pubs.bib

@article{chang_2017,
  author          = {Chang, Hsiao-Han AND Worby, Colin J. AND Yeka, Adoke AND
                  Nankabirwa, Joaniter AND Kamya, Moses R. AND Staedke, Sarah G.
                  AND Dorsey, Grant AND Murphy, Maxwell AND Neafsey, Daniel E.
                  AND Jeffreys, Anna E. AND Hubbart, Christina AND Rockett, Kirk
                  A. AND Amato, Roberto AND Kwiatkowski, Dominic P. AND Buckee,
                  Caroline O. AND Greenhouse, Bryan},
  journal         = {PLOS Computational Biology},
  publisher       = {Public Library of Science},
  title           = {THE REAL McCOIL: A method for the concurrent estimation of
                  the complexity of infection and SNP allele frequency for
                  malaria parasites},
  year            = 2017,
  month           = 01,
  volume          = 13,
  url             = {https://doi.org/10.1371/journal.pcbi.1005348},
  pages           = {1-18},
  number          = 1,
  doi             = {10.1371/journal.pcbi.1005348}
}

@article{chen_2018,
  author          = {Chen, Ingrid and Diawara, Halimatou and Mahamar,
                  Almahamoudou and Sanogo, Koualy and Keita, Sekouba and Kone,
                  Daouda and Diarra, Kalifa and Djimde, Moussa and Keita,
                  Mohamed and Brown, Joelle and Roh, Michelle E and Hwang, Jimee
                  and Pett, Helmi and Murphy, Maxwell and Niemi, Mikko and
                  Greenhouse, Bryan and Bousema, Teun and Gosling, Roly and
                  Dicko, Alassane},
  title           = "{Safety of Single-Dose Primaquine in G6PD-Deficient and
                  G6PD-Normal Males in Mali Without Malaria: An Open-Label,
                  Phase 1, Dose-Adjustment Trial}",
  journal         = {The Journal of Infectious Diseases},
  volume          = 217,
  number          = 8,
  pages           = {1298-1308},
  year            = 2018,
  month           = 01,
  issn            = {0022-1899},
  doi             = {10.1093/infdis/jiy014},
  url             = {https://doi.org/10.1093/infdis/jiy014},
}

@article{coutrier_2018,
  key             = {publication},
  title           = {Laboratory challenges of Plasmodium species identification
                  in Aceh Province, Indonesia, a malaria elimination setting
                  with newly discovered P. knowlesi.},
  author          = {Coutrier, Farah N and Tirta, Yusrifar K and Cotter, Chris
                  and Zarlinda, Iska and González, Iveth J and Schwartz, Alanna
                  and Maneh, Cut and Marfurt, Jutta and Murphy, Maxwell and
                  Herdiana, Herdiana and Anstey, Nicholas M and Greenhouse,
                  Bryan and Hsiang, Michelle S and Noviyanti, Rintis},
  url             = {http://dx.doi.org/10.1371/journal.pntd.0006924},
  year            = 2018,
  month           = 11,
  journal         = {PLoS Neglected Tropical Diseases},
  volume          = 12,
  number          = 11,
  doi             = {10.1371/journal.pntd.0006924},
  pmid            = 30500828,
  pmcid           = {PMC6291163},
  abstract        = {The discovery of the life-threatening zoonotic infection
                  Plasmodium knowlesi has added to the challenges of prompt and
                  accurate malaria diagnosis and surveillance. In this study
                  from Aceh Province, Indonesia, a malaria elimination setting
                  where P. knowlesi endemicity was not previously known, we
                  report the laboratory investigation and difficulties
                  encountered when using molecular detection methods for quality
                  assurance of microscopically identified clinical cases. From
                  2014 to 2015, 20 (49\%) P. falciparum, 16 (39\%) P. vivax, 3
                  (7\%) P. malariae, and 2 (5\%) indeterminate species were
                  identified by microscopy from four sentinel health facilities.
                  At a provincial-level reference laboratory, loop-mediated
                  isothermal amplification ({LAMP}), a field-friendly molecular
                  method, was performed and confirmed Plasmodium in all samples
                  though further species-identification was limited by the
                  unavailability of non-falciparum species-specific testing with
                  the platform used. At a national reference laboratory, several
                  molecular methods including nested {PCR} ({nPCR}) targeting
                  the 18 small sub-unit ({18S}) ribosomal {RNA}, {nPCR}
                  targeting the cytochrome-b (cytb) gene, a P. knowlesi-specific
                  {nPCR}, and finally sequencing, were necessary to ultimately
                  classify the samples as: 19 (46\%) P. knowlesi, 8 (20\%) P.
                  falciparum, 14 (34\%) P. vivax. Microscopy was unable to
                  identify or mis-classified up to 56\% of confirmed cases,
                  including all cases of P. knowlesi. With the {nPCR} methods
                  targeting the four human-only species, P. knowlesi was missed
                  ({18S} {rRNA} method) or showed cross-reactivity for P. vivax
                  (cytb method). To facilitate diagnosis and management of
                  potentially fatal P. knowlesi infection and surveillance for
                  elimination of human-only malaria in Indonesia and other
                  affected settings, new detection methods are needed for
                  testing at the point-of-care and in local reference
                  laboratories.}
}

