservice.ac.uk/854605/" + } + ], + "title": "Community health worker knowledge, attitudes and practices towards COVID-19: Learnings from an online cross-sectional survey using a digital health platform, UpSCALE, in Mozambique", + "issue": "2", + "volume": "16", + "publisher": "Public Library of Science (PLoS)", + "published": "2021-02-10", + "author": [ + "Feldman M.", + "Lacey Krylova V.", + "Farrow P.", + "Donovan L.", + "Zandamela E." + ] + }, + { + "doi": "10.1016/j.imu.2021.100529", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Results of the efficacy of FDA approved antiviral drugs on SARS-CoV-2 spike glycoprotein.", + "data_type": ["Protein data", "Drug discovery data"], + "data_url": "http://fulir.irb.hr/6161/" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "The Vini in silico model of cancer.", + "data_type": ["Protein data", "Drug discovery data"], + "data_url": "https://github.com/draskot/Vini" + } + ], + "title": "The screening and evaluation of potential clinically significant HIV drug combinations against the SARS-CoV-2 virus", + "issue": "", + "volume": "23", + "publisher": "Elsevier BV", + "published": "2022-07-23", + "author": [ + "Tomić D.", + "Davidović D.", + "Szasz A. M.", + "Rezeli M.", + "Pirkić B." + ] + }, + { + "doi": "10.1038/s41598-020-80352-8", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Raw data for amplification curves, and Ct values for clinical samples.", + "data_type": ["Genomics & transcriptomics data", "Other data"], + "data_url": "https://static-content.springer.com/esm/art%3A10.1038%2Fs41598-020-80352-8/MediaObjects/41598_2020_80352_MOESM2_ESM.xlsx" + } + ], + "title": "Direct detection of SARS-CoV-2 using non-commercial RT-LAMP reagents on heat-inactivated samples", + "issue": "1", + "volume": "11", + "publisher": "Springer Science and Business Media LLC", + "published": "2021-01-19", + "author": [ + "Alekseenko A.", + "Barrett D.", + "Pareja-Sanchez Y.", + "Howard R. J.", + "Strandback E." + ] + }, + { + "doi": "10.1073/pnas.2020732118", + "available_items": [ + { + "type": "data", + "repo_name": "Protein Data Bank", + "accession_number": "7AJP", + "description": "Crystal Structure of Human Adenovirus 56 Fiber Knob.", + "data_type": ["Protein data", "Biochemistry data"], + "data_url": "https://www.rcsb.org/structure/7AJP" + } + ], + "title": "Human species D adenovirus hexon capsid protein mediates cell entry through a direct interaction with CD46", + "issue": "3", + "volume": "118", + "publisher": "Proceedings of the National Academy of Sciences", + "published": "2020-12-31", + "author": [ + "Persson B. D.", + "John L.", + "Rafie K.", + "Strebl M.", + "Frängsmyr L." + ] + }, + { + "doi": "10.1101/2021.01.13.21249429", + "available_items": [ + { + "type": "data", + "repo_name": "Figshare", + "accession_number": "", + "description": "Most data in paper, but metadata record is available as an access point for individual data requests.", + "data_type": ["Health data"], + "data_url": "https://doi.org/10.17044/scilifelab.14229410" + } + ], + "title": "Elevated Angiopoietin-2 inhibits thrombomodulin-mediated anticoagulation in critically ill COVID-19 patients", + "issue": "", + "volume": "", + "publisher": "Cold Spring Harbor Laboratory", + "published": "2021-01-15", + "author": [ + "Hultstrom M.", + "Fromell K.", + "Larsson A.", + "Quaggin S. E.", + "Betsholtz C." + ] + }, + { + "doi": "10.1038/s41467-020-20653-8", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Source data behind study.", + "data_type": ["Biochemistry data", "Drug discovery data"], + "data_url": "https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-020-20653-8/MediaObjects/41467_2020_20653_MOESM4_ESM.xlsx" + } + ], + "title": "SARS-CoV-2 spike glycoprotein vaccine candidate NVX-CoV2373 immunogenicity in baboons and protection in mice", + "issue": "1", + "volume": "12", + "publisher": "Springer Science and Business Media LLC", + "published": "2021-01-14", + "author": ["Tian J.", "Patel N.", "Haupt R.", "Zhou H.", "Weston S."] + }, + { + "doi": "10.1186/s12912-021-00540-3", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Data cannot be publicly shared, but applications can be made for access.", + "data_type": ["Public health data", "Other data"], + "data_url": "https://bmcnurs.biomedcentral.com/articles/10.1186/s12912-021-00540-3#availability-of-data-and-materials" + } + ], + "title": "Malpractice claimed calls within the Swedish Healthcare Direct: a descriptive – comparative case study", + "issue": "1", + "volume": "20", + "publisher": "Springer Science and Business Media LLC", + "published": "2021-01-14", + "author": ["Björkman A.", "Engström M.", "Winblad U.", "Holmström I. K."] + }, + { + "doi": "10.1016/j.ijid.2021.01.023", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Patient demographics, management and outcome in 42 kidney recipients with COVID-19.", + "data_type": ["Health data"], + "data_url": "https://www.ijidonline.com/cms/10.1016/j.ijid.2021.01.023/attachment/10ccf84a-9c50-4457-b428-6a46ea9babe3/mmc1.docx" + } + ], + "title": "COVID-19 after kidney transplantation: Early outcomes and renal function following antiviral treatment", + "issue": "", + "volume": "104", + "publisher": "Elsevier BV", + "published": "2021-06-12", + "author": [ + "Elec A. D.", + "Oltean M.", + "Goldis P.", + "Cismaru C.", + "Lupse M." + ] + }, + { + "doi": "10.1038/s41598-021-95968-7", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Data cannot be shared publicly, but applications can be made for access.", + "data_type": ["Health data", "Biochemistry data"], + "data_url": "https://www.nature.com/articles/s41598-021-95968-7#data-availability" + } + ], + "title": "Acquired olfactory loss alters functional connectivity and morphology", + "issue": "1", + "volume": "11", + "publisher": "Springer Science and Business Media LLC", + "published": "2021-08-12", + "author": [ + "Iravani B.", + "Peter M. G.", + "Arshamian A.", + "Olsson M. J.", + "Hummel T." + ] + }, + { + "doi": "10.1126/science.abe6230", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Data generated/analysed are in the article or supplementary materials.", + "data_type": ["Protein data", "Biochemistry data", "Imaging data"], + "data_url": "https://www.science.org/doi/10.1126/science.abe6230" + }, + { + "type": "data", + "repo_name": "Protein Data Bank", + "accession_number": "7KN5", + "description": "Crystal structure of SARS-CoV-2 receptor binding domain complexed with nanobodies VHH E and U.", + "data_type": ["Protein data", "Biochemistry data", "Imaging data"], + "data_url": "https://www.rcsb.org/structure/7KN5" + }, + { + "type": "data", + "repo_name": "Protein Data Bank", + "accession_number": "7KN6", + "description": "Crystal structure of SARS-CoV-2 receptor binding domain complexed with nanobody VHH V and antibody Fab CC12.3.", + "data_type": ["Protein data", "Biochemistry data", "Imaging data"], + "data_url": "https://www.rcsb.org/structure/7KN6" + }, + { + "type": "data", + "repo_name": "Protein Data Bank", + "accession_number": "7KN7", + "description": "Crystal structure of SARS-CoV-2 receptor binding domain complexed with nanobody VHH W and antibody Fab CC12.3.", + "data_type": ["Protein data", "Biochemistry data", "Imaging data"], + "data_url": "https://www.rcsb.org/structure/7KN7" + }, + { + "type": "data", + "repo_name": "Protein Data Bank", + "accession_number": "7KSG", + "description": "SARS-CoV-2 spike in complex with nanobodies E.", + "data_type": ["Protein data", "Biochemistry data", "Imaging data"], + "data_url": "https://www.rcsb.org/structure/7KSG" + }, + { + "type": "data", + "repo_name": "Protein Data Bank", + "accession_number": "7B14", + "description": "Nanobody E bound to Spike-RBD in a localized reconstruction.", + "data_type": ["Protein data", "Biochemistry data", "Imaging data"], + "data_url": "https://www.rcsb.org/structure/7B14" + }, + { + "type": "data", + "repo_name": "Protein Data Bank", + "accession_number": "7B11", + "description": "SARS-CoV-spike with two RBDs up bound to VHH V on all RBDs.", + "data_type": ["Protein data", "Biochemistry data", "Imaging data"], + "data_url": "https://www.rcsb.org/structure/unreleased/7B11" + }, + { + "type": "data", + "repo_name": "Protein Data Bank", + "accession_number": "7B18", + "description": "SARS-CoV-spike bound to two neutralising nanobodies.", + "data_type": ["Protein data", "Biochemistry data", "Imaging data"], + "data_url": "https://www.rcsb.org/structure/7B18" + }, + { + "type": "data", + "repo_name": "Protein Data Bank", + "accession_number": "7B17", + "description": "SARS-CoV-spike RBD bound to two neutralising nanobodies.", + "data_type": ["Protein data", "Biochemistry data", "Imaging data"], + "data_url": "https://www.rcsb.org/structure/7B17" + }, + { + "type": "data", + "repo_name": "Electron Microscopy Data Bank", + "accession_number": "EMD-23018", + "description": "SARS-CoV-2 spike in complex with nanobodies E.", + "data_type": ["Protein data", "Biochemistry data", "Imaging data"], + "data_url": "https://www.ebi.ac.uk/emdb/EMD-23018" + }, + { + "type": "data", + "repo_name": "Electron Microscopy Data Bank", + "accession_number": "EMD-11978", + "description": "Nanobody E bound to Spike-RBD in a localized reconstruction.", + "data_type": ["Protein data", "Biochemistry data", "Imaging data"], + "data_url": "https://www.ebi.ac.uk/emdb/EMD-11978" + }, + { + "type": "data", + "repo_name": "Electron Microscopy Data Bank", + "accession_number": "EMD-11981", + "description": "SARS-CoV-spike bound to two neutralising nanobodies.", + "data_type": ["Protein data", "Biochemistry data", "Imaging data"], + "data_url": "https://www.ebi.ac.uk/emdb/EMD-11981" + }, + { + "type": "data", + "repo_name": "Electron Microscopy Data Bank", + "accession_number": "EMD-11980", + "description": "SARS-CoV-spike RBD bound to two neutralising nanobodies.", + "data_type": ["Protein data", "Biochemistry data", "Imaging data"], + "data_url": "https://www.ebi.ac.uk/emdb/EMD-11980" + }, + { + "type": "data", + "repo_name": "BioProject", + "accession_number": "PRJNA679438", + "description": "Structure-guided multivalent nanobodies block SARS-CoV-2 infection and suppress mutational escape.", + "data_type": ["Protein data", "Biochemistry data", "Imaging data"], + "data_url": "https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA679438" + } + ], + "title": "Structure-guided multivalent nanobodies block SARS-CoV-2 infection and suppress mutational escape", + "issue": "6530", + "volume": "371", + "publisher": "American Association for the Advancement of Science (AAAS)", + "published": "2021-02-12", + "author": [ + "Koenig P.", + "Das H.", + "Liu H.", + "Kümmerer B. M.", + "Gohr F. N." + ] + }, + { + "doi": "10.3390/vaccines9010042", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Data cannot be shared publicly, but applications can be made for access.", + "data_type": [ + "Public health data", + "Social science and humanities data" + ], + "data_url": "https://www.mdpi.com/2076-393X/9/1/42/htm" + } + ], + "title": "High Rates of COVID-19 Vaccine Hesitancy and Its Association