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Improving the value of public RNA-seq expression data by phenotype prediction.

Ellis SE, Collado-Torres L, Jaffe A, Leek JT.

Nucleic Acids Res. 2018 Mar 5. doi: 10.1093/nar/gky102. [Epub ahead of print]


Five ways to fix statistics.

Leek J, McShane BB, Gelman A, Colquhoun D, Nuijten MB, Goodman SN.

Nature. 2017 Nov 30;551(7682):557-559. doi: 10.1038/d41586-017-07522-z. No abstract available.


Effects of AAV-mediated knockdown of nNOS and GPx-1 gene expression in rat hippocampus after traumatic brain injury.

Boone DR, Leek JM, Falduto MT, Torres KEO, Sell SL, Parsley MA, Cowart JC, Uchida T, Micci MA, DeWitt DS, Prough DS, Hellmich HL.

PLoS One. 2017 Oct 10;12(10):e0185943. doi: 10.1371/journal.pone.0185943. eCollection 2017.


qSVA framework for RNA quality correction in differential expression analysis.

Jaffe AE, Tao R, Norris AL, Kealhofer M, Nellore A, Shin JH, Kim D, Jia Y, Hyde TM, Kleinman JE, Straub RE, Leek JT, Weinberger DR.

Proc Natl Acad Sci U S A. 2017 Jul 3;114(27):7130-7135. doi: 10.1073/pnas.1617384114. Epub 2017 Jun 20.


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.

Nat Biotechnol. 2017 Apr 11;35(4):319-321. doi: 10.1038/nbt.3838. No abstract available.


Widespread splicing of repetitive element loci into coding regions of gene transcripts.

Darby MM, Leek JT, Langmead B, Yolken RH, Sabunciyan S.

Hum Mol Genet. 2016 Nov 15;25(22):4962-4982. doi: 10.1093/hmg/ddw321.


Integrity of Induced Pluripotent Stem Cell (iPSC) Derived Megakaryocytes as Assessed by Genetic and Transcriptomic Analysis.

Kammers K, Taub MA, Ruczinski I, Martin J, Yanek LR, Frazee A, Gao Y, Hoyle D, Faraday N, Becker DM, Cheng L, Wang ZZ, Leek JT, Becker LC, Mathias RA.

PLoS One. 2017 Jan 20;12(1):e0167794. doi: 10.1371/journal.pone.0167794. eCollection 2017.


Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive.

Nellore A, Jaffe AE, Fortin JP, Alquicira-Hernández J, Collado-Torres L, Wang S, Phillips RA III, Karbhari N, Hansen KD, Langmead B, Leek JT.

Genome Biol. 2016 Dec 30;17(1):266. doi: 10.1186/s13059-016-1118-6.


Flexible expressed region analysis for RNA-seq with derfinder.

Collado-Torres L, Nellore A, Frazee AC, Wilks C, Love MI, Langmead B, Irizarry RA, Leek JT, Jaffe AE.

Nucleic Acids Res. 2017 Jan 25;45(2):e9. doi: 10.1093/nar/gkw852. Epub 2016 Sep 29.


Rail-RNA: scalable analysis of RNA-seq splicing and coverage.

Nellore A, Collado-Torres L, Jaffe AE, Alquicira-Hernández J, Wilks C, Pritt J, Morton J, Leek JT, Langmead B.

Bioinformatics. 2017 Dec 15;33(24):4033-4040. doi: 10.1093/bioinformatics/btw575.


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

Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL.

Nat Protoc. 2016 Sep;11(9):1650-67. doi: 10.1038/nprot.2016.095. Epub 2016 Aug 11.


BatchQC: interactive software for evaluating sample and batch effects in genomic data.

Manimaran S, Selby HM, Okrah K, Ruberman C, Leek JT, Quackenbush J, Haibe-Kains B, Bravo HC, Johnson WE.

Bioinformatics. 2016 Dec 15;32(24):3836-3838. Epub 2016 Aug 18.


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

Jaffe AE, Hyde T, Kleinman J, Weinberger DR, Chenoweth JG, McKay RD, Leek JT, Colantuoni C.

BMC Bioinformatics. 2016 Aug 10;17:302. doi: 10.1186/s12859-016-1152-0. No abstract available.


What Should Researchers Expect When They Replicate Studies? A Statistical View of Replicability in Psychological Science.

Patil P, Peng RD, Leek JT.

Perspect Psychol Sci. 2016 Jul;11(4):539-44. doi: 10.1177/1745691616646366.


Rail-dbGaP: analyzing dbGaP-protected data in the cloud with Amazon Elastic MapReduce.

