| Adjusting batch effects in microarray expression data using empirical Bayes methods WE Johnson, C Li, A Rabinovic Biostatistics 8 (1), 118-127, 2007 | 6305 | 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 | 3584 | 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 | 1927 | 2010 |
| 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 (3), 1-18, 2013 | 529 | 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 | 499 | 2006 |
| ComBat-seq: batch effect adjustment for RNA-seq count data Y Zhang, G Parmigiani, WE Johnson NAR genomics and bioinformatics 2 (3), lqaa078, 2020 | 399 | 2020 |
| 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 | 265 | 2011 |
| 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 | 243 | 2012 |
| 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 | 208 | 2009 |
| 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 | 191 | 2015 |
| 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), 1-15, 2014 | 183 | 2014 |
| Batch effects and noise in microarray experiments: sources and solutions A Scherer John Wiley & Sons, 2009 | 173 | 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 | 157 | 2013 |
| 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 | 146 | 2020 |
| 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 | 145 | 2013 |
| 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 | 142 | 2020 |
| 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 (8), 1-13, 2007 | 137 | 2007 |
| 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 | 125 | 2017 |
| The GNUMAP algorithm: unbiased probabilistic mapping of oligonucleotides from next-generation sequencing NL Clement, Q Snell, MJ Clement, PC Hollenhorst, J Purwar, BJ Graves, ... Bioinformatics 26 (1), 38-45, 2010 | 108 | 2010 |
| Multiplatform single-sample estimates of transcriptional activation SR Piccolo, MR Withers, OE Francis, AH Bild, WE Johnson Proceedings of the National Academy of Sciences 110 (44), 17778-17783, 2013 | 105 | 2013 |
Jeff LeekChief Data Officer, VP, and J Orin Edson Foundation Professor, Fred Hutchinson Cancer CenterVerified email at fredhutch.org