with Conspiracy Beliefs: A Study in Jordan and Kuwait among Other Arab Countries", + "issue": "1", + "volume": "9", + "publisher": "MDPI AG", + "published": "2021-01-12", + "author": [ + "Sallam M.", + "Dababseh D.", + "Eid H.", + "Al-Mahzoum K.", + "Al-Haidar A." + ] + }, + { + "doi": "10.1186/s12931-020-01605-8", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Data cannot be shared publicly, but applications can be made for access.", + "data_type": ["Biochemistry data", "Health data"], + "data_url": "https://respiratory-research.biomedcentral.com/articles/10.1186/s12931-020-01605-8" + } + ], + "title": "Sputum ACE2, TMPRSS2 and FURIN gene expression in severe neutrophilic asthma", + "issue": "1", + "volume": "22", + "publisher": "Springer Science and Business Media LLC", + "published": "2021-01-07", + "author": ["Kermani N. Z.", "Song W.", "Badi Y.", "Versi A.", "Guo Y."] + }, + { + "doi": "10.1371/journal.pone.0244824", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Data are available in the article and supplementary materials (including Ct values & gel images).", + "data_type": ["Genomics & transcriptomics data", "Health data"], + "data_url": "https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0244824" + } + ], + "title": "A direct RT-qPCR approach to test large numbers of individuals for SARS-CoV-2", + "issue": "12", + "volume": "15", + "publisher": "Public Library of Science (PLoS)", + "published": "2020-12-31", + "author": [ + "Maricic T.", + "Nickel O.", + "Aximu-Petri A.", + "Essel E.", + "Gansauge M." + ] + }, + { + "doi": "10.3390/v13010037", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Data are available in the article and supplementary materials (effect of novel antiviral compounds against ZIKV in several cell models).", + "data_type": ["Biochemistry data", "Other data"], + "data_url": "https://www.mdpi.com/1999-4915/13/1/37/s1" + } + ], + "title": "Broadly Active Antiviral Compounds Disturb Zika Virus Progeny Release Rescuing Virus-Induced Toxicity in Brain Organoids", + "issue": "1", + "volume": "13", + "publisher": "MDPI AG", + "published": "2020-12-29", + "author": ["Pettke A.", "Tampere M.", "Pronk R.", "Wallner O.", "Falk A."] + }, + { + "doi": "10.1111/joim.13304", + "available_items": [ + { + "type": "data", + "repo_name": "GitHub", + "accession_number": "", + "description": "Data related to discriminative bayesian seroprevalence", + "data_type": ["Health data", "Serology data"], + "data_url": "https://github.com/MurrellGroup/DiscriminativeSeroprevalence" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Code related to discriminative bayesian seroprevalence (see notebook).", + "data_type": ["Health data", "Serology data"], + "data_url": "https://github.com/MurrellGroup/DiscriminativeSeroprevalence" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Code used in analysis of seroprevalence data (R)", + "data_type": ["Health data", "Serology data"], + "data_url": "https://github.com/chr1swallace/seroprevalence-paper" + }, + { + "type": "data", + "repo_name": "GitHub", + "accession_number": "", + "description": "Seroprevalence data related to R code", + "data_type": ["Health data", "Serology data"], + "data_url": "https://github.com/chr1swallace/seroprevalence-paper" + } + ], + "title": "Seropositivity in blood donors and pregnant women during the first year of SARS‐CoV‐2 transmission in Stockholm, Sweden", + "issue": "3", + "volume": "290", + "publisher": "Wiley", + "published": "2021-05-18", + "author": [ + "Castro Dopico X.", + "Muschiol S.", + "Christian M.", + "Hanke L.", + "Sheward D. J." + ] + }, + { + "doi": "10.1093/rheumatology/keaa771", + "available_items": [ + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Study protocol and analysis source code", + "data_type": [ + "Drug discovery data", + "Health data", + "Social science and humanities data" + ], + "data_url": "https://github.com/ohdsi-studies/Covid19EstimationHydroxychloroquine2" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Analysis tools used in study", + "data_type": [ + "Drug discovery data", + "Health data", + "Social science and humanities data" + ], + "data_url": "https://github.com/OHDSI/" + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Data and results artefacts that do not include patient-level health information", + "data_type": [ + "Drug discovery data", + "Health data", + "Social science and humanities data" + ], + "data_url": "http://data.ohdsi.org/Covid19EstimationHydroxychloroquine2" + } + ], + "title": "Risk of depression, suicide and psychosis with hydroxychloroquine treatment for rheumatoid arthritis: a multinational network cohort study", + "issue": "", + "volume": "", + "publisher": "Oxford University Press (OUP)", + "published": "2020-12-25", + "author": [ + "Lane J. C. E.", + "Weaver J.", + "Kostka K.", + "Duarte-Salles T.", + "Abrahao M. T. F." + ] + }, + { + "doi": "10.1016/j.ebiom.2021.103277", + "available_items": [ + { + "type": "data", + "repo_name": "GitHub", + "accession_number": "", + "description": "Data on collaborative genetic studies of idiopathic pulmonary fibrosis.", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://github.com/genomicsITER/PFgenetics" + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "COVID19-hg GWAS meta-analyses data.", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://github.com/genomicsITER/PFgenetics" + } + ], + "title": "Shared genetic etiology between idiopathic pulmonary fibrosis and COVID-19 severity", + "issue": "", + "volume": "65", + "publisher": "Elsevier BV", + "published": "2022-07-22", + "author": [ + "Fadista J.", + "Kraven L. M.", + "Karjalainen J.", + "Andrews S. J.", + "Geller F." + ] + }, + { + "doi": "10.1101/2020.12.15.20248247", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Data cannot be made publicly available, but those with written permission from the Swedish Ethical Review Authority may be granted access.", + "data_type": ["Health data"], + "data_url": "https://www.medrxiv.org/node/189563.external-links.html" + } + ], + "title": "Large differences in community COVID-19 testing across geographic areas in a Swedish region with 385,000 inhabitants", + "issue": "", + "volume": "", + "publisher": "Cold Spring Harbor Laboratory", + "published": "2020-12-16", + "author": [ + "Kennedy B.", + "Martinell M.", + "Hammar U.", + "van Zoest V.", + "Kristiansson R. S." + ] + }, + { + "doi": "10.1101/2020.12.13.20248122", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Data cannot be made publicly available, but applications can be made for individual-level pseudonymised data.", + "data_type": ["Health data"], + "data_url": "https://www.medrxiv.org/node/189563.external-links.html" + } + ], + "title": "Screening for high amounts of SARS-CoV-2 identifies pre-symptomatic subjects among healthy healthcare workers", + "issue": "", + "volume": "", + "publisher": "Cold Spring Harbor Laboratory", + "published": "2020-12-14", + "author": [ + "Dillner J.", + "Elfström K. M.", + "Blomqvist J.", + "Engstrand L.", + "Uhlén M." + ] + }, + { + "doi": "10.1101/2020.12.11.422139", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Croatian Neandertal genome.", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "http://cdna.eva.mpg.de/neandertal/Vindija/VCF/" + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Croatian Neandertal genome (alternate source).", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://bioinf.eva.mpg.de/jbrowse/" + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Modern human genome.", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/" + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "GWAS summary statistics (round 4 release: A/B2_ALL_eur_leave_23andme).", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://www.covid19hg.org/results/" + } + ], + "title": "The MERS-CoV receptor gene is among COVID-19 risk factors inherited from Neandertals", + "issue": "", + "volume": "", + "publisher": "Cold Spring Harbor Laboratory", + "published": "2020-12-12", + "author": ["Zeberg H.", "Pääbo S."] + }, + { + "doi": "10.1002/jcp.30206", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "All data are included in the paper.", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://onlinelibrary.wiley.com/doi/10.1002/jcp.30206" + } + ], + "title": "Thermal inactivation of COVID‐19 specimens improves RNA quality and quantity", + "issue": "7", + "volume": "236", + "publisher": "Wiley", + "published": "2020-12-11", + "author": [ + "Hemati M.", + "Soosanabadi M.", + "Ghorashi T.", + "Ghaffari H.", + "Vahedi A." + ] + }, + { + "doi": "10.1038/s41597-020-00778-7", + "available_items": [ + { + "type": "data", + "repo_name": "Zenodo", + "accession_number": "", + "description": "Raw dataset: perceived likelihoods and impacts, individual and authorities’ preparedness and knowledge, socio-demographic characteristics in August 2020 (N=2,033 in Italy, N=2,121 in Sweden)", + "data_type": [ + "Public health data", + "Social science and humanities data" + ], + "data_url": "https://zenodo.org/record/4034277#.YsfjOS8RpTY" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Code for reading, processing and graphically representing the data", + "data_type": [ + "Public health data", + "Social science and humanities data" + ], + "data_url": "https://github.com/elenamondino/nationwide_survey" + } + ], + "title": "Public perceptions of multiple risks during the COVID-19 pandemic in Italy and Sweden", + "issue": "1", + "volume": "7", + "publisher": "Springer Science and Business Media LLC", + "published": "2021-12-02", + "author": [ + "Mondino E.", + "Di Baldassarre G.", + "Mård J.", + "Ridolfi E.", + "Rusca M." + ] + }, + { + "doi": "10.1080/2162402X.2020.1857112", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Allelic frequencies of FPR1 SNPs and characteristics of patient population from Hôpital Cochin and Hôpital Européen George Pompidou", + "data_type": ["Genomics & transcriptomics data", "Health data"], + "data_url": "https://www.tandfonline.com/doi/figure/10.1080/2162402X.2020.1857112?scroll=top&needAccess=true" + } + ], + "title": "No impact of cancer and plague-relevant FPR1 polymorphisms on COVID-19", + "issue": "1", + "volume": "9", + "publisher": "Informa UK Limited", + "published": "2020-01-01", + "author": [ + "Petrazzuolo A.", + "Le Naour J.", + "Vacchelli E.", + "Gaussem P.", + "Ellouze S." + ] + }, + { + "doi": "10.3390/v12121423", + "available_items": [ + { + "type": "data", + "repo_name": "Figshare", + "accession_number": "", + "description": "Thermal Proteome Profiling dataset from Hazara virus infected SW13 cells treated with DMSO or antiviral inhibitor 20 µM TH6744", + "data_type": [ + "Genomics & transcriptomics data", + "Biochemistry data", + "Protein data", + "Drug discovery data" + ], + "data_url": "https://scilifelab.figshare.com/articles/dataset/Thermal_Proteome_Profiling_dataset_from_Hazara_virus_infected_SW13_cells_treated_with_DMSO_or_antiviral_inhibitor_20_M_TH6744_/13089023" + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Antiviral screening; Dose-response treatment of TH6744 