| Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown M Pertea, D Kim, GM Pertea, JT Leek, SL Salzberg Nature protocols 11 (9), 1650-1667, 2016 | 5329 | 2016 |
| 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 | 4973 | 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 | 2205 | 2010 |
| Capturing heterogeneity in gene expression studies by surrogate variable analysis JT Leek, JD Storey PLoS genetics 3 (9), e161, 2007 | 2122 | 2007 |
| Temporal dynamics and genetic control of transcription in the human prefrontal cortex C Colantuoni, BK Lipska, T Ye, TM Hyde, R Tao, JT Leek, EA Colantuoni, ... Nature 478 (7370), 519-523, 2011 | 776 | 2011 |
| Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies AE Jaffe, P Murakami, H Lee, JT Leek, MD Fallin, AP Feinberg, RA Irizarry International journal of epidemiology 41 (1), 200-209, 2012 | 743 | 2012 |
| Ballgown bridges the gap between transcriptome assembly and expression analysis AC Frazee, G Pertea, AE Jaffe, B Langmead, SL Salzberg, JT Leek Nature biotechnology 33 (3), 243-246, 2015 | 738 | 2015 |
| Significance analysis of time course microarray experiments JD Storey, W Xiao, JT Leek, RG Tompkins, RW Davis Proceedings of the National Academy of Sciences 102 (36), 12837-12842, 2005 | 729 | 2005 |
| 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 | 507 | 2019 |
| A general framework for multiple testing dependence JT Leek, JD Storey Proceedings of the National Academy of Sciences 105 (48), 18718-18723, 2008 | 448 | 2008 |
| Cloud-scale RNA-sequencing differential expression analysis with Myrna B Langmead, KD Hansen, JT Leek Genome biology 11, 1-11, 2010 | 437 | 2010 |
| Reproducible RNA-seq analysis using recount2 L Collado-Torres, A Nellore, K Kammers, SE Ellis, MA Taub, KD Hansen, ... Nature biotechnology 35 (4), 319-321, 2017 | 415 | 2017 |
| Transparency and reproducibility in artificial intelligence B Haibe-Kains, GA Adam, A Hosny, F Khodakarami, ... Nature 586 (7829), E14-E16, 2020 | 398 | 2020 |
| Svaseq: removing batch effects and other unwanted noise from sequencing data JT Leek Nucleic acids research 42 (21), e161-e161, 2014 | 395 | 2014 |
| On the design and analysis of gene expression studies in human populations JM Akey, S Biswas, JT Leek, JD Storey Nature genetics 39 (7), 807-808, 2007 | 346 | 2007 |
| Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis AE Jaffe, RE Straub, JH Shin, R Tao, Y Gao, L Collado-Torres, ... Nature neuroscience 21 (8), 1117-1125, 2018 | 338 | 2018 |
| Systems-level dynamic analyses of fate change in murine embryonic stem cells R Lu, F Markowetz, RD Unwin, JT Leek, EM Airoldi, BD MacArthur, ... Nature 462 (7271), 358-362, 2009 | 338 | 2009 |
| EDGE: extraction and analysis of differential gene expression JT Leek, E Monsen, AR Dabney, JD Storey Bioinformatics 22 (4), 507-508, 2006 | 325 | 2006 |
| Polyester: simulating RNA-seq datasets with differential transcript expression AC Frazee, AE Jaffe, B Langmead, JT Leek Bioinformatics 31 (17), 2778-2784, 2015 | 313 | 2015 |
| What should researchers expect when they replicate studies? A statistical view of replicability in psychological science P Patil, RD Peng, JT Leek Perspectives on Psychological Science 11 (4), 539-544, 2016 | 268 | 2016 |