ComBat-seq: batch effect adjustment for RNA-seq count data
Zhang, Yuqing, Parmigiani, Giovanni, Johnson, W Evan
Published in NAR genomics and bioinformatics (01.09.2020)
Published in NAR genomics and bioinformatics (01.09.2020)
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Journal Article
Decontamination of ambient RNA in single-cell RNA-seq with DecontX
Yang, Shiyi, Corbett, Sean E, Koga, Yusuke, Wang, Zhe, Johnson, W Evan, Yajima, Masanao, Campbell, Joshua D
Published in Genome Biology (05.03.2020)
Published in Genome Biology (05.03.2020)
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Journal Article
Adjusting batch effects in microarray expression data using empirical Bayes methods
Johnson, W Evan, Li, Cheng, Rabinovic, Ariel
Published in Biostatistics (Oxford, England) (01.01.2007)
Published in Biostatistics (Oxford, England) (01.01.2007)
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Journal Article
Alternative empirical Bayes models for adjusting for batch effects in genomic studies
Zhang, Yuqing, Jenkins, David F, Manimaran, Solaiappan, Johnson, W Evan
Published in BMC bioinformatics (13.07.2018)
Published in BMC bioinformatics (13.07.2018)
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Journal Article
Tackling the widespread and critical impact of batch effects in high-throughput data
Irizarry, Rafael A, Leek, Jeffrey T, Scharpf, Robert B, Bravo, Héctor Corrada, Simcha, David, Langmead, Benjamin, Johnson, W. Evan, Geman, Donald, Baggerly, Keith
Published in Nature reviews. Genetics (01.10.2010)
Published in Nature reviews. Genetics (01.10.2010)
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Journal Article
Alternative preprocessing of RNA-Sequencing data in The Cancer Genome Atlas leads to improved analysis results
Rahman, Mumtahena, Jackson, Laurie K, Johnson, W Evan, Li, Dean Y, Bild, Andrea H, Piccolo, Stephen R
Published in Bioinformatics (Oxford, England) (15.11.2015)
Published in Bioinformatics (Oxford, England) (15.11.2015)
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Journal Article
Metagenomic profiling pipelines improve taxonomic classification for 16S amplicon sequencing data
Odom, Aubrey R, Faits, Tyler, Castro-Nallar, Eduardo, Crandall, Keith A, Johnson, W Evan
Published in Scientific reports (26.08.2023)
Published in Scientific reports (26.08.2023)
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Journal Article
Comprehensive generation, visualization, and reporting of quality control metrics for single-cell RNA sequencing data
Hong, Rui, Koga, Yusuke, Bandyadka, Shruthi, Leshchyk, Anastasia, Wang, Yichen, Akavoor, Vidya, Cao, Xinyun, Sarfraz, Irzam, Wang, Zhe, Alabdullatif, Salam, Jansen, Frederick, Yajima, Masanao, Johnson, W Evan, Campbell, Joshua D
Published in Nature communications (30.03.2022)
Published in Nature communications (30.03.2022)
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Journal Article
BatchQC: interactive software for evaluating sample and batch effects in genomic data
Manimaran, Solaiappan, Selby, Heather Marie, Okrah, Kwame, Ruberman, Claire, Leek, Jeffrey T, Quackenbush, John, Haibe-Kains, Benjamin, Bravo, Hector Corrada, Johnson, W Evan
Published in Bioinformatics (Oxford, England) (15.12.2016)
Published in Bioinformatics (Oxford, England) (15.12.2016)
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Journal Article
Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing
O'Rawe, Jason, Jiang, Tao, Sun, Guangqing, Wu, Yiyang, Wang, Wei, Hu, Jingchu, Bodily, Paul, Tian, Lifeng, Hakonarson, Hakon, Johnson, W Evan, Wei, Zhi, Wang, Kai, Lyon, Gholson J
Published in Genome medicine (27.03.2013)
Published in Genome medicine (27.03.2013)
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Journal Article
Model-Based Analysis of Tiling-Arrays for ChIP-Chip
Johnson, W. Evan, Li, Wei, Meyer, Clifford A., Gottardo, Raphael, Carroll, Jason S., Brown, Myles, Liu, X. Shirley
Published in Proceedings of the National Academy of Sciences - PNAS (15.08.2006)
Published in Proceedings of the National Academy of Sciences - PNAS (15.08.2006)
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Journal Article
