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Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown.

Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL. Pertea M, et al. Among authors: leek jt. Nat Protoc. 2016 Sep;11(9):1650-67. doi: 10.1038/nprot.2016.095. Epub 2016 Aug 11. Nat Protoc. 2016. PMID: 27560171 Free PMC article.

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Transparency and reproducibility in artificial intelligence.

Haibe-Kains B, Adam GA, Hosny A, Khodakarami F; Massive Analysis Quality Control (MAQC) Society Board of Directors, Waldron L, Wang B, McIntosh C, Goldenberg A, Kundaje A, Greene CS, Broderick T, Hoffman MM, Leek JT, Korthauer K, Huber W, Brazma A, Pineau J, Tibshirani R, Hastie T, Ioannidis JPA, Quackenbush J, Aerts HJWL. Haibe-Kains B, et al. Among authors: leek jt. Nature. 2020 Oct;586(7829):E14-E16. doi: 10.1038/s41586-020-2766-y. Epub 2020 Oct 14. Nature. 2020. PMID: 33057217 Free PMC article.

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The sva package for removing batch effects and other unwanted variation in high-throughput experiments.

Leek JT, Johnson WE, Parker HS, Jaffe AE, Storey JD. Leek JT, et al. Bioinformatics. 2012 Mar 15;28(6):882-3. doi: 10.1093/bioinformatics/bts034. Epub 2012 Jan 17. Bioinformatics. 2012. PMID: 22257669 Free PMC article.

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Tackling the widespread and critical impact of batch effects in high-throughput data.

Leek JT, Scharpf RB, Bravo HC, Simcha D, Langmead B, Johnson WE, Geman D, Baggerly K, Irizarry RA. Leek JT, et al. Nat Rev Genet. 2010 Oct;11(10):733-9. doi: 10.1038/nrg2825. Epub 2010 Sep 14. Nat Rev Genet. 2010. PMID: 20838408 Free PMC article. Review.

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Developmental and genetic regulation of the human cortex transcriptome illuminate schizophrenia pathogenesis.

Jaffe AE, Straub RE, Shin JH, Tao R, Gao Y, Collado-Torres L, Kam-Thong T, Xi HS, Quan J, Chen Q, Colantuoni C, Ulrich WS, Maher BJ, Deep-Soboslay A; BrainSeq Consortium, Cross AJ, Brandon NJ, Leek JT, Hyde TM, Kleinman JE, Weinberger DR. Jaffe AE, et al. Among authors: leek jt. Nat Neurosci. 2018 Aug;21(8):1117-1125. doi: 10.1038/s41593-018-0197-y. Epub 2018 Jul 26. Nat Neurosci. 2018. PMID: 30050107 Free PMC article.

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svaseq: removing batch effects and other unwanted noise from sequencing data.

Leek JT. Leek JT. Nucleic Acids Res. 2014 Dec 1;42(21):e161. doi: 10.1093/nar/gku864. Epub 2014 Oct 7. Nucleic Acids Res. 2014. PMID: 25294822 Free PMC article.

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Practical impacts of genomic data "cleaning" on biological discovery using surrogate variable analysis.

Jaffe AE, Hyde T, Kleinman J, Weinbergern DR, Chenoweth JG, McKay RD, Leek JT, Colantuoni C. Jaffe AE, et al. Among authors: leek jt. BMC Bioinformatics. 2015 Nov 6;16:372. doi: 10.1186/s12859-015-0808-5. BMC Bioinformatics. 2015. PMID: 26545828 Free PMC article.

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Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies.

Jaffe AE, Murakami P, Lee H, Leek JT, Fallin MD, Feinberg AP, Irizarry RA. Jaffe AE, et al. Among authors: leek jt. Int J Epidemiol. 2012 Feb;41(1):200-9. doi: 10.1093/ije/dyr238. Int J Epidemiol. 2012. PMID: 22422453 Free PMC article.

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Capturing heterogeneity in gene expression studies by surrogate variable analysis.

Leek JT, Storey JD. Leek JT, et al. PLoS Genet. 2007 Sep;3(9):1724-35. doi: 10.1371/journal.pgen.0030161. Epub 2007 Aug 1. PLoS Genet. 2007. PMID: 17907809 Free PMC article.

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Recounting the FANTOM CAGE-Associated Transcriptome.

Imada EL, Sanchez DF, Collado-Torres L, Wilks C, Matam T, Dinalankara W, Stupnikov A, Lobo-Pereira F, Yip CW, Yasuzawa K, Kondo N, Itoh M, Suzuki H, Kasukawa T, Hon CC, de Hoon MJL, Shin JW, Carninci P, Jaffe AE, Leek JT, Favorov A, Franco GR, Langmead B, Marchionni L. Imada EL, et al. Among authors: leek jt. Genome Res. 2020 Jul;30(7):1073-1081. doi: 10.1101/gr.254656.119. Epub 2020 Feb 20. Genome Res. 2020. PMID: 32079618 Free PMC article.

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