and TH3289; List of proteins from 2D-TPP analysis in U87 cells (FDR); List of proteins from 2D-TPP analysis in U87 cells (Fold-change); Uniprot annotation of overlapping TPP-TR and 2D-TPP hits", + "data_type": [ + "Genomics & transcriptomics data", + "Biochemistry data", + "Protein data", + "Drug discovery data" + ], + "data_url": "https://www.mdpi.com/1999-4915/12/12/1423/s1" + }, + { + "type": "data", + "repo_name": "ProteomeXchange Consortium", + "accession_number": "PXD021494", + "description": "Raw mass spectrometry data", + "data_type": [ + "Genomics & transcriptomics data", + "Biochemistry data", + "Protein data", + "Drug discovery data" + ], + "data_url": "http://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD021494" + } + ], + "title": "Novel Broad-Spectrum Antiviral Inhibitors Targeting Host Factors Essential for Replication of Pathogenic RNA Viruses", + "issue": "12", + "volume": "12", + "publisher": "MDPI AG", + "published": "2020-12-10", + "author": [ + "Tampere M.", + "Pettke A.", + "Salata C.", + "Wallner O.", + "Koolmeister T." + ] + }, + { + "doi": "10.1007/s10875-020-00928-x", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "General laboratory tests, immunologic investigation, computed tomographies of the chest of 17 primary immunodeficient patients infected with COVID-19", + "data_type": [ + "Genomics & transcriptomics data", + "Public health data" + ], + "data_url": "https://static-content.springer.com/esm/art%3A10.1007%2Fs10875-020-00928-x/MediaObjects/10875_2020_928_MOESM1_ESM.docx" + } + ], + "title": "Impact of SARS-CoV-2 Pandemic on Patients with Primary Immunodeficiency", + "issue": "2", + "volume": "41", + "publisher": "Springer Science and Business Media LLC", + "published": "2020-12-01", + "author": [ + "Delavari S.", + "Abolhassani H.", + "Abolnezhadian F.", + "Babaha F.", + "Iranparast S." + ] + }, + { + "doi": "10.1016/s2589-7500(20)30289-2", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Much of the data cannot be shared publicly, but applications can be made for access", + "data_type": ["Health data"], + "data_url": "https://data.ohdsi.org/IcariusSusceptibility/" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "start-to-finish open and executable source code", + "data_type": ["Health data"], + "data_url": "https://github.com/ohdsi-studies/Covid19Icarius" + } + ], + "title": "Renin–angiotensin system blockers and susceptibility to COVID-19: an international, open science, cohort analysis", + "issue": "2", + "volume": "3", + "publisher": "Elsevier BV", + "published": "2022-07-24", + "author": [ + "Morales D. R.", + "Conover M. M.", + "You S. C.", + "Pratt N.", + "Kostka K." + ] + }, + { + "doi": "10.1002/psp4.12568", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Experimental data are in the supplementary material", + "data_type": ["Biochemistry data", "Other data"], + "data_url": "https://ascpt.onlinelibrary.wiley.com/action/downloadSupplement?doi=10.1002%2Fpsp4.12568&file=psp412568-sup-0002-Suppinfo2.zip" + }, + { + "type": "code", + "repo_name": "GitLab", + "accession_number": "", + "description": "Code for macrophage model (matlab)", + "data_type": ["Biochemistry data", "Other data"], + "data_url": "https://gitlab.liu.se/eliny61/macrophage-model" + } + ], + "title": "Mechanisms of a Sustained Anti‐inflammatory Drug Response in Alveolar Macrophages Unraveled with Mathematical Modeling", + "issue": "12", + "volume": "9", + "publisher": "Wiley", + "published": "2020-12-26", + "author": [ + "Nyman E.", + "Lindh M.", + "Lövfors W.", + "Simonsson C.", + "Persson A." + ] + }, + { + "doi": "10.1080/22221751.2020.1799723", + "available_items": [ + { + "type": "data", + "repo_name": "BioProject", + "accession_number": "", + "description": "Raw RNAseq data", + "data_type": [ + "Genomics & transcriptomics data", + "Protein data", + "Health data" + ], + "data_url": "https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA627100" + }, + { + "type": "data", + "repo_name": "Zenodo", + "accession_number": "", + "description": "Proteomics data", + "data_type": [ + "Genomics & transcriptomics data", + "Protein data", + "Health data" + ], + "data_url": "https://zenodo.org/record/3754719#.Ysf11C8RrOR" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "All pre-processing and analysis code", + "data_type": [ + "Genomics & transcriptomics data", + "Protein data", + "Health data" + ], + "data_url": "https://github.com/neogilab/COVID19" + } + ], + "title": "Dysregulation in Akt/mTOR/HIF-1 signaling identified by proteo-transcriptomics of SARS-CoV-2 infected cells", + "issue": "1", + "volume": "9", + "publisher": "Informa UK Limited", + "published": "2020-01-01", + "author": [ + "Appelberg S.", + "Gupta S.", + "Svensson Akusjärvi S.", + "Ambikan A. T.", + "Mikaeloff F." + ] + }, + { + "doi": "10.1111/nan.12677", + "available_items": [ + { + "type": "data", + "repo_name": "Figshare", + "accession_number": "", + "description": "Whole slide scans of ACE2 immunohistochemistry from 4 COVID-19 patients and 3 pre-pandemic controls (named PAT1-4 and CONT1-4, respectively)", + "data_type": ["Health data"], + "data_url": "https://doi.org/10.6084/m9.figshare.13089383" + }, + { + "type": "data", + "repo_name": "Figshare", + "accession_number": "", + "description": "R script to analyze ACE2 expression in basal ganglian from GTEx project", + "data_type": ["Health data"], + "data_url": "https://doi.org/10.6084/m9.figshare.13089383" + } + ], + "title": "Intracerebral endotheliitis and microbleeds are neuropathological features of COVID‐19", + "issue": "3", + "volume": "47", + "publisher": "Wiley", + "published": "2020-12-14", + "author": [ + "Kirschenbaum D.", + "Imbach L. L.", + "Rushing E. J.", + "Frauenknecht K. B. M.", + "Gascho D." + ] + }, + { + "doi": "10.1016/j.dib.2020.106621", + "available_items": [ + { + "type": "data", + "repo_name": "Harvard Dataverse", + "accession_number": "", + "description": "Raw dataset: socio-demographic characteristics, sources of information regarding COVID-19, knowledge concerning COVID-19, behavior in preventing COVID-19, etc. (n=10,067)", + "data_type": [ + "Public health data", + "Social science and humanities data" + ], + "data_url": "https://doi.org/10.7910/DVN/YKH9C1" + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Detailed description of all study variables", + "data_type": [ + "Public health data", + "Social science and humanities data" + ], + "data_url": "https://ars.els-cdn.com/content/image/1-s2.0-S2352340920315018-mmc1.docx" + } + ], + "title": "A population-based nationwide dataset concerning the COVID-19 pandemic and serious psychological consequences in Bangladesh", + "issue": "", + "volume": "33", + "publisher": "Elsevier BV", + "published": "2021-03-20", + "author": [ + "Pakpour A. H.", + "Al Mamun F.", + "Hosen I.", + "Griffiths M. D.", + "Mamun M. A." + ] + }, + { + "doi": "10.3389/fpubh.2020.571364", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Data cannot be publicly shared, though it is is possible to apply for access.", + "data_type": [ + "Public health data", + "Social science and humanities data" + ], + "data_url": "https://www.frontiersin.org/articles/10.3389/fpubh.2020.571364/full" + } + ], + "title": "Social Determinants Predict Outcomes in Data From a Multi-Ethnic Cohort of 20,899 Patients Investigated for COVID-19", + "issue": "", + "volume": "8", + "publisher": "Frontiers Media SA", + "published": "2020-11-24", + "author": [ + "Lundon D. J.", + "Mohamed N.", + "Lantz A.", + "Goltz H. H.", + "Kelly B. D." + ] + }, + { + "doi": "10.1186/s13054-020-03375-7", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Data cannot be publicly shared, though it is is possible to apply for access.", + "data_type": ["Health data"], + "data_url": "https://ccforum.biomedcentral.com/articles/10.1186/s13054-020-03375-7#availability-of-data-and-materials" + } + ], + "title": "Dosing of thromboprophylaxis and mortality in critically ill COVID-19 patients", + "issue": "1", + "volume": "24", + "publisher": "Springer Science and Business Media LLC", + "published": "2020-11-23", + "author": [ + "Jonmarker S.", + "Hollenberg J.", + "Dahlberg M.", + "Stackelberg O.", + "Litorell J." + ] + }, + { + "doi": "10.1101/2020.11.18.20233767", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Supplementary materials include a list of GISAID accession numbers for the sequences used, and a summary of public intervention actions adopted in Nordic countries.", + "data_type": ["Health data", "Social science and humanities data"], + "data_url": "https://www.medrxiv.org/content/10.1101/2020.11.18.20233767v2.supplementary-material" + } + ], + "title": "The impact of early public health interventions on SARS-CoV-2 transmission and evolution", + "issue": "", + "volume": "", + "publisher": "Cold Spring Harbor Laboratory", + "published": "2020-11-18", + "author": [ + "Duchene S.", + "Featherstone L.", + "de Blasio B. F.", + "Holmes E. C.", + "Bohlin J." + ] + }, + { + "doi": "10.1101/2020.07.03.20145649", + "available_items": [ + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Code for modeling the impact of NPI implementations and lifting in all US states", + "data_type": ["Social science and humanities data", "Health data"], + "data_url": "https://github.com/patrickbryant1/COVID19.github.io/tree/master/simulations/mobility/dev/US" + }, + { + "type": "data", + "repo_name": "GitHub", + "accession_number": "", + "description": "Data for modeling the impact of NPI implementations and lifting in all US states", + "data_type": ["Social science and humanities data", "Health data"], + "data_url": "https://github.com/patrickbryant1/COVID19.github.io/tree/master/simulations/mobility/dev/US" + } + ], + "title": "The effect of opening up the US on COVID-19 spread", + "issue": "", + "volume": "", + "publisher": "Cold Spring Harbor Laboratory", + "published": "2020-07-04", + "author": ["Bryant P.", "Elofsson A."] + }, + { + "doi": "10.1111/ejh.13502", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Provided in the article: Characteristics, treatments, COVID-19-related outcomes, additional laboratory and clinical data for 9 patients", + "data_type": ["Health data"], + "data_url": "https://onlinelibrary.wiley.com/doi/10.1111/ejh.13502" + } + ], + "title": "Outcome of COVID‐19 in multiple myeloma patients in relation to treatment", + "issue": "6", + "volume": "105", + "publisher": "Wiley", + "published": "2020-08-18", + "author": [ + "Susek K. H.", + "Gran C.", + "Ljunggren H.", + "Alici E.", + "Nahi H." + ] + }, + { + "doi": "10.1101/2020.10.19.20215046", + "available_items": [ + { + "type": "data", + "repo_name": "GitHub", + "accession_number": "", + "description": "Code related to modelling the spread of COVID-19 on a dynamic social network with spread reduction according to Google mobility changes", + "data_type": [ + "Genomics & transcriptomics data", + "Social science and humanities data" + ], + "data_url": "https://github.com/patrickbryant1/epidemic_net" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Raw data and results related to modelling the spread of