scruff: an R/Bioconductor package for preprocessing single-cell RNA-sequencing data
Wang, Zhe, Hu, Junming, Johnson, W Evan, Campbell, Joshua D
Published in BMC bioinformatics (02.05.2019)
Published in BMC bioinformatics (02.05.2019)
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Journal Article
Respiratory syncytial virus M2-1 protein associates non-specifically with viral messenger RNA and with specific cellular messenger RNA transcripts
Braun, Molly R, Noton, Sarah L, Blanchard, Emmeline L, Shareef, Afzaal, Santangelo, Philip J, Johnson, W Evan, Fearns, Rachel
Published in PLoS pathogens (01.05.2021)
Published in PLoS pathogens (01.05.2021)
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Journal Article
Wolframin-1-expressing neurons in the entorhinal cortex propagate tau to CA1 neurons and impair hippocampal memory in mice
Delpech, Jean-Christophe, Pathak, Dhruba, Varghese, Merina, Kalavai, Srinidhi Venkatesan, Hays, Emma C, Hof, Patrick R, Johnson, W Evan, Ikezu, Seiko, Medalla, Maria, Luebke, Jennifer I, Ikezu, Tsuneya
Published in Science translational medicine (15.09.2021)
Published in Science translational medicine (15.09.2021)
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Journal Article
Combating subclonal evolution of resistant cancer phenotypes
Brady, Samuel W, McQuerry, Jasmine A, Qiao, Yi, Piccolo, Stephen R, Shrestha, Gajendra, Jenkins, David F, Layer, Ryan M, Pedersen, Brent S, Miller, Ryan H, Esch, Amanda, Selitsky, Sara R, Parker, Joel S, Anderson, Layla A, Dalley, Brian K, Factor, Rachel E, Reddy, Chakravarthy B, Boltax, Jonathan P, Li, Dean Y, Moos, Philip J, Gray, Joe W, Heiser, Laura M, Buys, Saundra S, Cohen, Adam L, Johnson, W Evan, Quinlan, Aaron R, Marth, Gabor, Werner, Theresa L, Bild, Andrea H
Published in Nature communications (01.11.2017)
Published in Nature communications (01.11.2017)
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Journal Article
A comprehensive update to the Mycobacterium tuberculosis H37Rv reference genome
Chitale, Poonam, Lemenze, Alexander D, Fogarty, Emily C, Shah, Avi, Grady, Courtney, Odom-Mabey, Aubrey R, Johnson, W Evan, Yang, Jason H, Eren, A Murat, Brosch, Roland, Kumar, Pradeep, Alland, David
Published in Nature communications (18.11.2022)
Published in Nature communications (18.11.2022)
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Journal Article
The Cancer Microbiome: Distinguishing Direct and Indirect Effects Requires a Systemic View
Xavier, Joao B, Young, Vincent B, Skufca, Joseph, Ginty, Fiona, Testerman, Traci, Pearson, Alexander T, Macklin, Paul, Mitchell, Amir, Shmulevich, Ilya, Xie, Lei, Caporaso, J Gregory, Crandall, Keith A, Simone, Nicole L, Godoy-Vitorino, Filipa, Griffin, Timothy J, Whiteson, Katrine L, Gustafson, Heather H, Slade, Daniel J, Schmidt, Thomas M, Walther-Antonio, Marina R S, Korem, Tal, Webb-Robertson, Bobbie-Jo M, Styczynski, Mark P, Johnson, W Evan, Jobin, Christian, Ridlon, Jason M, Koh, Andrew Y, Yu, Michael, Kelly, Libusha, Wargo, Jennifer A
Published in Trends in cancer (01.03.2020)
Published in Trends in cancer (01.03.2020)
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The oral microbiome in relation to pancreatic cancer risk in African Americans
Petrick, Jessica L, Wilkinson, Jeremy E, Michaud, Dominique S, Cai, Qiuyin, Gerlovin, Hanna, Signorello, Lisa B, Wolpin, Brian M, Ruiz-Narváez, Edward A, Long, Jirong, Yang, Yaohua, Johnson, W Evan, Shu, Xiao-Ou, Huttenhower, Curtis, Palmer, Julie R
Published in British journal of cancer (01.02.2022)
Published in British journal of cancer (01.02.2022)
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Journal Article
Nascent peptides that block protein synthesis in bacteria
Woolstenhulme, Christopher J, Parajuli, Shankar, Healey, David W, Valverde, Diana P, Petersen, E Nicholas, Starosta, Agata L, Guydosh, Nicholas R, Johnson, W Evan, Wilson, Daniel N, Buskirk, Allen R
Published in Proceedings of the National Academy of Sciences - PNAS (05.03.2013)
Published in Proceedings of the National Academy of Sciences - PNAS (05.03.2013)
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