@article{das_2017,
  author          = "Das, Smita and Jang, Ihn Kyung and Barney, Becky and Peck,
                  Roger and Rek, John C. and Arinaitwe, Emmanuel and Adrama,
                  Harriet and Murphy, Maxwell and Imwong, Mallika and Ling,
                  Clare L. and Proux, Stephane and Haohankhunnatham, Warat and
                  Rist, Melissa and Seilie, Annette M. and Hanron, Amelia and
                  Daza, Glenda and Chang, Ming and Nakamura, Tomoka and Kalnoky,
                  Michael and Labarre, Paul and Murphy, Sean C. and McCarthy,
                  James S. and Nosten, Francois and Greenhouse, Bryan and
                  Allauzen, Sophie and Domingo, Gonzalo J.",
  title           = "Performance of a High-Sensitivity Rapid Diagnostic Test for
                  Plasmodium falciparum Malaria in Asymptomatic Individuals from
                  Uganda and Myanmar and Naive Human Challenge Infections",
  journal         = "The American Journal of Tropical Medicine and Hygiene",
  year            = 2017,
  volume          = 97,
  number          = 5,
  pages           = "1540-1550",
  doi             = "https://doi.org/10.4269/ajtmh.17-0245",
  url             =
                  "http://www.ajtmh.org/content/journals/10.4269/ajtmh.17-0245",
  publisher       = "The American Society of Tropical Medicine and Hygiene",
  issn            = "0002-9637",
  type            = "Journal Article"
}

@inproceedings{hamre2016changes,
  title           = {Changes in population genetic parameters of Plasmodium
                  falciparum before and after a period of low or interrupted
                  malaria transmission in Kenyan highlands},
  author          = {Hamre, Karen E.S. and Tessema, Sofonias K. and Murphy,
                  Maxwell and Ayodo, George and Tran, Tuan M. and Schwartz,
                  Alanna and John, Chandy C. and Greenhouse, Bryan},
  booktitle       = {American Journal of Tropical Medicine and Hygiene},
  year            = 2016,
  organization    = {American Society of Tropical Medicine and Hygiene},
  key             = {poster}
}

@article{hsiang2020active,
  author          = {Hsiang, Michelle S and Ntshalintshali, Nyasatu and Kang
                  Dufour, Mi-Suk and Dlamini, Nomcebo and Nhlabathi, Nomcebo and
                  Vilakati, Sibonakaliso and Malambe, Calsile and Zulu, Zulisile
                  and Maphalala, Gugu and Novotny, Joseph and Murphy, Maxwell
                  and Schwartz, Alanna and Sturrock, Hugh and Gosling, Roly and
                  Dorsey, Grant and Kunene, Simon and Greenhouse, Bryan},
  title           = "{Active Case Finding for Malaria: A 3-Year National
                  Evaluation of Optimal Approaches to Detect Infections and
                  Hotspots Through Reactive Case Detection in the
                  Low-transmission Setting of Eswatini}",
  journal         = {Clinical Infectious Diseases},
  volume          = 70,
  number          = 7,
  pages           = {1316-1325},
  year            = 2019,
  month           = 05,
  issn            = {1058-4838},
  doi             = {10.1093/cid/ciz403},
  url             = {https://doi.org/10.1093/cid/ciz403},
}

@article{huber2020inferring,
  title           = {Inferring person-to-person networks of pathogen
                  transmission: is routine surveillance data up to the task?},
  author          = {Huber, John H and Hsiang, Michelle S and Dlamini, Nomcebo
                  and Murphy, Maxwell and Vilakati, Sibonakaliso and Nhlabathi,
                  Nomcebo and Lerch, Anita and Nielsen, Rasmus and
                  Ntshalintshali, Nyasatu and Greenhouse, Bryan and others},
  journal         = {medRxiv},
  year            = 2020,
  publisher       = {Cold Spring Harbor Laboratory Press}
}

@inproceedings{jang2017development,
  title           = {Development of a Multiplex Assay for Simultaneous
                  Quantification of Plasmodium Vivax and P. Falciparum
                  Infection},
  author          = {Jang, Ihn Kyung E and Kahn, Maria and Barney, Becky and
                  Kalnoky, Michael and Das, Smita and Peck, Roger and Tyler,
                  Abby and Lyman, Chris and Rek, John and Murphy, Maxwell and
                  others},
  booktitle       = {American Journal of Tropical Medicine and Hygiene},
  year            = 2017,
  organization    = {American Society of Tropical Medicine and Hygiene},
  key             = {poster}
}