COVID-19 on a dynamic social network with spread reduction according to Google mobility changes", + "data_type": [ + "Genomics & transcriptomics data", + "Social science and humanities data" + ], + "data_url": "https://github.com/patrickbryant1/epidemic_net" + } + ], + "title": "Modelling the dispersion of SARS-CoV-2 on a dynamic network graph", + "issue": "", + "volume": "", + "publisher": "Cold Spring Harbor Laboratory", + "published": "2020-10-21", + "author": ["Bryant P.", "Elofsson A."] + }, + { + "doi": "10.1073/pnas.2012331117", + "available_items": [ + { + "type": "data", + "repo_name": "GitHub", + "accession_number": "", + "description": "Data & circos plots related to multiple sequence alignments", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://github.com/hlzeng/Filtered_MSA_SARS_CoV_2" + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Data on GISAID accession numbers and multiple sequence alignments also available in the paper", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://www.pnas.org/doi/full/10.1073/pnas.2012331117" + } + ], + "title": "Global analysis of more than 50,000 SARS-CoV-2 genomes reveals epistasis between eight viral genes", + "issue": "49", + "volume": "117", + "publisher": "Proceedings of the National Academy of Sciences", + "published": "2020-11-17", + "author": [ + "Zeng H.", + "Dichio V.", + "Rodríguez Horta E.", + "Thorell K.", + "Aurell E." + ] + }, + { + "doi": "10.1111/apa.15673", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Case report of 5 Swedish children aged 9-15, as well as parental reported symptoms occurring over 2 months after diagnosis.", + "data_type": ["Health data"], + "data_url": "https://onlinelibrary.wiley.com/doi/10.1111/apa.15673" + } + ], + "title": "Case report and systematic review suggest that children may experience similar long‐term effects to adults after clinical COVID‐19", + "issue": "3", + "volume": "110", + "publisher": "Wiley", + "published": "2020-12-03", + "author": ["Ludvigsson J. F."] + }, + { + "doi": "10.1126/sciadv.abe4724", + "available_items": [ + { + "type": "data", + "repo_name": "ArrayExpress", + "accession_number": "E-MTAB-9711", + "description": "RNA-seq of SARS-CoV-2-infected human primary hepatocyte-derived spheroids upon interferon a2 and baricitinib treatment.", + "data_type": [ + "Biochemistry data", + "Genomics & transcriptomics data", + "Health data" + ], + "data_url": "https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-9711/" + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Patient information are contained in the paper and supplementary information.", + "data_type": [ + "Biochemistry data", + "Genomics & transcriptomics data", + "Health data" + ], + "data_url": "https://www.science.org/doi/10.1126/sciadv.abe4724" + } + ], + "title": "JAK inhibition reduces SARS-CoV-2 liver infectivity and modulates inflammatory responses to reduce morbidity and mortality", + "issue": "1", + "volume": "7", + "publisher": "American Association for the Advancement of Science (AAAS)", + "published": "2022-01-14", + "author": [ + "Stebbing J.", + "Sánchez Nievas G.", + "Falcone M.", + "Youhanna S.", + "Richardson P." + ] + }, + { + "doi": "10.1016/j.watres.2020.116620", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Amount of SARS-CoV-2 in wastewater in Gothenburg per week between February and June 2020 (data available in the article).", + "data_type": ["Public health data"], + "data_url": "https://www.sciencedirect.com/science/article/pii/S0043135420311556?via%3Dihub" + } + ], + "title": "Surveillance of wastewater revealed peaks of SARS-CoV-2 preceding those of hospitalized patients with COVID-19", + "issue": "", + "volume": "189", + "publisher": "Elsevier BV", + "published": "2021-01-19", + "author": [ + "Saguti F.", + "Magnil E.", + "Enache L.", + "Churqui M. P.", + "Johansson A." + ] + }, + { + "doi": "10.1093/nar/gkaa1013", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Nuclear magnetic resonance (NMR) experimental data deposited in COVID19-NMR project", + "data_type": ["Biochemistry data", "Other data"], + "data_url": "http://covid19-nmr.de" + }, + { + "type": "data", + "repo_name": "BioMagResBank", + "accession_number": "", + "description": "Chemical shift data deposited in BMRB (multiple accession numbers, given in Table 1 in the article).", + "data_type": ["Biochemistry data", "Other data"], + "data_url": "http://www.bmrb.wisc.edu/" + } + ], + "title": "Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy", + "issue": "22", + "volume": "48", + "publisher": "Oxford University Press (OUP)", + "published": "2020-11-10", + "author": [ + "Wacker A.", + "Weigand J. E.", + "Akabayov S. R.", + "Altincekic N.", + "Bains J. K." + ] + }, + { + "doi": "10.1038/s41467-020-19204-y", + "available_items": [ + { + "type": "data", + "repo_name": "GitHub", + "accession_number": "", + "description": "Microscale thermophoresis (MST) and biolayer interferometry (BLI) data.", + "data_type": ["Biochemistry data", "Protein data", "Other data"], + "data_url": "https://github.com/tania-custodio/Sb23" + }, + { + "type": "data", + "repo_name": "SASBDB", + "accession_number": "SASDJF4", + "description": "Synthetic nanobody Sybody 23 (Sy23).", + "data_type": ["Biochemistry data", "Protein data", "Other data"], + "data_url": "https://www.sasbdb.org/data/SASDJF4/" + }, + { + "type": "data", + "repo_name": "SASBDB", + "accession_number": "SASDJG4", + "description": "SARS-CoV-2 spike protein ACE2 receptor binding domain (RBD).", + "data_type": ["Biochemistry data", "Protein data", "Other data"], + "data_url": "https://www.sasbdb.org/data/SASDJG4/" + }, + { + "type": "data", + "repo_name": "SASBDB", + "accession_number": "SASDJH4", + "description": "SARS-CoV-2 spike protein ACE2 receptor binding domain (RBD) bound to the synthetic nanobody Sybody 23 (Sy23).", + "data_type": ["Biochemistry data", "Protein data", "Other data"], + "data_url": "https://www.sasbdb.org/data/SASDJH4/" + }, + { + "type": "data", + "repo_name": "Electron Microscopy Data Bank", + "accession_number": "EMD-11616", + "description": "Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing sybodies (Sb23).", + "data_type": ["Biochemistry data", "Protein data", "Other data"], + "data_url": "https://www.ebi.ac.uk/emdb/EMD-11616" + }, + { + "type": "data", + "repo_name": "Electron Microscopy Data Bank", + "accession_number": "EMD-11617", + "description": "Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing sybodies (Sb23) 2-up conformation.", + "data_type": ["Biochemistry data", "Protein data", "Other data"], + "data_url": "https://www.ebi.ac.uk/emdb/EMD-11617" + }, + { + "type": "data", + "repo_name": "Protein Data Bank", + "accession_number": "7A25", + "description": "Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing sybodies (Sb23).", + "data_type": ["Biochemistry data", "Protein data", "Other data"], + "data_url": "https://www.rcsb.org/structure/7A25" + }, + { + "type": "data", + "repo_name": "Protein Data Bank", + "accession_number": "7A29", + "description": "Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing sybodies (Sb23) 2-up conformation.", + "data_type": ["Biochemistry data", "Protein data", "Other data"], + "data_url": "https://www.rcsb.org/structure/7A29" + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Sequences of all the selected sybodies.", + "data_type": ["Biochemistry data", "Protein data", "Other data"], + "data_url": "https://www.nature.com/articles/s41467-020-19204-y#MOESM4" + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Source data.", + "data_type": ["Biochemistry data", "Protein data", "Other data"], + "data_url": "https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-020-19204-y/MediaObjects/41467_2020_19204_MOESM6_ESM.xlsx" + } + ], + "title": "Selection, biophysical and structural analysis of synthetic nanobodies that effectively neutralize SARS-CoV-2", + "issue": "1", + "volume": "11", + "publisher": "Springer Science and Business Media LLC", + "published": "2020-11-04", + "author": [ + "Custódio T. F.", + "Das H.", + "Sheward D. J.", + "Hanke L.", + "Pazicky S." + ] + }, + { + "doi": "10.1002/cti2.1224", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Karolinska KI/K Covid19 Immune atlas.", + "data_type": ["Biochemistry data", "Health data"], + "data_url": "https://covid19cellatlas.com/#/" + } + ], + "title": "Innate lymphoid cell composition associates with COVID‐19 disease severity", + "issue": "12", + "volume": "9", + "publisher": "Wiley", + "published": "2021-02-08", + "author": [ + "García M.", + "Kokkinou E.", + "Carrasco García A.", + "Parrot T.", + "Palma Medina L. M." + ] + }, + { + "doi": "10.1186/s13054-020-03351-1", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Data cannot be shared publicly due to issues with sensitivity, but it is possible to request access.", + "data_type": ["Health data"], + "data_url": "https://ccforum.biomedcentral.com/articles/10.1186/s13054-020-03351-1#availability-of-data-materials" + } + ], + "title": "Circulating bioactive adrenomedullin as a marker of sepsis, septic shock and critical illness", + "issue": "1", + "volume": "24", + "publisher": "Springer Science and Business Media LLC", + "published": "2020-11-04", + "author": [ + "Lundberg O. H. M.", + "Lengquist M.", + "Spångfors M.", + "Annborn M.", + "Bergmann D." + ] + }, + { + "doi": "10.1016/S2665-9913(20)30276-9", + "available_items": [ + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "All analysis tools used by Observational Health Data Sciences and Informatics.", + "data_type": ["Health data"], + "data_url": "https://github.com/OHDSI/" + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Data and results artefacts that do not include patient-level health information.", + "data_type": ["Health data"], + "data_url": "http://evidence.ohdsi.org:3838/Covid19EstimationHydroxychloroquine/" + } + ], + "title": "Risk of hydroxychloroquine alone and in combination with azithromycin in the treatment of rheumatoid arthritis: a multinational, retrospective study", + "issue": "11", + "volume": "2", + "publisher": "Elsevier BV", + "published": "2022-07-24", + "author": [ + "Lane J. C. E.", + "Weaver J.", + "Kostka K.", + "Duarte-Salles T.", + "Abrahao M. T. F." + ] + }, + { + "doi": "10.3389/fdata.2020.00032", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Data related to Austrian social media during COVID-19.", + "data_type": [ + "Social science and humanities data", + "Public health data" + ], + "data_url": "https://mpellert.at/covid19_monitor_austria/" + } + ], + "title": "Dashboard of Sentiment in Austrian Social Media During COVID-19", + "issue": "", + "volume": "3", + "publisher": "Frontiers Media SA", + "published": "2020-10-26", + "author": ["Pellert M.", "Lasser J.", "Metzler H.", "Garcia D."] + }, + { + "doi": "10.1126/science.abd4570", + "available_items": [ + { + "type": "data", + "repo_name": "dbGaP", + "accession_number": "phs002245.v1.p1", + "description": "Genetic Determinants of Susceptibility to Severe COVID-19 Infection.", + "data_type": ["Genomics & transcriptomics data", "Health