Jeff Leek
Jeff Leek
Chief Data Officer, VP, and J Orin Edson Foundation Professor, Fred Hutchinson Cancer Center
Verified email at - Homepage
Cited by
Cited by
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
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
Capturing heterogeneity in gene expression studies by surrogate variable analysis
JT Leek, JD Storey
PLoS genetics 3 (9), e161, 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
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
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
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
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
A general framework for multiple testing dependence
JT Leek, JD Storey
Proceedings of the National Academy of Sciences 105 (48), 18718-18723, 2008
Cloud-scale RNA-sequencing differential expression analysis with Myrna
B Langmead, KD Hansen, JT Leek
Genome biology 11, 1-11, 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
Svaseq: removing batch effects and other unwanted noise from sequencing data
JT Leek
Nucleic acids research 42 (21), e161-e161, 2014
Transparency and reproducibility in artificial intelligence
B Haibe-Kains, GA Adam, A Hosny, F Khodakarami, ...
Nature 586 (7829), E14-E16, 2020
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
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
EDGE: extraction and analysis of differential gene expression
JT Leek, E Monsen, AR Dabney, JD Storey
Bioinformatics 22 (4), 507-508, 2006
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
Polyester: simulating RNA-seq datasets with differential transcript expression
AC Frazee, AE Jaffe, B Langmead, JT Leek
Bioinformatics 31 (17), 2778-2784, 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
The system can't perform the operation now. Try again later.
Articles 1–20