@article{jang2020multiplex,
  author          = "Jang, Ihn Kyung and Tyler, Abby and Lyman, Chris and Rek,
                  John C. and Arinaitwe, Emmanuel and Adrama, Harriet and
                  Murphy, Maxwell and Imwong, Mallika and Proux, Stephane and
                  Haohankhunnatham, Warat and Barney, Rebecca and Rashid, Andrew
                  and Kalnoky, Michael and Kahn, Maria and Golden, Allison and
                  Nosten, François and Greenhouse, Bryan and Gamboa, Dionicia
                  and Domingo, Gonzalo J.",
  title           = "Multiplex Human Malaria Array: Quantifying Antigens for
                  Malaria Rapid Diagnostics",
  journal         = "The American Journal of Tropical Medicine and Hygiene",
  issn            = "0002-9637",
  year            = 2020,
  publisher       = "The American Society of Tropical Medicine and Hygiene",
  url             =
                  "https://www.ajtmh.org/content/journals/10.4269/ajtmh.19-0763",
  doi             = "https://doi.org/10.4269/ajtmh.19-0763"
}

@article{jang2021assessment,
  title           = {Assessment of Plasmodium antigens and CRP in dried blood
                  spots with multiplex malaria array},
  author          = {Jang, Ihn Kyung and Aranda, Sara and Barney, Rebecca and
                  Rashid, Andrew and Helwany, Muhammad and Rek, John C and
                  Arinaitwe, Emmanuel and Adrama, Harriet and Murphy, Maxwell
                  and Imwong, Mallika and others},
  journal         = {Journal of Parasitic Diseases},
  pages           = {1--11},
  year            = 2021,
  publisher       = {Springer India}
}

@article{jang_2018,
  key             = {publication},
  title           = {A new highly sensitive enzyme-linked immunosorbent assay
                  for the detection of Plasmodium falciparum histidine-rich
                  protein 2 in whole blood.},
  author          = {Jang, Ihn Kyung and Das, Smita and Barney, Rebecca S and
                  Peck, Roger B and Rashid, Andrew and Proux, Stephane and
                  Arinaitwe, Emmanuel and Rek, John and Murphy, Maxwell and
                  Bowers, Katherine and Boadi, Samuel and Watson, Julie and
                  Nosten, Francois and Greenhouse, Bryan and Chiodini, Peter L
                  and Domingo, Gonzalo J},
  url             = {http://dx.doi.org/10.1186/s12936-018-2545-5},
  year            = 2018,
  month           = 11,
  journal         = {Malaria Journal},
  volume          = 17,
  number          = 1,
  doi             = {10.1186/s12936-018-2545-5},
  pmid            = 30384849,
  pmcid           = {PMC6211401},
}

@article{jang_2018a,
  author          = {Jang, Ihn Kyung and Tyler, Abby and Lyman, Chris and Kahn,
                  Maria and Kalnoky, Michael and Rek, John C. and Arinaitwe,
                  Emmanuel and Adrama, Harriet and Murphy, Maxwell and Imwong,
                  Mallika and Ling, Clare L. and Proux, Stephane and
                  Haohankhunnatham, Warat and Rist, Melissa and Seilie, Annette
                  M. and Hanron, Amelia and Daza, Glenda and Chang, Ming and
                  Das, Smita and Barney, Rebecca and Rashid, Andrew and Landier,
                  Jordi and Boyle, David S. and Murphy, Sean C. and McCarthy,
                  James S. and Nosten, Fran{\c c}ois and Greenhouse, Bryan and
                  Domingo, Gonzalo J.},
  editor          = {Loeffelholz, Michael J.},
  title           = {Simultaneous Quantification of Plasmodium Antigens and Host
                  Factor C-Reactive Protein in Asymptomatic Individuals with
                  Confirmed Malaria by Use of a Novel Multiplex Immunoassay},
  volume          = 57,
  number          = 1,
  elocation-id    = {e00948-18},
  year            = 2019,
  doi             = {10.1128/JCM.00948-18},
  publisher       = {American Society for Microbiology Journals},
  abstract        = {Malaria rapid diagnostic tests (RDTs) primarily detect
                  Plasmodium falciparum antigen histidine-rich protein 2 (HRP2)
                  and the malaria-conserved antigen lactate dehydrogenase (LDH)
                  for P. vivax and other malaria species. The performance of
                  RDTs and their utility is dependent on circulating antigen
                  concentration distributions in infected individuals in a
                  population in which malaria is endemic and on the limit of
                  detection of the RDT for the antigens. A multiplexed
                  immunoassay for the quantification of HRP2, P. vivax LDH, and
                  all-malaria LDH (pan LDH) was developed to accurately measure
                  circulating antigen concentration and antigen distribution in
                  a population with endemic malaria. The assay also measures
                  C-reactive protein (CRP) levels as an indicator of
                  inflammation. Validation was conducted with clinical specimens
                  from 397 asymptomatic donors from Myanmar and Uganda,
                  confirmed by PCR for infection, and from participants in
                  induced blood-stage malaria challenge studies. The assay lower
                  limits of detection for HRP2, pan LDH, P. vivax LDH, and CRP
                  were 0.2 pg/ml, 9.3 pg/ml, 1.5 pg/ml, and 26.6 ng/ml,
                  respectively. At thresholds for HRP2, pan LDH, and P. vivax
                  LDH of 2.3 pg/ml, 47.8 pg/ml, and 75.1 pg/ml, respectively,
                  and a specificity >=98.5\%, the sensitivities for
                  ultrasensitive PCR-confirmed infections were 93.4\%, 84.9\%,
                  and 48.9\%, respectively. Plasmodium LDH (pLDH) concentration,
                  in contrast to that of HRP2, correlated closely with parasite
                  density. CRP levels were moderately higher in P. falciparum
                  infections with confirmed antigenemia versus those in clinical
                  specimens with no antigen. The 4-plex array is a sensitive
                  tool for quantifying diagnostic antigens in malaria infections
                  and supporting the evaluation of new ultrasensitive RDTs.},
  issn            = {0095-1137},
  URL             = {https://jcm.asm.org/content/57/1/e00948-18},
  journal         = {Journal of Clinical Microbiology}
}