data"], + "data_url": "https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs002245.v1.p1" + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Plasma, cells, genomic DNA, and other materials/samples are available upon request from authors or the Amsterdam UMC Covid-19 Biobank.", + "data_type": ["Genomics & transcriptomics data", "Health data"], + "data_url": "https://www.science.org/doi/10.1126/science.abd4570" + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "All additional data are in the supplementary material.", + "data_type": ["Genomics & transcriptomics data", "Health data"], + "data_url": "https://www.science.org/doi/10.1126/science.abd4570" + } + ], + "title": "Inborn errors of type I IFN immunity in patients with life-threatening COVID-19", + "issue": "6515", + "volume": "370", + "publisher": "American Association for the Advancement of Science (AAAS)", + "published": "2020-10-23", + "author": [ + "Zhang Q.", + "Bastard P.", + "Liu Z.", + "Le Pen J.", + "Moncada-Velez M." + ] + }, + { + "doi": "10.1126/science.abd4585", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Plasma, cells, and genomic DNA, as well as other materials can be provided via material transfer agreements.", + "data_type": ["Genomics & transcriptomics data", "Health data"], + "data_url": "https://www.science.org/doi/10.1126/science.abd4585" + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Clinical, epidemiological characteristics of 101 patients, as well as information on neutralising capacity and assays are provided in the article and supplementary materials.", + "data_type": ["Genomics & transcriptomics data", "Health data"], + "data_url": "https://www.science.org/doi/10.1126/science.abd4585" + } + ], + "title": "Autoantibodies against type I IFNs in patients with life-threatening COVID-19", + "issue": "6515", + "volume": "370", + "publisher": "American Association for the Advancement of Science (AAAS)", + "published": "2020-10-23", + "author": [ + "Bastard P.", + "Rosen L. B.", + "Zhang Q.", + "Michailidis E.", + "Hoffmann H." + ] + }, + { + "doi": "10.1371/journal.pone.0241104", + "available_items": [ + { + "type": "data", + "repo_name": "Zenodo", + "accession_number": "", + "description": "Serum-IgG responses to SARS-CoV-2 after mild and severe COVID-19 infection.", + "data_type": ["Biochemistry data", "Serology data", "Health data"], + "data_url": "https://zenodo.org/record/3994670#.YsveGC8RpTY" + } + ], + "title": "Serum-IgG responses to SARS-CoV-2 after mild and severe COVID-19 infection and analysis of IgG non-responders", + "issue": "10", + "volume": "15", + "publisher": "Public Library of Science (PLoS)", + "published": "2020-10-21", + "author": [ + "Marklund E.", + "Leach S.", + "Axelsson H.", + "Nyström K.", + "Norder H." + ] + }, + { + "doi": "10.1101/2020.07.17.20155937", + "available_items": [ + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Code for discriminative bayesian seroprevalence.", + "data_type": ["Serology data", "Biochemistry data", "Health data"], + "data_url": "https://github.com/MurrellGroup/DiscriminativeSeroprevalence/" + }, + { + "type": "data", + "repo_name": "GitHub", + "accession_number": "", + "description": "Data for discriminative bayesian seroprevalence.", + "data_type": ["Serology data", "Biochemistry data", "Health data"], + "data_url": "https://github.com/MurrellGroup/DiscriminativeSeroprevalence/" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Code used in analysis of seroprevalence data.", + "data_type": ["Serology data", "Biochemistry data", "Health data"], + "data_url": "https://github.com/chr1swallace/seroprevalence-paper" + }, + { + "type": "data", + "repo_name": "GitHub", + "accession_number": "", + "description": "Seroprevalence data.", + "data_type": ["Serology data", "Biochemistry data", "Health data"], + "data_url": "https://github.com/chr1swallace/seroprevalence-paper" + } + ], + "title": "Probabilistic approaches for classifying highly variable anti-SARS-CoV-2 antibody responses", + "issue": "", + "volume": "", + "publisher": "Cold Spring Harbor Laboratory", + "published": "2020-07-17", + "author": [ + "Dopico X. C.", + "Hanke L.", + "Sheward D. J.", + "Muschiol S.", + "Aleman S." + ] + }, + { + "doi": "10.1007/s11239-020-02312-3", + "available_items": [ + { + "type": "data", + "repo_name": "Swedish national dataservice", + "accession_number": "", + "description": "All raw data underlying the study.", + "data_type": ["Health data"], + "data_url": "https://snd.gu.se/sv/catalogue/study/2020-43/1/1#dataset" + } + ], + "title": "Rotational thromboelastometry results are associated with care level in COVID-19", + "issue": "2", + "volume": "51", + "publisher": "Springer Science and Business Media LLC", + "published": "2020-10-17", + "author": [ + "Almskog L. M.", + "Wikman A.", + "Svensson J.", + "Wanecek M.", + "Bottai M." + ] + }, + { + "doi": "10.1038/s41467-020-18848-0", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Source data related to symptoms and some aggregated patient data.", + "data_type": ["Serology data", "Health data"], + "data_url": "https://static-content.springer.com/esm/art%3A10.1038%2Fs41467-020-18848-0/MediaObjects/41467_2020_18848_MOESM4_ESM.xlsx" + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Data cannot be made publicly available, but can be made available upon request.", + "data_type": ["Serology data", "Health data"], + "data_url": "https://www.nature.com/articles/s41467-020-18848-0#data-availability" + } + ], + "title": "SARS-CoV-2 exposure, symptoms and seroprevalence in healthcare workers in Sweden", + "issue": "1", + "volume": "11", + "publisher": "Springer Science and Business Media LLC", + "published": "2020-10-08", + "author": [ + "Rudberg A.", + "Havervall S.", + "Månberg A.", + "Jernbom Falk A.", + "Aguilera K." + ] + }, + { + "doi": "10.1038/s41467-020-18849-z", + "available_items": [ + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Data analysis code used in the study.", + "data_type": ["Public health data"], + "data_url": "https://github.com/ohdsi-studies/Covid19HospitalizationCharacterization." + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Aggregated results are available. Individual patient-level data cannot be made publicly available, but requests may be submitted for access.", + "data_type": ["Public health data"], + "data_url": "http://evidence.ohdsi.org/Covid19CharacterizationHospitalization/" + } + ], + "title": "Deep phenotyping of 34,128 adult patients hospitalised with COVID-19 in an international network study", + "issue": "1", + "volume": "11", + "publisher": "Springer Science and Business Media LLC", + "published": "2020-10-06", + "author": [ + "Burn E.", + "You S. C.", + "Sena A. G.", + "Kostka K.", + "Abedtash H." + ] + }, + { + "doi": "10.3390/ijms21197375", + "available_items": [ + { + "type": "data", + "repo_name": "Protein Data Bank", + "accession_number": "6ZPE", + "description": "Nonstructural protein 10 (nsp10) from SARS CoV-2, 1.58Å resolution.", + "data_type": ["Protein data"], + "data_url": "https://www.rcsb.org/structure/6ZPE" + }, + { + "type": "data", + "repo_name": "Protein Data Bank", + "accession_number": "6ZCT", + "description": "Nonstructural protein 10 (nsp10) from SARS CoV-2, 2.55Å resolution.", + "data_type": ["Protein data"], + "data_url": "https://www.rcsb.org/structure/6ZCT" + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Nsp10 unfolding temperatures determined by DSF.", + "data_type": ["Protein data"], + "data_url": "http://www.mdpi.com/1422-0067/21/19/7375/s1" + } + ], + "title": "Crystal Structure of Non-Structural Protein 10 from Severe Acute Respiratory Syndrome Coronavirus-2", + "issue": "19", + "volume": "21", + "publisher": "MDPI AG", + "published": "2020-10-06", + "author": [ + "Rogstam A.", + "Nyblom M.", + "Christensen S.", + "Sele C.", + "Talibov V. O." + ] + }, + { + "doi": "10.1016/j.cell.2020.08.017", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "All data generated during the study (predicted binding affinities, donor characteristics, sample information, and some analyses) are available in the article.", + "data_type": [ + "Genomics & transcriptomics data", + "Protein data", + "Other data" + ], + "data_url": "https://www.cell.com/cell/fulltext/S0092-8674(20)31008-4?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867420310084%3Fshowall%3Dtrue#secsectitle0060" + } + ], + "title": "Robust T Cell Immunity in Convalescent Individuals with Asymptomatic or Mild COVID-19", + "issue": "1", + "volume": "183", + "publisher": "Elsevier BV", + "published": "2020-10-01", + "author": [ + "Sekine T.", + "Perez-Potti A.", + "Rivera-Ballesteros O.", + "Strålin K.", + "Gorin J." + ] + }, + { + "doi": "10.1212/WNL.0000000000010977", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Data cannot be made publicly available, but access to anonymised data can be requested.", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://n.neurology.org/content/96/2/e294/tab-figures-data" + } + ], + "title": "CSF biomarkers in patients with COVID-19 and neurological symptoms", + "issue": "", + "volume": "", + "publisher": "Ovid Technologies (Wolters Kluwer Health)", + "published": "2020-10-01", + "author": [ + "Edén A.", + "Kanberg N.", + "Gostner J.", + "Fuchs D.", + "Hagberg L." + ] + }, + { + "doi": "10.1038/s41586-020-2818-3", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Summary statistics of the genome-wide association study are available from the COVID-19 Host Genetics Initiative (round 3, ANA_B2_V2: hospitalized patients with COVID-19 compared with population controls).", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://www.covid19hg.org/" + } + ], + "title": "The major genetic risk factor for severe COVID-19 is inherited from Neanderthals", + "issue": "7835", + "volume": "587", + "publisher": "Springer Science and Business Media LLC", + "published": "2020-09-30", + "author": ["Zeberg H.", "Pääbo S."] + }, + { + "doi": "10.1126/sciimmunol.abe1670", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Curated flow cytometry data are available for exploration via the Karolinska COVID-19 Immune Atlas.", + "data_type": [ + "Health data", + "Protein data", + "Genomics & transcriptomics data" + ], + "data_url": "https://covid19cellatlas.com/#/" + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "All other data are available in the article itself or the supplementary materials.", + "data_type": [ + "Health data", + "Protein data", + "Genomics & transcriptomics data" + ], + "data_url": "https://www.science.org/doi/10.1126/sciimmunol.abe1670" + } + ], + "title": "MAIT cell activation and dynamics associated with COVID-19 disease severity", + "issue": "51", + "volume": "5", + "publisher": "American Association for the Advancement of Science (AAAS)", + "published": "2020-09-18", + "author": [ + "Parrot T.", + "Gorin J.", + "Ponzetta A.", + "Maleki K. T.", + "Kammann T." + ] + }, + { + "doi": "10.1074/jbc.AC120.015967", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Color light micrographs of autopsy lung tissue from the three Covid-19 cases, all