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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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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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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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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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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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How to share data for collaboration.

Ellis SE, Leek JT. Ellis SE, et al. Among authors: leek jt. Am Stat. 2018;72(1):53-57. doi: 10.1080/00031305.2017.1375987. Epub 2018 Apr 24. Am Stat. 2018. PMID: 32981941 Free PMC article.

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recount3: summaries and queries for large-scale RNA-seq expression and splicing.

Wilks C, Zheng SC, Chen FY, Charles R, Solomon B, Ling JP, Imada EL, Zhang D, Joseph L, Leek JT, Jaffe AE, Nellore A, Collado-Torres L, Hansen KD, Langmead B. Wilks C, et al. Among authors: leek jt. Genome Biol. 2021 Nov 29;22(1):323. doi: 10.1186/s13059-021-02533-6. Genome Biol. 2021. PMID: 34844637 Free PMC article.

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Reproducible RNA-seq analysis using recount2.

Collado-Torres L, Nellore A, Kammers K, Ellis SE, Taub MA, Hansen KD, Jaffe AE, Langmead B, Leek JT. Collado-Torres L, et al. Among authors: leek jt. Nat Biotechnol. 2017 Apr 11;35(4):319-321. doi: 10.1038/nbt.3838. Nat Biotechnol. 2017. PMID: 28398307 Free PMC article. No abstract available.

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A visual tool for defining reproducibility and replicability.

Patil P, Peng RD, Leek JT. Patil P, et al. Among authors: leek jt. Nat Hum Behav. 2019 Jul;3(7):650-652. doi: 10.1038/s41562-019-0629-z. Nat Hum Behav. 2019. PMID: 31209370 No abstract available.

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Transcriptional profile of platelets and iPSC-derived megakaryocytes from whole-genome and RNA sequencing.

Kammers K, Taub MA, Rodriguez B, Yanek LR, Ruczinski I, Martin J, Kanchan K, Battle A, Cheng L, Wang ZZ, Johnson AD, Leek JT, Faraday N, Becker LC, Mathias RA. Kammers K, et al. Among authors: leek jt. Blood. 2021 Feb 18;137(7):959-968. doi: 10.1182/blood.2020006115. Blood. 2021. PMID: 33094331 Free PMC article.

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