@article{katrak_2017,
  author          = "Katrak, Shereen and Murphy, Maxwell and Nayebare, Patience
                  and Rek, John and Smith, Mary and Arinaitwe, Emmanuel and
                  Nankabirwa, Joaniter I. and Kamya, Moses and Dorsey, Grant and
                  Rosenthal, Philip J. and Greenhouse, Bryan",
  title           = "Performance of Loop-Mediated Isothermal Amplification for
                  the Identification of Submicroscopic Plasmodium falciparum
                  Infection in Uganda",
  journal         = "The American Journal of Tropical Medicine and Hygiene",
  year            = 2017,
  volume          = 97,
  number          = 6,
  pages           = "1777-1781",
  doi             = "https://doi.org/10.4269/ajtmh.17-0225",
  url             =
                  "http://www.ajtmh.org/content/journals/10.4269/ajtmh.17-0225",
  publisher       = "The American Society of Tropical Medicine and Hygiene",
  issn            = "0002-9637",
  type            = "Journal Article",
}

@inproceedings{kuchta2017cas,
  title           = {Cas-9 Based Sequencing Enrichment for Malaria Genotyping},
  author          = {Kuchta, Alison and Crawford, Emily and Quan, Jenai and
                  Wilheim, Jordan and Murphy, Maxwell and Tessema, Sofonias K
                  and Derisi, Joe and Greenhouse, Bryan},
  booktitle       = {American Journal of Tropical Medicine and Hygiene},
  year            = 2017,
  organization    = {American Society of Tropical Medicine and Hygiene},
  key             = {poster}
}

@inproceedings{kuchta2017population,
  title           = {Population Structure of Plasmoidum Falciparum is Detectable
                  at Small Spatial Scales in Kihihi, Uganda},
  author          = {Kuchta, Alison and Murphy, Maxwell and Arinaitwe, Emmanuel
                  and Rek, John and Chen, Anna and Wilheim, Jordan and Tessema,
                  Sofonias K and Bousema, Teun and Kamya, Moses and Staedke,
                  Sarah and others},
  booktitle       = {American Journal of Tropical Medicine and Hygiene},
  year            = 2017,
  organization    = {American Society of Tropical Medicine and Hygiene},
  key             = {poster}
}

@article{liu2020confirmation,
  title           = {Confirmation of the absence of local transmission and
                  geographic assignment of imported falciparum malaria cases to
                  China using microsatellite panel},
  author          = {Liu, Yaobao and Tessema, Sofonias K and Murphy, Maxwell and
                  Xu, Sui and Schwartz, Alanna and Wang, Weiming and Cao,
                  Yuanyuan and Lu, Feng and Tang, Jianxia and Gu, Yaping and
                  others},
  journal         = {Malaria journal},
  volume          = 19,
  number          = 1,
  pages           = {1--11},
  year            = 2020,
  publisher       = {BioMed Central}
}