Nellore A, Wilks C, Hansen KD, Leek JT, Langmead B.

Bioinformatics. 2016 Aug 15;32(16):2551-3. doi: 10.1093/bioinformatics/btw177. Epub 2016 Apr 21.


Evolution of cellular morpho-phenotypes in cancer metastasis.

Wu PH, Phillip JM, Khatau SB, Chen WC, Stirman J, Rosseel S, Tschudi K, Van Patten J, Wong M, Gupta S, Baras AS, Leek JT, Maitra A, Wirtz D.

Sci Rep. 2015 Dec 17;5:18437. doi: 10.1038/srep18437.


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.

BMC Bioinformatics. 2015 Nov 6;16:372. doi: 10.1186/s12859-015-0808-5. Erratum in: BMC Bioinformatics. 2016;17:302.


Polyester: simulating RNA-seq datasets with differential transcript expression.

Frazee AC, Jaffe AE, Langmead B, Leek JT.

Bioinformatics. 2015 Sep 1;31(17):2778-84. doi: 10.1093/bioinformatics/btv272. Epub 2015 Apr 28.


Statistics: P values are just the tip of the iceberg.

Leek JT, Peng RD.

Nature. 2015 Apr 30;520(7549):612. doi: 10.1038/520612a. No abstract available.


Test set bias affects reproducibility of gene signatures.

Patil P, Bachant-Winner PO, Haibe-Kains B, Leek JT.

Bioinformatics. 2015 Jul 15;31(14):2318-23. doi: 10.1093/bioinformatics/btv157. Epub 2015 Mar 18.


Ballgown bridges the gap between transcriptome assembly and expression analysis.

Frazee AC, Pertea G, Jaffe AE, Langmead B, Salzberg SL, Leek JT.

Nat Biotechnol. 2015 Mar;33(3):243-6. doi: 10.1038/nbt.3172. No abstract available.


Statistics. What is the question?

Leek JT, Peng RD.

Science. 2015 Mar 20;347(6228):1314-5. doi: 10.1126/science.aaa6146. Epub 2015 Feb 26. No abstract available.


Opinion: Reproducible research can still be wrong: adopting a prevention approach.

Leek JT, Peng RD.

Proc Natl Acad Sci U S A. 2015 Feb 10;112(6):1645-6. doi: 10.1073/pnas.1421412111. No abstract available.


regionReport: Interactive reports for region-level and feature-level genomic analyses.

Collado-Torres L, Jaffe AE, Leek JT.

Version 2. F1000Res. 2015 May 1 [revised 2016 Jan 1];4:105. doi: 10.12688/f1000research.6379.2. eCollection 2015.


Developmental regulation of human cortex transcription and its clinical relevance at single base resolution.

Jaffe AE, Shin J, Collado-Torres L, Leek JT, Tao R, Li C, Gao Y, Jia Y, Maher BJ, Hyde TM, Kleinman JE, Weinberger DR.

Nat Neurosci. 2015 Jan;18(1):154-161. doi: 10.1038/nn.3898. Epub 2014 Dec 15.


Removing batch effects for prediction problems with frozen surrogate variable analysis.

Parker HS, Corrada Bravo H, Leek JT.

PeerJ. 2014 Sep 23;2:e561. doi: 10.7717/peerj.561. eCollection 2014.


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

Leek JT.

Nucleic Acids Res. 2014 Dec 1;42(21). doi: 10.1093/nar/gku864. Epub 2014 Oct 7.


Preserving biological heterogeneity with a permuted surrogate variable analysis for genomics batch correction.

Parker HS, Leek JT, Favorov AV, Considine M, Xia X, Chavan S, Chung CH, Fertig EJ.

Bioinformatics. 2014 Oct;30(19):2757-63. doi: 10.1093/bioinformatics/btu375. Epub 2014 Jun 6.


Inflammatory molecular signature associated with infectious agents in psychosis.

Hayes LN, Severance EG, Leek JT, Gressitt KL, Rohleder C, Coughlin JM, Leweke FM, Yolken RH, Sawa A.

Schizophr Bull. 2014 Sep;40(5):963-72. doi: 10.1093/schbul/sbu052. Epub 2014 Apr 17.


Differential expression analysis of RNA-seq data at single-base resolution.

Frazee AC, Sabunciyan S, Hansen KD, Irizarry RA, Leek JT.

Biostatistics. 2014 Jul;15(3):413-26. doi: 10.1093/biostatistics/kxt053. Epub 2014 Jan 6. Erratum in: Biostatistics. 2014 Jul;15(3):584-5.


Gene set bagging for estimating the probability a statistically significant result will replicate.

Jaffe AE, Storey JD, Ji H, Leek JT.

