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@article{Chevrier2017,
title = {Compensation of Signal Spillover in Suspension and Imaging Mass Cytometry},
author = "Chevrier, Stéphane and Crowell, Helena L. and Zanotelli, Vito R.T. and Engler, Stefanie and Robinson, Mark D. and Bodenmiller, Bernd",
journal = "Cell Systems",
volume = 6,
pages = "612--620",
year = 2017
}
@article{Bendall2011,
title = {Single-cell mass cytometry of differential immune and drug responses across a human hematopoietic continuum},
author = "Bendall, Sean C. and Simonds, Erin F. and Qiu, Peng and Amir, El Ad D. and Krutzik, Peter O. and Finck, Rachel and Bruggner, Robert V. and Melamed, Rachel and Trejo, Angelica and Ornatsky, Olga I. and Balderas, Robert S. and Plevritis, Sylvia K. and Sachs, Karen and Pe'er, Dana and Tanner, Scott D. and Nolan, Garry P.",
journal = "Science",
volume = 332,
pages = "687--696",
year = 2011
}
@article{Giesen2014,
Author = {Giesen, Charlotte and Wang, Hao A.O. and Schapiro, Denis and Zivanovic, Nevena and Jacobs, Andrea and Hattendorf, Bodo and Schüffler, Peter J. and Grolimund, Daniel and Buhmann, Joachim M. and Brandt, Simone and Varga, Zsuzsanna and Wild, Peter J. and Günther, Detlef and Bodenmiller, Bernd},
Journal = {Nature {M}ethods},
Number = {4},
Pages = {417-422},
Title = {Highly multiplexed imaging of tumor tissues with subcellular resolution by mass cytometry},
Volume = {11},
Year = {2014}
}
@article{Schulz2018,
title = {Simultaneous Multiplexed Imaging of mRNA and Proteins with Subcellular Resolution in Breast Cancer Tissue Samples by Mass Cytometry.},
author = "Schulz, Daniel and Zanotelli, Vito RT and Fischer, Rana R and Schapiro, Denis and Engler, Stefanie and Lun, Xiao-Kang and Jackson, Hartland W and Bodenmiller, Bernd",
journal = "Cell Systems",
volume = 6,
pages = "25--36.e5",
year = 2018
}
@article{Shapiro2017,
title = {histoCAT: analysis of cell phenotypes and interactions in multiplex image cytometry data.},
author = "Schapiro, Denis and Jackson, Hartland W and Raghuraman, Swetha and Fischer, Jana R and Zanotelli, Vito RT and Schulz, Daniel and Giesen, Charlotte and Catena, Raúl and Varga, Zsuzsanna and Bodenmiller, Bernd",
journal = "Nature Methods",
volume = 14,
pages = "873–-876",
year = 2017
}
@article{Angelo2014,
Author = {Angelo, Michael and Bendall, Sean C. and Finck, Rachel and Hale, Matthew B. and Hitzman, Chuck and Borowsky, Alexander D. and Levenson, Richard M. and Lowe, John B. and Liu, Scot D. and Zhao, Shuchun and Natkunam, Yasodha and Nolan, Garry P.},
Journal = {Nature Medicine},
Number = {4},
Pages = {436-442},
Title = {Multiplexed ion beam imaging of human breast tumors},
Volume = {20},
Year = {2014}
}
@article{Lin2018,
Author = {Lin, Jia-Ren and Izar, Benjamin and Wang, Shu and Yapp, Clarence and Mei, Shaolin and Shah, Parin M. and Santagata, Sandro and Sorger, Peter K.},
Journal = {eLife},
Pages = {1-46},
Title = {Highly multiplexed immunofluorescence imaging of human tissues and tumors using t-CyCIF and conventional optical microscopes},
Volume = {7},
Year = {2018}
}
@article{Gut2018,
Author = {Gut, Gabriele and Herrmann, Markus D and Pelkmans, Lucas},
Journal = {Science},
Pages = {1-13},
Title = {Multiplexed protein maps link subcellular organization to cellular states},
Volume = {361},
Year = {2018}
}