@inproceedings{mccreesh2015identifying,
  title           = {Identifying risk factors for malaria in the Zambezi region
                  of Namibia: A cross-sectional study using rapid diagnostic
                  testing (RDT) and loop mediated isothermal amplification
                  (LAMP)},
  author          = {McCreesh, Patrick and Roberts, Kathryn and Tambo,
                  Munyaradzi and Bennett, Adam and Smith, Jennifer and Kelly,
                  Gerard and Cueto, Carmen and Moe, Caitlin and Haindongo,
                  Erastus Unity and Chisenga, Mukosha and Murphy, Maxwell and
                  Kleinschmidt, Immo and Sturrock, Hugh and Uusiku, Petrina and
                  Gosling, Roland and Mumbengegwi, Davis and Hsiang, Michelle},
  booktitle       = {American Journal of Tropical Medicine and Hygiene},
  year            = 2015,
  organization    = {American Society of Tropical Medicine and Hygiene},
  key             = {poster}
}

@article{mccreesh_2018,
  key             = {publication},
  title           = {Subpatent malaria in a low transmission African setting: a
                  cross-sectional study using rapid diagnostic testing ({RDT})
                  and loop-mediated isothermal amplification ({LAMP}) from
                  Zambezi region, Namibia.},
  author          = {{McCreesh}, Patrick and Mumbengegwi, Davis and Roberts,
                  Kathryn and Tambo, Munyaradzi and Smith, Jennifer and
                  Whittemore, Brooke and Kelly, Gerard and Moe, Caitlin and
                  Murphy, Maxwell and Chisenga, Mukosha and Greenhouse, Bryan
                  and Ntuku, Henry and Kleinschmidt, Immo and Sturrock, Hugh and
                  Uusiku, Petrina and Gosling, Roland and Bennett, Adam and
                  Hsiang, Michelle S},
  url             = {http://dx.doi.org/10.1186/s12936-018-2626-5},
  year            = 2018,
  month           = 12,
  journal         = {Malaria Journal},
  volume          = 17,
  number          = 1,
  doi             = {10.1186/s12936-018-2626-5},
  pmid            = 30567537,
  pmcid           = {PMC6299963},
}

@inproceedings{murphy2015automated,
  title           = {Automated Methods for High-Throughput Analysis of
                  Plasmodium Microsatellite Genotyping Data},
  author          = {Murphy, Maxwell and Schwartz, Alanna and Liu, Yaobao and
                  Kemere, Jordan and Hsiang, Michelle and Greenhouse, Bryan},
  booktitle       = {American Journal of Tropical Medicine and Hygiene},
  year            = 2015,
  organization    = {American Society of Tropical Medicine and Hygiene},
  key             = {poster}
}

@inproceedings{murphy2018geographic,
  title           = {Geographic assignment of P. falciparum and P. vivax
                  infections using genetic data},
  author          = {Murphy, Maxwell and Tessema, Sofonias and Mupiri,
                  Anna-Rossa and Tambo, Munyaradzi and Smith, Jennifer L. and
                  Bennett, Adam and Sturrock, Hugh J. and Gosling, Roland and
                  Mumbengegwi, Davis and Hsiang, Michelle S. and Noviyanti,
                  Rintis and Trimarsanto, Hidayat and Price, Ric and
                  Rodríguez-Barraquer, Isabel and Auburn, Sarah and Greenhouse,
                  Bryan},
  booktitle       = {American Journal of Tropical Medicine and Hygiene},
  year            = 2018,
  organization    = {American Society of Tropical Medicine and Hygiene},
  key             = {poster}
}

@article{pringle_2018,
  author          = {Pringle, Julia C and Tessema, Sofonias and Wesolowski, Amy
                  and Chen, Anna and Murphy, Maxwell and Carpi, Giovanna and
                  Shields, Timothy M and Hamapumbu, Harry and Searle, Kelly M
                  and Kobayashi, Tamaki and Katowa, Ben and Musonda, Michael and
                  Stevenson, Jennifer C and Thuma, Philip E and Greenhouse,
                  Bryan and Moss, William J and Norris, Douglas E},
  title           = "{Genetic Evidence of Focal Plasmodium falciparum
                  Transmission in a Pre-elimination Setting in Southern
                  Province, Zambia}",
  journal         = {The Journal of Infectious Diseases},
  volume          = 219,
  number          = 8,
  pages           = {1254-1263},
  year            = 2018,
  month           = 11,
  abstract        = "{Southern Province, Zambia has experienced a dramatic
                  decline in Plasmodium falciparum malaria transmission in the
                  past decade and is targeted for elimination. Zambia’s National
                  Malaria Elimination Program recommends reactive case detection
                  (RCD) within 140 m of index households to enhance surveillance
                  and eliminate remaining transmission foci.To evaluate whether
                  RCD captures local transmission, we genotyped 26
                  microsatellites from 106 samples collected from index (n = 27)
                  and secondary (n = 79) cases detected through RCD in the Macha
                  Hospital catchment area between January 2015 and April
                  2016.Participants from the same RCD event harbored more
                  genetically related parasites than those from different RCD
                  events, suggesting that RCD captures, at least in part,
                  infections related through local transmission. Related
                  parasites clustered in space and time, up to at least 250 m
                  from index households. Spatial analysis identified a putative
                  focal transmission hotspot.The current RCD strategy detects
                  focal transmission events, although programmatic guidelines to
                  screen within 140 m of index households may fail to capture
                  all secondary cases. This study highlights the utility of
                  parasite genetic data in assessing programmatic interventions,
                  and similar approaches may be useful to malaria elimination
                  programs seeking to tailor intervention strategies to the
                  underlying transmission epidemiology.}",
  issn            = {0022-1899},
  doi             = {10.1093/infdis/jiy640},
  url             = {https://doi.org/10.1093/infdis/jiy640},
}