included in the article.", + "data_type": ["Imaging data", "Genomics & transcriptomics data"], + "data_url": "https://www.jbc.org/article/S0021-9258(17)50371-3/fulltext#seccestitle40" + } + ], + "title": "Presence of hyaluronan in lung alveoli in severe Covid-19: An opening for new treatment options?", + "issue": "45", + "volume": "295", + "publisher": "Elsevier BV", + "published": "2021-12-18", + "author": [ + "Hellman U.", + "Karlsson M. G.", + "Engström-Laurent A.", + "Cajander S.", + "Dorofte L." + ] + }, + { + "doi": "10.1038/s41467-020-18611-5", + "available_items": [ + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Analysis code used in the study.", + "data_type": [ + "Public health data", + "Genomics & transcriptomics data" + ], + "data_url": "https://github.com/reiniuslab/COVID19" + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Source data, including all raw data (primarily Ct values) are included in the article.", + "data_type": [ + "Public health data", + "Genomics & transcriptomics data" + ], + "data_url": "https://www.nature.com/articles/s41467-020-18611-5" + } + ], + "title": "Massive and rapid COVID-19 testing is feasible by extraction-free SARS-CoV-2 RT-PCR", + "issue": "1", + "volume": "11", + "publisher": "Springer Science and Business Media LLC", + "published": "2020-09-23", + "author": [ + "Smyrlaki I.", + "Ekman M.", + "Lentini A.", + "Rufino de Sousa N.", + "Papanicolaou N." + ] + }, + { + "doi": "10.1212/WNL.0000000000010111", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Data cannot be publicly shared, but applications can be made for access to anonymised data.", + "data_type": ["Health data", "Biochemistry data"], + "data_url": "https://github.com/reiniuslab/COVID19" + } + ], + "title": "Neurochemical evidence of astrocytic and neuronal injury commonly found in COVID-19", + "issue": "12", + "volume": "95", + "publisher": "Ovid Technologies (Wolters Kluwer Health)", + "published": "2020-06-16", + "author": [ + "Kanberg N.", + "Ashton N. J.", + "Andersson L.", + "Yilmaz A.", + "Lindh M." + ] + }, + { + "doi": "10.7717/peerj.9879", + "available_items": [ + { + "type": "data", + "repo_name": "GitHub", + "accession_number": "", + "description": "Data required to reproduce the results. The data was largely produced using Google mobility data.", + "data_type": ["Biochemistry data", "Health data"], + "data_url": "https://github.com/patrickbryant1/COVID19.github.io/tree/master/simulations/mobility" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Analysis code required for modelliing (primarily using R).", + "data_type": ["Biochemistry data", "Health data"], + "data_url": "https://github.com/patrickbryant1/COVID19.github.io/tree/master/simulations/mobility" + } + ], + "title": "Estimating the impact of mobility patterns on COVID-19 infection rates in 11 European countries", + "issue": "", + "volume": "8", + "publisher": "PeerJ", + "published": "2020-09-15", + "author": ["Bryant P.", "Elofsson A."] + }, + { + "doi": "10.3390/v12091026", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Supplementary materials include information about phylogenetic models, mutational profiles, and spatio-temporal appearance of each variant.", + "data_type": [ + "Biochemistry data", + "Genomics & transcriptomics data", + "Health data" + ], + "data_url": "https://www.mdpi.com/1999-4915/12/9/1026/htm" + } + ], + "title": "Spatio-Temporal Mutational Profile Appearances of Swedish SARS-CoV-2 during the Early Pandemic", + "issue": "9", + "volume": "12", + "publisher": "MDPI AG", + "published": "2020-09-14", + "author": ["Ling J.", "Hickman R. A.", "Li J.", "Lu X.", "Lindahl J. F."] + }, + { + "doi": "10.1128/mSphere.00224-21", + "available_items": [ + { + "type": "data", + "repo_name": "GitHub", + "accession_number": "", + "description": "Input data related to ELISA tests.", + "data_type": ["Biochemistry data", "Serology data", "Health data"], + "data_url": "https://github.com/chandranlab/Ig_titer_sigmoid_fit" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Code related to modelling antibody titer quantification from single dilution points.", + "data_type": ["Biochemistry data", "Serology data", "Health data"], + "data_url": "https://github.com/chandranlab/Ig_titer_sigmoid_fit" + } + ], + "title": "Single-Dilution COVID-19 Antibody Test with Qualitative and Quantitative Readouts", + "issue": "2", + "volume": "6", + "publisher": "American Society for Microbiology", + "published": "2021-04-28", + "author": [ + "Bortz R. H.", + "Florez C.", + "Laudermilch E.", + "Wirchnianski A. S.", + "Lasso G." + ] + }, + { + "doi": "10.1212/wnl.0000000000010250", + "available_items": [ + { + "type": "data", + "repo_name": "Dryad", + "accession_number": "", + "description": "Proteomics data.", + "data_type": ["Health data", "Protein data"], + "data_url": "https://datadryad.org/stash/dataset/doi:10.5061/dryad.xwdbrv1bb" + } + ], + "title": "Acute necrotizing encephalopathy with SARS-CoV-2 RNA confirmed in cerebrospinal fluid", + "issue": "10", + "volume": "95", + "publisher": "Ovid Technologies (Wolters Kluwer Health)", + "published": "2020-06-25", + "author": [ + "Virhammar J.", + "Kumlien E.", + "Fällmar D.", + "Frithiof R.", + "Jackmann S." + ] + }, + { + "doi": "10.1016/j.cell.2020.09.016", + "available_items": [ + { + "type": "data", + "repo_name": "Mendeley", + "accession_number": "", + "description": "Data organised by figures presented in the article.", + "data_type": ["Serology data", "Protein data", "Health data"], + "data_url": "https://data.mendeley.com/datasets/ds6g796xyg/1" + }, + { + "type": "data", + "repo_name": "Figshare", + "accession_number": "", + "description": "Plasma protein expression (Olink - NPX values), FACS, Autoantibodies.", + "data_type": ["Serology data", "Protein data", "Health data"], + "data_url": "https://doi.org/10.17044/scilifelab.13181273" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Scripts to complete analyses and produce figures.", + "data_type": ["Serology data", "Protein data", "Health data"], + "data_url": "https://doi.org/10.17044/scilifelab.13181273" + } + ], + "title": "The Immunology of Multisystem Inflammatory Syndrome in Children with COVID-19", + "issue": "4", + "volume": "183", + "publisher": "Elsevier BV", + "published": "2022-06-25", + "author": [ + "Consiglio C. R.", + "Cotugno N.", + "Sardh F.", + "Pou C.", + "Amodio D." + ] + }, + { + "doi": "10.1038/s41467-020-18174-5", + "available_items": [ + { + "type": "data", + "repo_name": "GenBank", + "accession_number": "MT784731", + "description": "Sequence of Ty1.", + "data_type": [ + "Biochemistry data", + "Protein data", + "Genomics & transcriptomics data" + ], + "data_url": "https://www.ncbi.nlm.nih.gov/nuccore/MT784731" + }, + { + "type": "data", + "repo_name": "GitHub", + "accession_number": "", + "description": "Bio layer interferometry (BLI) data.", + "data_type": [ + "Biochemistry data", + "Protein data", + "Genomics & transcriptomics data" + ], + "data_url": "https://github.com/derpaule/Ty1_octet_itc" + }, + { + "type": "data", + "repo_name": "GitHub", + "accession_number": "", + "description": "Isothermal titration calorimetry (ITC) data.", + "data_type": [ + "Biochemistry data", + "Protein data", + "Genomics & transcriptomics data" + ], + "data_url": "https://github.com/derpaule/Ty1_octet_itc/tree/master/data_itc" + }, + { + "type": "data", + "repo_name": "BioProject", + "accession_number": "PRJNA638614", + "description": "Next generation sequencing (NGS) data.", + "data_type": [ + "Biochemistry data", + "Protein data", + "Genomics & transcriptomics data" + ], + "data_url": "https://www.ncbi.nlm.nih.gov/bioproject/PRJNA638614" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Jupyter notebooks to reproduce next generation sequencing (NGS) data.", + "data_type": [ + "Biochemistry data", + "Protein data", + "Genomics & transcriptomics data" + ], + "data_url": "https://github.com/MurrellGroup/Ty1" + }, + { + "type": "data", + "repo_name": "Electron Microscopy Data Bank", + "accession_number": "EMD-11526", + "description": "Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing nanobodies (Ty1).", + "data_type": [ + "Biochemistry data", + "Protein data", + "Genomics & transcriptomics data" + ], + "data_url": "https://www.ebi.ac.uk/emdb/EMD-11526" + }, + { + "type": "data", + "repo_name": "Protein Data Bank", + "accession_number": "6ZXN", + "description": "Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing nanobodies (Ty1).", + "data_type": [ + "Biochemistry data", + "Protein data", + "Genomics & transcriptomics data" + ], + "data_url": "https://www.rcsb.org/structure/6zxn" + } + ], + "title": "An alpaca nanobody neutralizes SARS-CoV-2 by blocking receptor interaction", + "issue": "1", + "volume": "11", + "publisher": "Springer Science and Business Media LLC", + "published": "2020-09-04", + "author": [ + "Hanke L.", + "Vidakovics Perez L.", + "Sheward D. J.", + "Das H.", + "Schulte T." + ] + }, + { + "doi": "10.1371/journal.pone.0238217", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Number of COVID-19 deaths contributed by specific age group and population characteristics for 14 countries and 13 US states.", + "data_type": [ + "Social science and humanities data", + "Public health data" + ], + "data_url": "https://ars.els-cdn.com/content/image/1-s2.0-S0013935120307854-mmc2.pdf" + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Healthcare professionals’ responses about perceptions, exposure, and workload during the COVID-19 pandemic.", + "data_type": [ + "Social science and humanities data", + "Public health data" + ], + "data_url": "https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0238217#sec011" + } + ], + "title": "Factors contributing to healthcare professional burnout during the COVID-19 pandemic: A rapid turnaround global survey", + "issue": "9", + "volume": "15", + "publisher": "Public Library of Science (PLoS)", + "published": "2020-09-03", + "author": [ + "Morgantini L. A.", + "Naha U.", + "Wang H.", + "Francavilla S.", + "Acar Ö." + ] + }, + { + "doi": "10.1016/j.xcrm.2020.100078", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Raw mass cytometry data and the Olink protein data generated during this study.", + "data_type": ["Protein data", "Health data"], + "data_url": "https://brodinlab.com/data-repository/" + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Immunoglobulin G (IgG) data.", + "data_type": ["Protein data", "Health data"], + "data_url": "https://www.cell.com/cms/10.1016/j.xcrm.2020.100078/attachment/53aca693-33e7-4b26-881f-ea11c7c15ad1/mmc1" + }, + { + "type": "data", + "repo_name": "GitHub", + "accession_number": "", + "description": "SARS-CoV2 longitudinal systems-level analyses code.", + "data_type": ["Protein data", "Health data"], + "data_url": "https://github.com/rodriluc/SARS-CoV2_study" + } + ], + "title": "Systems-Level Immunomonitoring from Acute to Recovery Phase of Severe COVID-19", + "issue": "5", + "volume": "1", + "publisher": "Elsevier BV", + "published": "2020-08-25", + "author": [ + "Rodriguez L.", + "Pekkarinen P. T.", + "Lakshmikanth