W. Evan Johnson
W. Evan Johnson
Professor of Medicine
Verified email at
Cited by
Cited by
Adjusting batch effects in microarray expression data using empirical Bayes methods
WE Johnson, C Li, A Rabinovic
Biostatistics 8 (1), 118-127, 2007
The sva package for removing batch effects and other unwanted variation in high-throughput experiments
JT Leek, WE Johnson, HS Parker, AE Jaffe, JD Storey
Bioinformatics 28 (6), 882-883, 2012
Tackling the widespread and critical impact of batch effects in high-throughput data
JT Leek, RB Scharpf, HC Bravo, D Simcha, B Langmead, WE Johnson, ...
Nature Reviews Genetics 11 (10), 733-739, 2010
ComBat-seq: batch effect adjustment for RNA-seq count data
Y Zhang, G Parmigiani, WE Johnson
NAR genomics and bioinformatics 2 (3), lqaa078, 2020
Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing
J O'Rawe, T Jiang, G Sun, Y Wu, W Wang, J Hu, P Bodily, L Tian, ...
Genome medicine 5, 1-18, 2013
Model-based analysis of tiling-arrays for ChIP-chip
WE Johnson, W Li, CA Meyer, R Gottardo, JS Carroll, M Brown, XS Liu
Proceedings of the National Academy of Sciences 103 (33), 12457-12462, 2006
sva: Surrogate variable analysis
JT Leek, WE Johnson, HS Parker, EJ Fertig, AE Jaffe, JD Storey, Y Zhang, ...
R package version 3 (0), 882-883, 2019
Using VAAST to identify an X-linked disorder resulting in lethality in male infants due to N-terminal acetyltransferase deficiency
AF Rope, K Wang, R Evjenth, J Xing, JJ Johnston, JJ Swensen, B Moore, ...
The American Journal of Human Genetics, 2011
Decontamination of ambient RNA in single-cell RNA-seq with DecontX
S Yang, SE Corbett, Y Koga, Z Wang, WE Johnson, M Yajima, ...
Genome biology 21, 1-15, 2020
A single-sample microarray normalization method to facilitate personalized-medicine workflows
SR Piccolo, Y Sun, JD Campbell, ME Lenburg, AH Bild, WE Johnson
Genomics 100 (6), 337-344, 2012
Alternative preprocessing of RNA-Sequencing data in The Cancer Genome Atlas leads to improved analysis results
M Rahman, LK Jackson, WE Johnson, DY Li, AH Bild, SR Piccolo
Bioinformatics 31 (22), 3666-3672, 2015
DNA specificity determinants associate with distinct transcription factor functions
PC Hollenhorst, KJ Chandler, RL Poulsen, WE Johnson, NA Speck, ...
PLoS genetics 5 (12), e1000778, 2009
PathoScope 2.0: a complete computational framework for strain identification in environmental or clinical sequencing samples
C Hong, S Manimaran, Y Shen, JF Perez-Rogers, AL Byrd, ...
Microbiome 2, 1-15, 2014
The cancer microbiome: distinguishing direct and indirect effects requires a systemic view
JB Xavier, VB Young, J Skufca, F Ginty, T Testerman, AT Pearson, ...
Trends in cancer 6 (3), 192-204, 2020
Batch effects and noise in microarray experiments: sources and solutions
A Scherer
Wiley, 2009
Nascent peptides that block protein synthesis in bacteria
CJ Woolstenhulme, S Parajuli, DW Healey, DP Valverde, EN Petersen, ...
Proceedings of the National Academy of Sciences 110 (10), E878-E887, 2013
Pathoscope: species identification and strain attribution with unassembled sequencing data
OE Francis, M Bendall, S Manimaran, C Hong, NL Clement, ...
Genome research 23 (10), 1721-1729, 2013
Combating subclonal evolution of resistant cancer phenotypes
SW Brady, JA McQuerry, Y Qiao, SR Piccolo, G Shrestha, DF Jenkins, ...
Nature communications 8 (1), 1231, 2017
Model-based analysis of two-color arrays (MA2C)
JS Song, WE Johnson, X Zhu, X Zhang, W Li, AK Manrai, JS Liu, R Chen, ...
Genome biology 8, 1-13, 2007
Metataxonomic and metagenomic approaches vs. culture-based techniques for clinical pathology
SK Hilton, E Castro-Nallar, M Pérez-Losada, I Toma, TA McCaffrey, ...
Frontiers in microbiology 7, 484, 2016
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