@article{quan_2018,
  author          = {Quan, Jenai and Langelier, Charles and Kuchta, Alison and
                  Batson, Joshua and Teyssier, Noam and Lyden, Amy and Caldera,
                  Saharai and McGeever, Aaron and Dimitrov, Boris and King, Ryan
                  and Wilheim, Jordan and Murphy, Maxwell and Ares, Lara Pesce
                  and Travisano, Katherine A and Sit, Rene and Amato, Roberto
                  and Mumbengegwi, Davis R and Smith, Jennifer L and Bennett,
                  Adam and Gosling, Roly and Mourani, Peter M and Calfee,
                  Carolyn S and Neff, Norma F and Chow, Eric D and Kim, Peter S
                  and Greenhouse, Bryan and DeRisi, Joseph L and Crawford, Emily
                  D},
  title           = "{FLASH: a next-generation CRISPR diagnostic for multiplexed
                  detection of antimicrobial resistance sequences}",
  journal         = {Nucleic Acids Research},
  volume          = 47,
  number          = 14,
  pages           = {e83-e83},
  year            = 2019,
  month           = 05,
  abstract        = "{The growing prevalence of deadly microbes with resistance
                  to previously life-saving drug therapies is a dire threat to
                  human health. Detection of low abundance pathogen sequences
                  remains a challenge for metagenomic Next Generation Sequencing
                  (NGS). We introduce FLASH (Finding Low Abundance Sequences by
                  Hybridization), a next-generation CRISPR/Cas9 diagnostic
                  method that takes advantage of the efficiency, specificity and
                  flexibility of Cas9 to enrich for a programmed set of
                  sequences. FLASH-NGS achieves up to 5 orders of magnitude of
                  enrichment and sub-attomolar gene detection with minimal
                  background. We provide an open-source software tool (FLASHit)
                  for guide RNA design. Here we applied it to detection of
                  antimicrobial resistance genes in respiratory fluid and dried
                  blood spots, but FLASH-NGS is applicable to all areas that
                  rely on multiplex PCR.}",
  issn            = {0305-1048},
  doi             = {10.1093/nar/gkz418},
  url             = {https://doi.org/10.1093/nar/gkz418},
}

@article{ranadive_2017,
  author          = {Ranadive, Nikhil and Kunene, Simon and Darteh, Sarah and
                  Ntshalintshali, Nyasatu and Nhlabathi, Nomcebo and Dlamini,
                  Nomcebo and Chitundu, Stanley and Saini, Manik and Murphy,
                  Maxwell and Soble, Adam and Schwartz, Alanna and Greenhouse,
                  Bryan and Hsiang, Michelle S.},
  title           = "{Limitations of Rapid Diagnostic Testing in Patients with
                  Suspected Malaria: A Diagnostic Accuracy Evaluation from
                  Swaziland, a Low-Endemicity Country Aiming for Malaria
                  Elimination}",
  journal         = {Clinical Infectious Diseases},
  volume          = 64,
  number          = 9,
  pages           = {1221-1227},
  year            = 2017,
  month           = 03,
  issn            = {1058-4838},
  doi             = {10.1093/cid/cix131},
  url             = {https://doi.org/10.1093/cid/cix131},
}

@inproceedings{roh2016influence,
  title           = {Influence of Malaria Importation on P. falciparum
                  Population Genetic Diversity: A Study from Pre-elimination
                  Setting of Swaziland},
  author          = {Roh, Michelle and Murphy, Maxwell and Tessema, Sofonias and
                  Ntshalintshali, Nyasatu and Saini, Manik and Prach, Lisa and
                  Maphalala, Gugu and Nhlabathi, Nomcebo and Mkonta, Nomcebo and
                  Kunene, Simon and Hsiang, Michelle and Greenhouse, Bryan},
  booktitle       = {American Journal of Tropical Medicine and Hygiene},
  year            = 2016,
  organization    = {American Society of Tropical Medicine and Hygiene},
  key             = {poster}
}