@article{Bodenmiller2016,
Author = {Bodenmiller, Bernd},
Journal = {Cell Systems},
Pages = {225-238},
Title = {Multiplexed Epitope-Based Tissue Imaging for Discovery and Healthcare Applications},
Volume = {2},
Year = {2016}
}
@article{Chen2015,
Author = {Chen, Kok Hao and Boettiger, Alistair N. and Moffitt, Jeffrey R. and Wang, Siyuan and Zhuang, Xiaowei},
Journal = {Science},
Pages = {aaa6090},
Title = {Spatially resolved, highly multiplexed RNA profiling in single cells},
Volume = {348},
Year = {2015}
}
@article{Greenwald2021,
Author = {Greenwald, Noah F and Miller, Geneva and Moen, Erick and Kong, Alex and Kagel, Adam and Camacho, Christine and Mcintosh, Brianna J and Leow, Ke and Schwartz, Morgan Sarah and Dougherty, Thomas and Cui, Sunny and Camplisson, Isabella and Bar-tal, Omer and Singh, Jaiveer and Fong, Mara and Chaudhry, Gautam and Abraham, Zion and Moseley, Jackson and Warshawsky, Shiri and Soon, Erin and Greenbaum, Shirley and Risom, Tyler and Hollmann, Travis and Keren, Leeat and Graf, Will and Angelo, Michael and Valen, David Van},
Journal = {bioRxiv},
Pages = {1-29},
Title = {Whole-cell segmentation of tissue images with human-level performance using large-scale data annotation and deep learning},
Year = {2021}
}
@article{Lubeck2014,
Author = {Lubeck, Eric and Coskun, Ahmet F and Zhiyentayev, Timur and Ahmad, Mubhij and Cai, Long},
Journal = {Nature Methods},
Pages = {360-361},
Title = {Single-cell in situ RNA profiling by sequential hybridization},
Volume = {11},
Year = {2014}
}
@article{Goltsev2018,
Author = {Goltsev, Yury and Samusik, Nikolay and Kennedy-Darling, Julia and Bhate, Salil and Hale, Matthew and Vazquez, Gustavo and Black, Sarah and Nolan, Garry P.},
Journal = {Cell},
Pages = {968--981},
Title = {Deep Profiling of Mouse Splenic Architecture with CODEX Multiplexed Imaging},
Volume = {174},
Year = {2018}
}
@article{Saka2019,
Author = {Saka, Sinem K. and Wang, Yu and Kishi, Jocelyn Y. and Zhu, Allen and Zeng, Yitian and Xie, Wenxin and Kirli, Koray and Yapp, Clarence and Cicconet, Marcelo and Beliveau, Brian J. and Lapan, Sylvain W. and Yin, Siyuan and Lin, Millicent and Boyden, Edward S. and Kaeser, Pascal S. and Pihan, German and Church, George M. and Yin, Peng},
Journal = {Nature Biotechnology},
Pages = {1080--1090},
Title = {Immuno-SABER enables highly multiplexed and amplified protein imaging in tissues},
Volume = {37},
Year = {2019}
}
@article{Ijsselsteijn2019,
year = {2019},
volume = {10},
author = {Ijsselsteijn, Marieke E. and van der Breggen, Ruud and Sarasqueta, Arantza F. and Koning, Frits and de Miranda, Noel F. C. C.},
title = {A 40-Marker Panel for High Dimensional Characterization of Cancer Immune Microenvironments by Imaging Mass Cytometry},
journal = {Frontiers in Immunology}
}
@article{Windhager2021,
year = {2021},
journal = {bioRxiv},
author = {Windhager,Jonas and Bodenmiller, Bernd and Eling, Nils},
title = {An end-to-end workflow for multiplexed image processing and analysis}
}
@article{Wolf2018,
year = {2018},
volume = {19},
author = {Wolf, Alexander F. and Angerer, Philipp and Theis, Fabian J.},
title = {{SCANPY}: large-scale single-cell gene expression data analysis},
journal = {Genome Biology}
}
@article{Shannon2003,
year = {2003},
volume = {13},
pages = {2498--2504},
