J
Jeffrey T. Leek
Researcher at Johns Hopkins University
Publications - 139
Citations - 20229
Jeffrey T. Leek is an academic researcher from Johns Hopkins University. The author has contributed to research in topics: Bioconductor & Gene. The author has an hindex of 44, co-authored 136 publications receiving 15256 citations. Previous affiliations of Jeffrey T. Leek include Johns Hopkins University School of Medicine & University of Washington.
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Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown
TL;DR: This protocol describes all the steps necessary to process a large set of raw sequencing reads and create lists of gene transcripts, expression levels, and differentially expressed genes and transcripts.
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The sva package for removing batch effects and other unwanted variation in high-throughput experiments
TL;DR: The sva package is described, which supports surrogate variable estimation with the sva function, direct adjustment for known batch effects with the ComBat function and adjustment for batch and latent variables in prediction problems with the fsva function.
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Capturing heterogeneity in gene expression studies by surrogate variable analysis.
Jeffrey T. Leek,John D. Storey +1 more
TL;DR: This work introduces “surrogate variable analysis” (SVA) to overcome the problems caused by heterogeneity in expression studies and shows that SVA increases the biological accuracy and reproducibility of analyses in genome-wide expression studies.
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Tackling the widespread and critical impact of batch effects in high-throughput data
Jeffrey T. Leek,Robert B. Scharpf,Héctor Corrada Bravo,Héctor Corrada Bravo,David M. Simcha,Benjamin Langmead,W. Evan Johnson,Donald Geman,Keith A. Baggerly,Rafael A. Irizarry +9 more
TL;DR: It is argued that batch effects (as well as other technical and biological artefacts) are widespread and critical to address and experimental and computational approaches for doing so are reviewed.
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Temporal dynamics and genetic control of transcription in the human prefrontal cortex
Carlo Colantuoni,Barbara K. Lipska,Tianzhang Ye,Thomas M. Hyde,Thomas M. Hyde,Ran Tao,Jeffrey T. Leek,Elizabeth Colantuoni,Abdel G. Elkahloun,Mary M. Herman,Daniel R. Weinberger,Daniel R. Weinberger,Joel E. Kleinman +12 more
TL;DR: The temporal dynamics and genetic control of transcription in human prefrontal cortex in an extensive series of post-mortem brains from fetal development through ageing is explored, finding a wave of gene expression changes occurring during fetal development which are reversed in early postnatal life.