@article{roh_2019,
  title           = {High Genetic Diversity of Plasmodium falciparum in the
                  Low-Transmission Setting of the Kingdom of Eswatini.},
  author          = {Roh, Michelle E and Tessema, Sofonias K and Murphy, Maxwell
                  and Nhlabathi, Nomcebo and Mkhonta, Nomcebo and Vilakati,
                  Sibonakaliso and Ntshalintshali, Nyasatu and Saini, Manik and
                  Maphalala, Gugu and Chen, Anna and Wilheim, Jordan and Prach,
                  Lisa and Gosling, Roly and Kunene, Simon and S Hsiang,
                  Michelle and Greenhouse, Bryan},
  pages           = {1346-1354},
  url             = {http://dx.doi.org/10.1093/infdis/jiz305},
  year            = 2019,
  month           = 9,
  day             = 13,
  urldate         = {2019-12-16},
  journal         = {J Infect Dis},
  volume          = 220,
  number          = 8,
  doi             = {10.1093/infdis/jiz305},
  pmid            = 31190073,
  pmcid           = {PMC6743842},
  f1000-projects  = {Your publications},
  abstract        = {{BACKGROUND}: To better understand transmission dynamics,
                  we characterized Plasmodium falciparum genetic diversity in
                  Eswatini, where transmission is low and sustained by
                  importation. {METHODS}: Twenty-six P. falciparum
                  microsatellites were genotyped in 66\% of confirmed cases
                  (2014-2016; N = 582). Population and within-host diversity
                  were used to characterize differences between imported and
                  locally acquired infections. Logistic regression was used to
                  assess the added value of diversity metrics to classify
                  imported and local infections beyond epidemiology data alone.
                  {RESULTS}: Parasite population in Eswatini was highly diverse
                  (expected heterozygosity [{HE}] = 0.75) and complex: 67\%
                  polyclonal infections, mean multiplicity of infection ({MOI})
                  2.2, and mean within-host infection fixation index ({FWS})
                  0.84. Imported cases had comparable diversity to local cases
                  but exhibited higher {MOI} (2.4 vs 2.0; P = .004) and lower
                  mean {FWS} (0.82 vs 0.85; P = .03). Addition of {MOI} and
                  {FWS} to multivariate analyses did not increase discrimination
                  between imported and local infections. {CONCLUSIONS}: In
                  contrast to the common perception that P. falciparum diversity
                  declines with decreasing transmission intensity, Eswatini
                  isolates exhibited high parasite diversity consistent with
                  high rates of malaria importation and limited local
                  transmission. Estimates of malaria transmission intensity from
                  genetic data need to consider the effect of importation,
                  especially as countries near elimination. \copyright The
                  Author(s) 2019. Published by Oxford University Press for the
                  Infectious Diseases Society of America.}
}

@inproceedings{sudathip2017malaria,
  title           = {Malaria elimination in Thailand: Using LAMP in reactive
                  case detection to increase infection detection.},
  author          = {Sudathip, Prayuth and Cotter, Chris and Kitchikarn,
                  Suravadee and Rattanapairoj, Orpreeya and Zelman, Brittany and
                  Maneesiri, Rachaneekorn and Sugaram, Rungniran and Schwartz,
                  Alanna and Murphy, Maxwell and Greenhouse, Bryan and Gonzalez,
                  Iveth J. and Vorster, Luna and Imwong, Mallika and Gosling,
                  Roly D. and Hsiang, Michelle S.},
  booktitle       = {American Journal of Tropical Medicine and Hygiene},
  year            = 2017,
  organization    = {American Society of Tropical Medicine and Hygiene},
  key             = {poster}
}

@article{taghavian_2018,
  author          = {Taghavian, Omid and Jain, Aarti and Joyner, Chester J. and
                  Ketchum, Sunny and Nakajima, Rie and Jasinskas, Algis and
                  Liang, Li and Fong, Rich and King, Christopher and Greenhouse,
                  Bryan and Murphy, Maxwell and Bailey, Jason and Galinski, Mary
                  R. and Barnwell, John W. and Plowe, Christopher V. and Davies,
                  D. Huw and Felgner, Philip L.},
  title           = {Antibody Profiling by Proteome Microarray with Multiplex
                  Isotype Detection Reveals Overlap between Human and Aotus
                  nancymaae Controlled Malaria Infections},
  journal         = {PROTEOMICS},
  volume          = 18,
  number          = 2,
  pages           = 1700277,
  keywords        = {antibody isotype, malaria, multiplex, protein microarray,
                  quantum dots},
  doi             = {10.1002/pmic.201700277},
  url             =
                  {https://onlinelibrary.wiley.com/doi/abs/10.1002/pmic.201700277},
  abstract        = {Abstract The development of vaccines against malaria and
                  serodiagnostic tests for detecting recent exposure requires
                  tools for antigen discovery and suitable animal models. The
                  protein microarray is a high-throughput, sample sparing
                  technique, with applications in infectious disease research,
                  clinical diagnostics, epidemiology, and vaccine development.
                  We recently demonstrated Qdot-based indirect
                  immunofluorescence together with portable optical imager
                  ArrayCAM using single isotype detection could replicate data
                  using the conventional laser confocal scanner system. We
                  developed a multiplexing protocol for simultaneous detection
                  of IgG, IgA, and IgM and compared samples from a controlled
                  human malaria infection model with those from controlled
                  malaria infections of Aotus nancymaae, a widely used non-human
                  primate model of human malaria. IgG profiles showed the
                  highest concordance in number of reactive antigens; thus, of
                  the 139 antigens recognized by human IgG antibody, 111 were
                  also recognized by Aotus monkeys. Interestingly, IgA profiles
                  were largely non-overlapping. Finally, on the path toward
                  wider deployment of the portable platform, we show excellent
                  correlations between array data obtained in five independent
                  laboratories around the United States using the multiplexing
                  protocol (R2: 0.60–0.92). This study supports the use of this
                  platform for wider deployment, particularly in endemic areas
                  where such a tool will have the greatest impact on global
                  human health.},
  year            = 2018
}