author = {Shannon, Paul and Markiel, Andrew and Ozier, Owen and Baliga, Nitin S. and Wang, Jonathan T. and Ramage, Daniel and Amin, Nada and Schwikowski, Benno and Ideker, Trey},
title = {Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks},
journal = {Genome Research}
}
@article{Amezquita2019,
year = {2019},
volume = {17},
pages = {137--145},
author = {Amezquita, Robert A. and Lun, Aaron T. L. and Becht, Etienne and Carey, Vince J. and Carpp, Lindsay N. and Geistlinger, Ludwig and Marini, Federico and Rue-Albrecht, Kevin and Risso, Davide and Soneson, Charlotte and Waldron, Levi and Pag{\`{e}}s, Herv{\'{e}} and Smith, Mike L. and Huber, Wolfgang and Morgan, Martin and Gottardo, Raphael and Hicks, Stephanie C.},
title = {Orchestrating single-cell analysis with Bioconductor},
journal = {Nature Methods}
}
@article{Righelli2021,
year = {2021},
author = {Righelli, Dario and Weber, Lukas M. and Crowell, Helena L. and Pardo, Brenda and Collado-Torres, Leonardo and Ghazanfar, Shila and Lun, Aaron T. L. and Hicks, Stephanie C. and Risso, Davide},
title = {{SpatialExperiment}: infrastructure for spatially resolved transcriptomics data in R using Bioconductor},
journal = {bioRxiv}
}
@article{Haghverdi2018,
year = {2018},
volume = {36},
pages = {421--427},
author = {Haghverdi, Laleh and Lun, Aaron T. L. and Morgan, Michael D. and Marioni, John C.},
title = {Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors},
journal = {Nature Biotechnology}
}
@article{Korsunsky2019,
year = {2019},
volume = {16},
pages = {1289--1296},
author = {Korsunsky, Ilya and Millard, Nghia and Fan, Jean and Slowikowski, Kamil and Zhang, Fan and Wei, Kevin and Baglaenko, Yuriy and Brenner, Michael and Loh, Po-ru and Raychaudhuri, Soumya},
title = {Fast, sensitive and accurate integration of single-cell data with Harmony},
journal = {Nature Methods}
}
@article{Stuart2019,
year = {2019},
volume = {177},
pages = {1888--1902},
author = {Stuart, Tim and Butler, Andrew and Hoffman, Paul and Hafemeister, Christoph and Papalexi, Efthymia and Mauck, William M. III and Hao, Yuhan and Stoeckius, Marlon and Smibert, Peter and Satija, Rahul},
title = {Comprehensive Integration of Single-Cell Data},
journal = {Cell}
}
@article{Bai2021,
year = {2021},
volume = {12},
author = {Bai, Yunhao and Zhu, Bokai and Rovira-Clave, Xavier and Chen, Han and Markovic, Maxim and Chan, Chi Ngai and Su, Tung-Hung and McIlwain, David R. and Estes, Jacob D. and Keren, Leeat and Nolan, Garry P. and Jiang, Sizun},
title = {Adjacent Cell Marker Lateral Spillover Compensation and Reinforcement for Multiplexed Images},
journal = {Frontiers in Immunology}
}
@article{Hoch2022,
year = {2022},
author = {Hoch, Tobias and Schulz, Daniel and Eling, Nils and Gómez, Julia Martínez and Levesque, Mitchell P. and Bodenmiller, Bernd},
title = {Multiplexed imaging mass cytometry of the chemokine milieus in melanoma characterizes features of the response to immunotherapy},
journal = {Science Immunology},
volume = {7},
number = {70},
pages = {eabk1692},
year = {2022},
doi = {10.1126/sciimmunol.abk1692},
}
@article{Weber2016,
year = {2016},
volume = {89A},
pages = {1084--1096},
author = {Weber, Lukas M. and Robinson, Mark D.},
title = {Comparison of Clustering Methods for High-Dimensional Single-Cell Flow and Mass Cytometry Data},
journal = {Cytometry Part A}
}
@article{Levine2015,
year = {2015},
volume = {162},