BMC Bioinformatics. 2013 Dec 12;14:360. doi: 10.1186/1471-2105-14-360.


Prevalence and counts of Salmonella and enterohemorrhagic Escherichia coli in raw, shelled runner peanuts.

Miksch RR, Leek J, Myoda S, Nguyen T, Tenney K, Svidenko V, Greeson K, Samadpour M.

J Food Prot. 2013 Oct;76(10):1668-75. doi: 10.4315/0362-028X.JFP-13-047.


An estimate of the science-wise false discovery rate and application to the top medical literature.

Jager LR, Leek JT.

Biostatistics. 2014 Jan;15(1):1-12. doi: 10.1093/biostatistics/kxt007. Epub 2013 Sep 25.


A decision-theory approach to interpretable set analysis for high-dimensional data.

Boca SM, Bravo HC, Caffo B, Leek JT, Parmigiani G.

Biometrics. 2013 Sep;69(3):614-23. doi: 10.1111/biom.12060. Epub 2013 Aug 2.


A simple and reproducible breast cancer prognostic test.

Marchionni L, Afsari B, Geman D, Leek JT.

BMC Genomics. 2013 May 17;14:336. doi: 10.1186/1471-2164-14-336.


Sequestration: inadvertently killing biomedical research to score political points.

Leek JT, Salzberg SL.

Genome Biol. 2013 Mar 27;14(3):109. doi: 10.1186/gb-2013-14-3-109. No abstract available.


SVAw - a web-based application tool for automated surrogate variable analysis of gene expression studies.

Pirooznia M, Seifuddin F, Goes FS, Leek JT, Zandi PP.

Source Code Biol Med. 2013 Mar 11;8(1):8. doi: 10.1186/1751-0473-8-8.


Making Sense of Extreme Longevity: Explorations Into the Spiritual Lives of Centenarians.

Manning LK, Leek JA, Radina ME.

J Relig Spiritual Aging. 2012 Jan 1;24(4):345-359. Epub 2012 Sep 27.


Gene expression anti-profiles as a basis for accurate universal cancer signatures.

Bravo HC, Pihur V, McCall M, Irizarry RA, Leek JT.

BMC Bioinformatics. 2012 Oct 22;13:272. doi: 10.1186/1471-2105-13-272.


A statistical approach to selecting and confirming validation targets in -omics experiments.

Leek JT, Taub MA, Rasgon JL.

BMC Bioinformatics. 2012 Jun 27;13:150.


The practical effect of batch on genomic prediction.

Parker HS, Leek JT.

Stat Appl Genet Mol Biol. 2012;11(3):Article 10.


Personalized medicine: Keep a way open for tailored treatments.

Leek JT, Peng RD, Anderson RR.

Nature. 2012 Apr 18;484(7394):318. doi: 10.1038/484318a. No abstract available.


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.

Int J Epidemiol. 2012 Feb;41(1):200-9. doi: 10.1093/ije/dyr238.


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.

Bioinformatics. 2012 Mar 15;28(6):882-3. doi: 10.1093/bioinformatics/bts034. Epub 2012 Jan 17.


Cooperation between referees and authors increases peer review accuracy.

Leek JT, Taub MA, Pineda FJ.

PLoS One. 2011;6(11):e26895. doi: 10.1371/journal.pone.0026895. Epub 2011 Nov 9.


ReCount: a multi-experiment resource of analysis-ready RNA-seq gene count datasets.

Frazee AC, Langmead B, Leek JT.

BMC Bioinformatics. 2011 Nov 16;12:449. doi: 10.1186/1471-2105-12-449.


Temporal dynamics and genetic control of transcription in the human prefrontal cortex.

Colantuoni C, Lipska BK, Ye T, Hyde TM, Tao R, Leek JT, Colantuoni EA, Elkahloun AG, Herman MM, Weinberger DR, Kleinman JE.

Nature. 2011 Oct 26;478(7370):519-23. doi: 10.1038/nature10524.


Dissecting inflammatory complications in critically injured patients by within-patient gene expression changes: a longitudinal clinical genomics study.

Desai KH, Tan CS, Leek JT, Maier RV, Tompkins RG, Storey JD; Inflammation and the Host Response to Injury Large-Scale Collaborative Research Program.

PLoS Med. 2011 Sep;8(9):e1001093. doi: 10.1371/journal.pmed.1001093. Epub 2011 Sep 13.


Sequencing technology does not eliminate biological variability.

Hansen KD, Wu Z, Irizarry RA, Leek JT.

Nat Biotechnol. 2011 Jul 11;29(7):572-3. doi: 10.1038/nbt.1910. No abstract available.

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