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Fumio Nakaki, James Sharpe

Miles Richardson, Shijie Zhao, Liyuan Lin, Ravi U. Sheth, Yiming Qu, Jeongchan Lee, Thomas Moody, Deirdre Ricaurte, Yiming Huang, Florencia Velez-Cortes, Guillaume Urtecho, Harris H. Wang

Fengying Sun, Haoyan Li, Dongqing Sun, Shaliu Fu, Lei Gu, Xin Shao, Qinqin Wang, Xin Dong, Bin Duan, Feiyang Xing, Jun Wu, Minmin Xiao, Fangqing Zhao, Jing-Dong J. Han, Qi Liu, Xiaohui Fan, Chen Li, Chenfei Wang, Tieliu Shi

Dongsheng Bai, Zhenkun Cao, Nivedita Attada, Jinghui Song, Chenxu Zhu

Aidan Leckie-Harre, Isabel Silverman, Haojia Wu, Benjamin D. Humphreys, Andrew F. Malone

Efthalia Preka, Alejandro Lastra Romero, Ying Sun, Yara Onetti Vilalta, Thea Seitz, Adamantia Fragkopoulou, Christer Betsholtz, Ahmed M. Osman, Klas Blomgren

Chen Zhao, Ruowen Zhao, Xinwen Wu, Kailin Tang, Pan Xu, Xin Chen, Pingyi Zhu, Yuan He

Hao Zhang, Ryan M. Mulqueen, Natalie Iannuzo, Dominique O. Farrera, Francesca Polverino, James J. Galligan, Julie G. Ledford, Andrew C. Adey, Darren A. Cusanovich

Wenying Wang, Tianran Li, Yue Cheng, Fei Li, Shuhong Qi, Min Mao, Jingjing Wu, Qing Liu, Xiaoning Zhang, Xuegang Li, Lu Zhang, Haoyue Qi, Lan Yang, Kaidi Yang, Zhicheng He, Shuaishuai Ding, Zhongyi Qin, Ying Yang, Xi Yang, Chunhua Luo, Ying Guo, Chao Wang, Xindong Liu, Lei Zhou, Yuqi Liu, Weikai Kong, Jingya Miao, Shuanghui Ye, Min Luo, Lele An, Lujing Wang, Linrong Che, Qin Niu, Qinghua Ma, Xia Zhang, Zhihong Zhang, Rong Hu, Hua Feng, Yi-Fang Ping, Xiu-Wu Bian, Yu Shi

David J Bacsik, Bernadeta Dadonaite, Andrew Butler, Allison J Greaney, Nicholas S Heaton, Jesse D Bloom

Helle Rus Povlsen, Amalie Kai Bentzen, Mohammad Kadivar, Leon Eyrich Jessen, Sine Reker Hadrup, Morten Nielsen

Ryan McNulty, Duluxan Sritharan, Seong Ho Pahng, Jeffrey P. Meisch, Shichen Liu, Melanie A. Brennan, Gerda Saxer, Sahand Hormoz, Adam Z. Rosenthal

Anukriti Singh, Brian P. Hermann

David J Bacsik, Bernadeta Dadonaite, Andrew Butler, Allison J Greaney, Nicholas S Heaton, Jesse D Bloom

Muhammad Rahmad Royan, Khadeeja Siddique, Rasoul Nourizadeh-Lillabadi, Finn-Arne Weltzien, Christiaan Henkel, Romain Fontaine

Miia Riihimäki, Kim Fegraeus, Jessica Nordlund, Ida Waern, Sara Wernersson, Srinivas Akula, Lars Hellman, Amanda Raine

Pierre-Luc Germain, Aaron Lun, Carlos Garcia Meixide, Will Macnair, Mark D. Robinson

Gregory J Boggy, G W McElfresh, Eisa Mahyari, Abigail B Ventura, Scott G Hansen, Louis J Picker, Benjamin N Bimber

Nan Miles Xi, Jingyi Jessica Li

Pierre-Luc Germain, Aaron Lun, Will Macnair, Mark D. Robinson

Silvia Domcke, Andrew J. Hill, Riza M. Daza, Junyue Cao, Diana R. O’Day, Hannah A. Pliner, Kimberly A. Aldinger, Dmitry Pokholok, Fan Zhang, Jennifer H. Milbank, Michael A. Zager, Ian A. Glass, Frank J. Steemers, Dan Doherty, Cole Trapnell, Darren A. Cusanovich, Jay Shendure

Aline Fastrès, Dimitri Pirottin, Laurence Fievez, Alexandru-Cosmin Tutunaru, Géraldine Bolen, Anne-Christine Merveille, Thomas Marichal, Christophe J. Desmet, Fabrice Bureau, Cécile Clercx