T.", + "Tan Z.", + "Consiglio C. R." + ] + }, + { + "doi": "10.1126/sciimmunol.abd6832", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Curated flow cytometry data available via the Karolinska COVID-19 Immune Atlas.", + "data_type": [ + "Protein data", + "Biochemistry data", + "Genomics & transcriptomics data", + "Health data", + "Imaging data", + "Other data" + ], + "data_url": "https://covid19cellatlas.com/#/" + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Raw data, clinical characteristics of patients, and various results files are available in supplementary data.", + "data_type": [ + "Protein data", + "Biochemistry data", + "Genomics & transcriptomics data", + "Health data", + "Imaging data", + "Other data" + ], + "data_url": "https://www.science.org/doi/10.1126/sciimmunol.abd6832" + } + ], + "title": "Natural killer cell immunotypes related to COVID-19 disease severity", + "issue": "50", + "volume": "5", + "publisher": "American Association for the Advancement of Science (AAAS)", + "published": "2020-08-14", + "author": [ + "Maucourant C.", + "Filipovic I.", + "Ponzetta A.", + "Aleman S.", + "Cornillet M." + ] + }, + { + "doi": "10.1101/2020.08.06.20169854", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Supplementary information contains information on publicly available data sources used, instruments used, data on loci associated with risk factors, and genetic correlations between lifespan-related traits and COVID-19.", + "data_type": ["Genomics & transcriptomics data", "Health data"], + "data_url": "https://www.medrxiv.org/content/10.1101/2020.08.06.20169854v2.supplementary-material" + } + ], + "title": "Genetic and Phenotypic Evidence for the Causal Relationship Between Aging and COVID-19", + "issue": "", + "volume": "", + "publisher": "Cold Spring Harbor Laboratory", + "published": "2020-08-07", + "author": [ + "Ying K.", + "Zhai R.", + "Pyrkov T. V.", + "Mariotti M.", + "Fedichev P. O." + ] + }, + { + "doi": "10.1080/20008686.2020.1789036", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Serological responses of 1,005 employees to SARS-CoV-2 at 22 different elderly care homes in Stockholm, Sweden, and the number of employees that reported known contacts with COVID-19.", + "data_type": ["Serology data", "Health data"], + "data_url": "https://www.tandfonline.com/action/downloadTable?id=t0001&doi=10.1080%2F20008686.2020.1789036&downloadType=CSV" + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Prevalence of IgM (either only IgM or combined with IgG) or only IgG among elderly care home employees with or without reported symptoms.", + "data_type": ["Serology data", "Health data"], + "data_url": "https://www.tandfonline.com/doi/figure/10.1080/20008686.2020.1789036?scroll=top&needAccess=true#" + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Predictors for seropositivity in both univariable and multivariable analyses.", + "data_type": ["Serology data", "Health data"], + "data_url": "https://www.tandfonline.com/action/downloadTable?id=t0003&doi=10.1080%2F20008686.2020.1789036&downloadType=CSV" + } + ], + "title": "High seroprevalence of SARS-CoV-2 in elderly care employees in Sweden", + "issue": "1", + "volume": "10", + "publisher": "Informa UK Limited", + "published": "2020-01-01", + "author": [ + "Lindahl J. F.", + "Hoffman T.", + "Esmaeilzadeh M.", + "Olsen B.", + "Winter R." + ] + }, + { + "doi": "10.1016/S1473-3099(20)30314-5", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Data on single nucleotide polymorphisms and characteristics of 16 laboratory-confirmed COVID-19 cases included in the article.", + "data_type": ["Health data", "Genomics & transcriptomics data"], + "data_url": "https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(20)30314-5/fulltext" + } + ], + "title": "Investigation of a COVID-19 outbreak in Germany resulting from a single travel-associated primary case: a case series", + "issue": "8", + "volume": "20", + "publisher": "Elsevier BV", + "published": "2020-11-02", + "author": [ + "Böhmer M. M.", + "Buchholz U.", + "Corman V. M.", + "Hoch M.", + "Katz K." + ] + }, + { + "doi": "10.1097/HJH.0000000000002531", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Biochemistry of patients ordered by days after intensive care admission (n = 9), included in the article.", + "data_type": ["Biochemistry data", "Health data"], + "data_url": "https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(20)30314-5/fulltext" + } + ], + "title": "Hyperreninemia and low total body water may contribute to acute kidney injury in COVID-19 patients in intensive care", + "issue": "8", + "volume": "38", + "publisher": "Ovid Technologies (Wolters Kluwer Health)", + "published": "2020-05-28", + "author": ["Hultström M.", "von Seth M.", "Frithiof R."] + }, + { + "doi": "10.1038/s41467-021-21085-8", + "available_items": [ + { + "type": "data", + "repo_name": "Figshare", + "accession_number": "", + "description": "Raw data with demographic and clinical characteristics of the patients, progress of treatment and control groups.", + "data_type": ["Biochemistry data", "Drug discovery data"], + "data_url": "https://figshare.com/articles/dataset/Source_Data_xls/13482810" + }, + { + "type": "code", + "repo_name": "Figshare", + "accession_number": "", + "description": "All relevant codes used in SAS software for statistical analysis.", + "data_type": ["Biochemistry data", "Drug discovery data"], + "data_url": "https://figshare.com/articles/dataset/Source_Data_xls/13482810" + } + ], + "title": "Efficacy and tolerability of bevacizumab in patients with severe Covid-19", + "issue": "1", + "volume": "12", + "publisher": "Springer Science and Business Media LLC", + "published": "2021-02-05", + "author": ["Pang J.", "Xu F.", "Aondio G.", "Li Y.", "Fumagalli A."] + }, + { + "doi": "10.1101/2020.07.27.224063", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Due to risk of de-identification, the pseudonymised RNA sequencing data will not be made publicly available, but it is possible to apply for access.", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://www.biorxiv.org/content/10.1101/2020.07.27.224063v2.full" + }, + { + "type": "data", + "repo_name": "ArrayExpress", + "accession_number": "E-MTAB-9357", + "description": "Processed data: RNA-seq of coding RNA from single cells.", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-9357/" + }, + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Data are integrated for further visualization and analysis in ISB COVID-19 data explorer.", + "data_type": ["Genomics & transcriptomics data"], + "data_url": "https://atlas.fredhutch.org/isb/covid/" + } + ], + "title": "Multiomic Immunophenotyping of COVID-19 Patients Reveals Early Infection Trajectories", + "issue": "", + "volume": "", + "publisher": "Cold Spring Harbor Laboratory", + "published": "2020-07-28", + "author": ["Su Y.", "Chen D.", "Lausted C.", "Yuan D.", "Choi J."] + }, + { + "doi": "10.3389/fmed.2020.00349", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Data are in the article, including exposure history and characterists of COVID-19 patients during hospitalisation and discharge, as well as information from a follow-up.", + "data_type": ["Health data"], + "data_url": "https://www.frontiersin.org/articles/10.3389/fmed.2020.00349/full#h6" + } + ], + "title": "Re-positive Cases of Nucleic Acid Tests in Discharged Patients With COVID-19: A Follow-Up Study", + "issue": "", + "volume": "7", + "publisher": "Frontiers Media SA", + "published": "2020-06-23", + "author": ["Qiao X.", "Xu X.", "Zi H.", "Liu G.", "Li B."] + }, + { + "doi": "10.1038/s41586-020-2284-y", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Population outflow data from Wuhan from January 1-24, 2020; COVID-19 case counts as of February 19 and other data for 296 prefectures in mainland China (additional data in the article).", + "data_type": ["Health data"], + "data_url": "https://static-content.springer.com/esm/art%3A10.1038%2Fs41586-020-2284-y/MediaObjects/41586_2020_2284_MOESM3_ESM.xlsx" + }, + { + "type": "code", + "repo_name": "", + "accession_number": "", + "description": "Analysis code included alongside other data in spplementary information.", + "data_type": ["Health data"], + "data_url": "https://static-content.springer.com/esm/art%3A10.1038%2Fs41586-020-2284-y/MediaObjects/41586_2020_2284_MOESM1_ESM.pdf" + } + ], + "title": "Population flow drives spatio-temporal distribution of COVID-19 in China", + "issue": "7812", + "volume": "582", + "publisher": "Springer Science and Business Media LLC", + "published": "2020-04-29", + "author": ["Jia J. S.", "Lu X.", "Yuan Y.", "Xu G.", "Jia J."] + }, + { + "doi": "10.1186/s12931-020-01363-7", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Provided in the article: CT images for 2 patients over 12 days.", + "data_type": ["Imaging data", "Health data"], + "data_url": "https://respiratory-research.biomedcentral.com/articles/10.1186/s12931-020-01363-7#availability-of-data-and-materials" + } + ], + "title": "The unsynchronized changes of CT image and nucleic acid detection in COVID-19: reports the two cases from Gansu, China", + "issue": "1", + "volume": "21", + "publisher": "Springer Science and Business Media LLC", + "published": "2020-04-22", + "author": ["Gao J.", "Liu J.", "Wen H.", "Liu H.", "Hu W."] + }, + { + "doi": "10.1371/journal.pone.0291146", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Data related to PCR probes, assessments of infectivity and RNA integrity, and ex-vivo challenges are included in the study.", + "data_type": ["Genomics & transcriptomics data", "Health data"], + "data_url": "https://europepmc.org/article/MED/37769001#sec015" + } + ], + "title": "Evaluation of a human mucosal tissue explant model for SARS-CoV-2 replication", + "issue": "9", + "volume": "18", + "publisher": "Public Library of Science (PLoS)", + "published": "2023-09-28", + "author": [ + "Gordhan B. G.", + "Herrera C.", + "Pillay A.", + "Seiphetlo T.", + "Ealand C. S." + ] + }, + { + "doi": "10.1038/s41467-023-41146-4", + "available_items": [ + { + "type": "data", + "repo_name": "PRIDE", + "accession_number": "PXD038394", + "description": "AKI DIA samples for generalized peakgroup scoring model application", + "data_type": [ + "Genomics & transcriptomics data", + "Health data", + "Protein data", + "Other data" + ], + "data_url": "https://www.ebi.ac.uk/pride/archive/projects/PXD038394" + }, + { + "type": "data", + "repo_name": "PRIDE", + "accession_number": "PXD025752", + "description": "A time-resolved proteomic and prognostic map of COVID-19", + "data_type": [ + "Genomics & transcriptomics data", + "Health data", + "Protein data", + "Other data" + ], + "data_url": "https://www.ebi.ac.uk/pride/archive/projects/PXD025752" + }, + { + "type": "data", + "repo_name": "Figshare", + "accession_number": "", + "description": "Olink Dataset", + "data_type": [ + "Genomics & transcriptomics data", + "Health data", + "Protein data", + "Other data" + ], + "data_url": "https://figshare.com/articles/dataset/dx_doi_org_10_6084_m9_figshare_6025748/6025748" + }, + { + "type": "data", + "repo_name": "PRIDE", + "accession_number": "PXD044264", + "description": "56 