pages = {184--197},
author = {Levine, Jacob H. and Simonds, Erin F. and Bendall, Sean C. and Davis, Kara L. and Amir, El-ad D. and Tadmor, Michelle D. and Litvin, Oren and Fienberg, Harris G. and Jager, Astraea and Zunder, Eli R. and Finck, Rachel and Gedman, Amanda L. and Radtke, Ina and
Downing, James R. and Pe’er, Dana and Nolan, Garry P.},
title = {Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis},
journal = {Cell}
}
@article{Jackson2020,
year = {2020},
volume = {578},
pages = {615--620},
author = {Jackson, Hartland W. and Fischer, Jana R. and Zanotelli, Vito R. T. and Ali, H. Raza and Mechera, Robert and Soysal, Savas D. and Moch, Holger and Muenst, Simone and Varga, Zsuzsanna and Weber, Walter P. and Bodenmiller, Bernd},
title = {The single-cell pathology landscape of breast cancer},
journal = {Nature}
}
@article{Tietscher2022,
year = {2022},
author = {Tietscher, Sandra and Wagner, Johanna and Anzeneder, Tobias and
Langwieder, Claus and Rees, Martin and Sobottka, Bettina and de Souza, Natalie
and Bodenmiller, Bernd},
title = {A comprehensive single-cell map of T cell exhaustion-associated immune environments in human breast cancer},
journal = {Research Square}
}
@article{Yu2022,
doi = {10.1186/s13059-022-02622-0},
url = {https://doi.org/10.1186/s13059-022-02622-0},
year = {2022},
volume = {23},
number = {1},
author = {Yu, Lijia and Cao, Yue and Yang, Jean Y. H. and Yang, Pengyi},
title = {Benchmarking clustering algorithms on estimating the number of cell types from single-cell {RNA}-sequencing data},
journal = {Genome Biology}
}
@article{Eling2020,
doi = {10.1093/bioinformatics/btaa1061},
url = {https://doi.org/10.1093/bioinformatics/btaa1061},
year = {2020},
volume = {36},
pages = {5706–-5708},
number = {24},
author = {Eling, Nils and Damond, Nicolas and Hoch, Tobias and Bodenmiller, Bernd},
title = {cytomapper: an R/Bioconductor package for visualization of highly multiplexed imaging data},
journal = {Bioinformatics}
}
@article{Schurch2020,
year = {2020},
volume = {182},
pages = {1341--1359},
author = {Schürch, Christian M and Bhate, Salil S and Barlow, Graham L and Phillips, Darci J and Noti, Luca and Zlobec, Inti and Chu, Pauline and Black, Sarah and Demeter, Janos and Mcilwain, David R and Kinoshita, Shigemi and Samusik, Nikolay and Goltsev, Yury and Nolan, Garry P},
title = {Coordinated Cellular Neighborhoods Orchestrate Antitumoral Immunity at the Colorectal Cancer Invasive Front},
journal = {Cell}
}
@article{Patrick2021,
year = {2021},
author = {Patrick, Ellis and Canete, Nicolas P. and Iyengar, Sourish S. and Harman, Andrew N. and Sutherland, Greg T. and Yang, Pengyi},
title = {Spatial analysis for highly multiplexed imaging data to identify tissue microenvironments},
journal = {bioRxiv}
}
@article{Bhate2022,
author = {Salil S. Bhate and Graham L. Barlow and Christian M. Schürch and Garry P. Nolan},
journal = {Cell Systems},
number = {2},
pages = {109-130},
title = {Tissue schematics map the specialization of immune tissue motifs and their appropriation by tumors},
volume = {13},
year = {2022}
}
@article{Gu2016,
author = {Zuguang Gu and Roland Eils and Matthias Schlesner},
journal = {Bioinformatics},
pages = {2847–2849},
title = {Complex heatmaps reveal patterns and correlations in multidimensional genomic data},
volume = {32},
year = {2016}
}