Sydney B. Blattman, Wenyan Jiang, Panos Oikonomou, Saeed Tavazoie

Pierre-Luc Germain, Anthony Sonrel, Mark D. Robinson

Hongyi Xin, Qiuyu Lian, Yale Jiang, Jiadi Luo, Xinjun Wang, Carla Erb, Zhongli Xu, Xiaoyi Zhang, Elisa Heidrich-O’Hare, Qi Yan, Richard H. Duerr, Kong Chen, Wei Chen

Christopher S. McGinnis, Lyndsay M. Murrow, Zev J. Gartner

Daniel Osorio, Xue Yu, Peng Yu, Erchin Serpedin, James J. Cai

Alistair B. Russell, Elizaveta Elshina, Jacob R. Kowalsky, Aartjan J. W. te Velthuis, Jesse D. Bloom

Shinnosuke Suzuki, Victoria D Diaz, Brian P Hermann

2025	Probability of stealth multiplets in sample-multiplexing for droplet-based single-cell analysis BMC Genomics Fumio Nakaki, James Sharpe
2025	SAMPL-seq reveals micron-scale spatial hubs in the human gut microbiome Nature Microbiology Miles Richardson, Shijie Zhao, Liyuan Lin, Ravi U. Sheth, Yiming Qu, Jeongchan Lee, Thomas Moody, Deirdre Ricaurte, Yiming Huang, Florencia Velez-Cortes, Guillaume Urtecho, Harris H. Wang
2025	Single-cell omics: experimental workflow, data analyses and applications Science China Life Sciences Fengying Sun, Haoyan Li, Dongqing Sun, Shaliu Fu, Lei Gu, Xin Shao, Qinqin Wang, Xin Dong, Bin Duan, Feiyang Xing, Jun Wu, Minmin Xiao, Fangqing Zhao, Jing-Dong J. Han, Qi Liu, Xiaohui Fan, Chen Li, Chenfei Wang, Tieliu Shi
2025	Single-cell parallel analysis of DNA damage and transcriptome reveals selective genome vulnerability Nature Methods Dongsheng Bai, Zhenkun Cao, Nivedita Attada, Jinghui Song, Chenxu Zhu
2024	Sequencing of Physically Interacting Cells in Human Kidney Allograft Rejection to Infer Contact-dependent Immune Cell Transcription Transplantation Aidan Leckie-Harre, Isabel Silverman, Haojia Wu, Benjamin D. Humphreys, Andrew F. Malone
2024	Rapid and robust isolation of microglia and vascular cells from brain subregions for integrative single-cell analyses Heliyon Efthalia Preka, Alejandro Lastra Romero, Ying Sun, Yara Onetti Vilalta, Thea Seitz, Adamantia Fragkopoulou, Christer Betsholtz, Ahmed M. Osman, Klas Blomgren
2024	Function of unconventional T cells in oral lichen planus revealed by single-cell RNA sequencing Inflammation Research Chen Zhao, Ruowen Zhao, Xinwen Wu, Kailin Tang, Pan Xu, Xin Chen, Pingyi Zhu, Yuan He
2024	txci-ATAC-seq: a massive-scale single-cell technique to profile chromatin accessibility Genome Biology Hao Zhang, Ryan M. Mulqueen, Natalie Iannuzo, Dominique O. Farrera, Francesca Polverino, James J. Galligan, Julie G. Ledford, Andrew C. Adey, Darren A. Cusanovich
2024	Identification of hypoxic macrophages in glioblastoma with therapeutic potential for vasculature normalization Cancer Cell Wenying Wang, Tianran Li, Yue Cheng, Fei Li, Shuhong Qi, Min Mao, Jingjing Wu, Qing Liu, Xiaoning Zhang, Xuegang Li, Lu Zhang, Haoyue Qi, Lan Yang, Kaidi Yang, Zhicheng He, Shuaishuai Ding, Zhongyi Qin, Ying Yang, Xi Yang, Chunhua Luo, Ying Guo, Chao Wang, Xindong Liu, Lei Zhou, Yuqi Liu, Weikai Kong, Jingya Miao, Shuanghui Ye, Min Luo, Lele An, Lujing Wang, Linrong Che, Qin Niu, Qinghua Ma, Xia Zhang, Zhihong Zhang, Rong Hu, Hua Feng, Yi-Fang Ping, Xiu-Wu Bian, Yu Shi
2023	Influenza virus transcription and progeny production are poorly correlated in single cells eLife David J Bacsik, Bernadeta Dadonaite, Andrew Butler, Allison J Greaney, Nicholas S Heaton, Jesse D Bloom
2023	Improved T cell receptor antigen pairing through data-driven filtering of sequencing information from single cells eLife Helle Rus Povlsen, Amalie Kai Bentzen, Mohammad Kadivar, Leon Eyrich Jessen, Sine Reker Hadrup, Morten Nielsen
2023	Probe-based bacterial single-cell RNA sequencing predicts toxin regulation Nature Microbiology Ryan McNulty, Duluxan Sritharan, Seong Ho Pahng, Jeffrey P. Meisch, Shichen Liu, Melanie A. Brennan, Gerda Saxer, Sahand Hormoz, Adam Z. Rosenthal