@inproceedings{tessema2017fine,
  title           = {Fine-Scale Population Genetics of Plasmoidum Falciparum in
                  Northern Namibia},
  author          = {Tessema, Sofonias and Murphy, Maxwell and Mupiri, Anna-Rosa
                  and Smith, Jennifer L and Chen, Anna and Wilheim, Jordan and
                  Hsiang, Michelle S and Sturrock, Hugh J and Mumbengegwi, Davis
                  and Greenhouse, Bryan},
  booktitle       = {American Journal of Tropical Medicine and Hygiene},
  year            = 2017,
  organization    = {American Society of Tropical Medicine and Hygiene},
  key             = {poster}
}

@article{tessema2020sensitive,
  author          = {Tessema, Sofonias K and Hathaway, Nicholas J and Teyssier,
                  Noam B and Murphy, Maxwell and Chen, Anna and Aydemir, Ozkan
                  and Duarte, Elias M and Simone, Wilson and Colborn, James and
                  Saute, Francisco and Crawford, Emily and Aide, Pedro and
                  Bailey, Jeffrey A and Greenhouse, Bryan},
  title           = {Sensitive, highly multiplexed sequencing of microhaplotypes
                  from the Plasmodium falciparum heterozygome},
  elocation-id    = {2020.02.25.964536},
  year            = 2020,
  doi             = {10.1101/2020.02.25.964536},
  publisher       = {Cold Spring Harbor Laboratory},
  URL             =
                  {https://www.biorxiv.org/content/early/2020/02/26/2020.02.25.964536},
  journal         = {bioRxiv}
}

@article{tessema_2019,
  title           = {Using parasite genetic and human mobility data to infer
                  local and cross-border malaria connectivity in Southern
                  Africa.},
  author          = {Tessema, Sofonias K and Wesolowski, Amy and Chen, Anna and
                  Murphy, Maxwell and Wilheim, Jordan and Mupiri, Anna-Rosa and
                  Ruktanonchai, Nick W and Alegana, Victor A and Tatem, Andrew J
                  and Tambo, Munyaradzi and Didier, Bradley and Cohen, Justin M
                  and Bennett, Adam and Sturrock, Hugh Jw and Gosling, Roland
                  and Hsiang, Michelle S and Smith, David L and Mumbengegwi,
                  Davis R and Smith, Jennifer L and Greenhouse, Bryan},
  url             = {http://dx.doi.org/10.7554/eLife.43510},
  year            = 2019,
  month           = 4,
  day             = 2,
  journal         = {eLife},
  volume          = 8,
  doi             = {10.7554/{eLife}.43510},
  pmid            = 30938286,
  pmcid           = {PMC6478435},
  f1000-projects  = {{PlasmoMap} and Your publications},
  abstract        = {Local and cross-border importation remain major challenges
                  to malaria elimination and are difficult to measure using
                  traditional surveillance data. To address this challenge, we
                  systematically collected parasite genetic data and travel
                  history from thousands of malaria cases across northeastern
                  Namibia and estimated human mobility from mobile phone data.
                  We observed strong fine-scale spatial structure in local
                  parasite populations, providing positive evidence that the
                  majority of cases were due to local transmission. This result
                  was largely consistent with estimates from mobile phone and
                  travel history data. However, genetic data identified more
                  detailed and extensive evidence of parasite connectivity over
                  hundreds of kilometers than the other data, within Namibia and
                  across the Angolan and Zambian borders. Our results provide a
                  framework for incorporating genetic data into malaria
                  surveillance and provide evidence that both strengthening of
                  local interventions and regional coordination are likely
                  necessary to eliminate malaria in this region of Southern
                  Africa. \copyright 2019, Tessema et al.}
}