samples from acute kidney injury patients (DIA-MS septic AKI dataset).", + "data_type": [ + "Genomics & transcriptomics data", + "Health data", + "Protein data", + "Other data" + ], + "data_url": "https://www.ebi.ac.uk/pride/archive/projects/PXD044264" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Biologically Informed Neural Network (BINN) code", + "data_type": [ + "Genomics & transcriptomics data", + "Health data", + "Protein data", + "Other data" + ], + "data_url": "https://github.com/InfectionMedicineProteomics/BINN" + }, + { + "type": "code", + "repo_name": "Zenodo", + "accession_number": "", + "description": "InfectionMedicineProteomics/BINN: First release", + "data_type": [ + "Genomics & transcriptomics data", + "Health data", + "Protein data", + "Other data" + ], + "data_url": "https://zenodo.org/record/8207421" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "DE-score algorithm has been implemented into the data processing package DPKS", + "data_type": [ + "Genomics & transcriptomics data", + "Health data", + "Protein data", + "Other data" + ], + "data_url": "https://github.com/InfectionMedicineProteomics/DPKS" + } + ], + "title": "Interpreting biologically informed neural networks for enhanced proteomic biomarker discovery and pathway analysis", + "issue": "1", + "volume": "14", + "publisher": "Springer Science and Business Media LLC", + "published": "2023-09-02", + "author": [ + "Hartman E.", + "Scott A. M.", + "Karlsson C.", + "Mohanty T.", + "Vaara S. T." + ] + }, + { + "doi": "10.1038/s41467-023-41541-x", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Data cannot be shared publicly, but those with appropriate ethical permissions can apply for access via helsedata.no/en.", + "data_type": ["Health data"], + "data_url": "" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Code used for analysis (in R)", + "data_type": ["Health data"], + "data_url": "https://github.com/remebjornatle/post_covid" + } + ], + "title": "Predictors of the post-COVID condition following mild SARS-CoV-2 infection", + "issue": "1", + "volume": "14", + "publisher": "Springer Science and Business Media LLC", + "published": "2023-09-20", + "author": ["Reme B.", "Gjesvik J.", "Magnusson K."] + }, + { + "doi": "10.1038/s41467-023-41159-z", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Results of the meta-analysis are available in a Shiny app.", + "data_type": ["Protein data"], + "data_url": "https://figshare.com/articles/online_resource/CoViD-19_Meta-Analysis_of_Plasma_Proteins_CoViMAPP_app/22293148" + }, + { + "type": "data", + "repo_name": "ProteomeXchange", + "accession_number": "PXD037486", + "description": "In-depth serum proteomics of hospitalized COVID-19 patients and PCR-negative healthy controls with HiRIEF LC-MS/MS", + "data_type": ["Protein data"], + "data_url": "https://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD037486" + }, + { + "type": "data", + "repo_name": "ProteomeXchange", + "accession_number": "PXD037451", + "description": "Mass-spectrometry proteomics of Calu-3 cell lines infected with SARS-CoV-2, in comparison to non-infected and UV mock-treated cell lines", + "data_type": ["Protein data"], + "data_url": "https://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD037451" + }, + { + "type": "data", + "repo_name": "ProteomeXchange", + "accession_number": "PXD040982", + "description": "Mass-spectrometry phosphoproteomics of Calu-3 cell lines infected with SARS-CoV-2, in comparison to non-infected and UV mock-treated cell lines", + "data_type": ["Protein data"], + "data_url": "https://proteomecentral.proteomexchange.org/cgi/GetDataset?ID=PXD040982" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Custom code for the Nextflow proteomics workflow", + "data_type": ["Protein data"], + "data_url": "https://europepmc.org/article/MED/37739942#id339581" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "R code used for analyses", + "data_type": ["Protein data"], + "data_url": "https://europepmc.org/article/MED/37739942#id339581" + } + ], + "title": "Comprehensive proteomics and meta-analysis of COVID-19 host response", + "issue": "1", + "volume": "14", + "publisher": "Springer Science and Business Media LLC", + "published": "2023-09-22", + "author": [ + "Babačić H.", + "Christ W.", + "Araújo J. E.", + "Mermelekas G.", + "Sharma N." + ] + }, + { + "doi": "10.1038/s41598-023-42127-9", + "available_items": [ + { + "type": "data", + "repo_name": "GitHub", + "accession_number": "", + "description": "Unsupervised learning methods to Identify essential genes associated with SARS-CoV-2", + "data_type": [ + "Genomics & transcriptomics data", + "Drug discovery data" + ], + "data_url": "https://github.com/MahnazHabibi/Gene_analysis" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Unsupervised learning methods to Identify essential genes associated with SARS-CoV-2", + "data_type": [ + "Genomics & transcriptomics data", + "Drug discovery data" + ], + "data_url": "https://github.com/MahnazHabibi/Gene_analysis" + } + ], + "title": "Identification of essential genes associated with SARS-CoV-2 infection as potential drug target candidates with machine learning algorithms", + "issue": "1", + "volume": "13", + "publisher": "Springer Science and Business Media LLC", + "published": "2023-09-13", + "author": ["Taheri G.", "Habibi M."] + }, + { + "doi": "10.1038/s41598-023-43412-3", + "available_items": [ + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Workflow developed during the COVID-19 pandemic with the purpose of COVID-19 vaccination Phase III trial data analysis and support through data quality control and automated reporting", + "data_type": ["Health data"], + "data_url": "https://github.com/rcvanwijk/ReproducibilityPMX" + } + ], + "title": "Reproducibility in pharmacometrics applied in a phase III trial of BCG-vaccination for COVID-19", + "issue": "1", + "volume": "13", + "publisher": "Springer Science and Business Media LLC", + "published": "2023-09-28", + "author": [ + "van Wijk R. C.", + "Mockeliunas L.", + "van den Hoogen G.", + "Upton C. M.", + "Diacon A. H." + ] + }, + { + "doi": "10.1371/journal.pone.0290974", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "All vaccination data are available on Ireland's COVID-19 Data Hub", + "data_type": ["Public health data"], + "data_url": "https://covid19ireland-geohive.hub.arcgis.com/" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Code to simulate the evolution of the COVID-19 pandemic with and without optimal vaccination.", + "data_type": ["Public health data"], + "data_url": "https://github.com/elenizavrakli/Optimal-Age-Specific-Vaccination-Control" + } + ], + "title": "Optimal age-specific vaccination control for COVID-19: An Irish case study", + "issue": "9", + "volume": "18", + "publisher": "Public Library of Science (PLoS)", + "published": "2023-09-05", + "author": ["Zavrakli E.", "Parnell A.", "Malone D.", "Duffy K.", "Dey S."] + }, + { + "doi": "10.1038/s41467-023-41312-8", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Library designs including the proteins, peptides and statistics", + "data_type": ["Protein data", "Biochemistry data"], + "data_url": "http://slim.icr.ac.uk/phage_libraries/human/" + } + ], + "title": "Identification of motif-based interactions between SARS-CoV-2 protein domains and human peptide ligands pinpoint antiviral targets", + "issue": "1", + "volume": "14", + "publisher": "Springer Science and Business Media LLC", + "published": "2023-09-13", + "author": [ + "Mihalič F.", + "Benz C.", + "Kassa E.", + "Lindqvist R.", + "Simonetti L." + ] + }, + { + "doi": "10.1038/s41398-023-02578-0", + "available_items": [ + { + "type": "data", + "repo_name": "Open Science Framework", + "accession_number": "", + "description": "Anonymised data, dictionary, analytical code, study protocol and frequentist statistical analysis plan", + "data_type": ["Social science and humanities data"], + "data_url": "https://osf.io/j9v2z/" + }, + { + "type": "code", + "repo_name": "Open Science Framework", + "accession_number": "", + "description": "Anonymised data, dictionary, analytical code, study protocol and frequentist statistical analysis plan", + "data_type": ["Social science and humanities data"], + "data_url": "https://osf.io/j9v2z/" + } + ], + "title": "Reducing intrusive memories after trauma via an imagery-competing task intervention in COVID-19 intensive care staff: a randomised controlled trial", + "issue": "1", + "volume": "13", + "publisher": "Springer Science and Business Media LLC", + "published": "2023-09-01", + "author": [ + "Iyadurai L.", + "Highfield J.", + "Kanstrup M.", + "Markham A.", + "Ramineni V." + ] + } + ] } From 438984fd8c95fe3773e166fd016feca4dbbe56bd Mon Sep 17 00:00:00 2001 From: LianeHughes <68756672+LianeHughes@users.noreply.github.com> Date: Fri, 19 Jan 2024 07:07:42 +0100 Subject: [PATCH 4/5] fix typo on news --- content/english/updates/wastewater_update_gothenburg.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/content/english/updates/wastewater_update_gothenburg.md b/content/english/updates/wastewater_update_gothenburg.md index a922fb8be..d500681b0 100644 --- a/content/english/updates/wastewater_update_gothenburg.md +++ b/content/english/updates/wastewater_update_gothenburg.md @@ -6,7 +6,7 @@ banner: /dashboard_thumbs/wastewater.jpg banner_caption: Photo of a Swedish wastewater treatment plant, by Kari Kohvakka (Stockholm Vatten). --- -We have been working with the Norder group at Uppsala university to update the [wastewater dashboard](/dashboards/wastewater/). +We have been working with the Norder group at Gothenburg University to update the [wastewater dashboard](/dashboards/wastewater/). The group have been working to test a new method for the quantification of SARS-CoV-2 and enteric viruses in wastewater. The group have been examining the levels of viruses in Gothenburg's wastewater for many years, including before the pandemic. In 2023, they began to collaborate directly with the portal in order to be able to share their data in near-real time. From bd174629367db572106ac365a05e03433e3b7a9f Mon Sep 17 00:00:00 2001 From: LianeHughes <68756672+LianeHughes@users.noreply.github.com> Date: Fri, 19 Jan 2024 07:39:48 +0100 Subject: [PATCH 5/5] Fix title --- content/english/highlights/covimapp.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/content/english/highlights/covimapp.md b/content/english/highlights/covimapp.md index 91163c703..6a50f505c 100644 --- a/content/english/highlights/covimapp.md +++ b/content/english/highlights/covimapp.md @@ -1,5 +1,5 @@ --- -title: CoViMAPP – analysing changes in soluble blood proteome alterations due to COVID-19 +title: CoViMAPP – analysing changes in the soluble blood proteome due to COVID-19 date: 2024-01-19 summary: Babačić and colleagues expanded the coverage of the soluble blood proteome using mass spectrometry. In order to support further research in this area, their results have been added to an open-access app. banner: /highlights/banners/covimapp_logo.png