2023	Methods in Molecular Biology Anukriti Singh, Brian P. Hermann
2023	Influenza virus transcription and progeny production are poorly correlated in single cells eLife David J Bacsik, Bernadeta Dadonaite, Andrew Butler, Allison J Greaney, Nicholas S Heaton, Jesse D Bloom
2023	Functional and developmental heterogeneity of pituitary lactotropes in medaka General and Comparative Endocrinology Muhammad Rahmad Royan, Khadeeja Siddique, Rasoul Nourizadeh-Lillabadi, Finn-Arne Weltzien, Christiaan Henkel, Romain Fontaine
2023	Single-cell transcriptomics delineates the immune cell landscape in equine lower airways and reveals upregulation of FKBP5 in horses with asthma Scientific Reports Miia Riihimäki, Kim Fegraeus, Jessica Nordlund, Ida Waern, Sara Wernersson, Srinivas Akula, Lars Hellman, Amanda Raine
2022	Doublet identification in single-cell sequencing data using scDblFinder F1000Research Pierre-Luc Germain, Aaron Lun, Carlos Garcia Meixide, Will Macnair, Mark D. Robinson
2022	BFF and cellhashR: analysis tools for accurate demultiplexing of cell hashing data Bioinformatics Gregory J Boggy, G W McElfresh, Eisa Mahyari, Abigail B Ventura, Scott G Hansen, Louis J Picker, Benjamin N Bimber
2021	Benchmarking Computational Doublet-Detection Methods for Single-Cell RNA Sequencing Data Cell Systems Nan Miles Xi, Jingyi Jessica Li
2021	Doublet identification in single-cell sequencing data using scDblFinder F1000Research Pierre-Luc Germain, Aaron Lun, Will Macnair, Mark D. Robinson
2020	A human cell atlas of fetal chromatin accessibility Science Silvia Domcke, Andrew J. Hill, Riza M. Daza, Junyue Cao, Diana R. O’Day, Hannah A. Pliner, Kimberly A. Aldinger, Dmitry Pokholok, Fan Zhang, Jennifer H. Milbank, Michael A. Zager, Ian A. Glass, Frank J. Steemers, Dan Doherty, Cole Trapnell, Darren A. Cusanovich, Jay Shendure
2020	Identification of Pro-Fibrotic Macrophage Populations by Single-Cell Transcriptomic Analysis in West Highland White Terriers Affected With Canine Idiopathic Pulmonary Fibrosis Frontiers in Immunology Aline Fastrès, Dimitri Pirottin, Laurence Fievez, Alexandru-Cosmin Tutunaru, Géraldine Bolen, Anne-Christine Merveille, Thomas Marichal, Christophe J. Desmet, Fabrice Bureau, Cécile Clercx
2020	Prokaryotic single-cell RNA sequencing by in situ combinatorial indexing Nature Microbiology Sydney B. Blattman, Wenyan Jiang, Panos Oikonomou, Saeed Tavazoie
2020	pipeComp, a general framework for the evaluation of computational pipelines, reveals performant single cell RNA-seq preprocessing tools Genome Biology Pierre-Luc Germain, Anthony Sonrel, Mark D. Robinson
2020	GMM-Demux: sample demultiplexing, multiplet detection, experiment planning, and novel cell-type verification in single cell sequencing Genome Biology Hongyi Xin, Qiuyu Lian, Yale Jiang, Jiadi Luo, Xinjun Wang, Carla Erb, Zhongli Xu, Xiaoyi Zhang, Elisa Heidrich-O’Hare, Qi Yan, Richard H. Duerr, Kong Chen, Wei Chen
2019	DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors Cell Systems Christopher S. McGinnis, Lyndsay M. Murrow, Zev J. Gartner
2019	Single-cell RNA sequencing of a European and an African lymphoblastoid cell line Scientific Data Daniel Osorio, Xue Yu, Peng Yu, Erchin Serpedin, James J. Cai
2019	Single-Cell Virus Sequencing of Influenza Infections That Trigger Innate Immunity Journal of Virology Alistair B. Russell, Elizaveta Elshina, Jacob R. Kowalsky, Aartjan J. W. te Velthuis, Jesse D. Bloom
2019	What has single-cell RNA-seq taught us about mammalian spermatogenesis? Biology of Reproduction Shinnosuke Suzuki, Victoria D Diaz, Brian P Hermann
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