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Papers

More info on my Google Scholar profile

Preprints

  • Jaffe AE, Tao R, Norris A, Kealhofer M, Nellore A, Jia Y, Hyde T, Kleinman J, Straub R, Leek JT, Weinberger D A framework for RNA quality correction in differential expression analysis bioRxiv doi: 10.1101/074245 [link]

  • Patil P, Peng RD, Leek JT (2016) A statistical definition for reproducibility and replicability bioRxiv doi: 10.1101/066803 [link]

  • Boca S and Leek JT (2015) A regression framework for the proportion of true null hypotheses bioRxiv doi:10.1101/035675 [link] [analysis code]

2017

  • 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 (2017) Integrity of induced pluripotent stem cell (iPSC) derived megakaryocytes as assessed by genetic and transcriptomic analysis [link] PLoS One. e0167794

  • Leek JT and Jager LR. (2017) Is most published research really false? [link] Annual Review of Statistics and its Applications 4:109-122.

  • Collado-Torres L, Nellore A, Kammers K, Ellis SE, Taub MA Hansen KD, Jaffe AE Langmead B, Leek JT (2017) recount: A large-scale resource of analysis-ready RNA-seq expression data bioRxiv doi: 10.1101/068478 [link] [database] [reproducible analysis] [software] accepted at Nature Biotechnology.

2016

  • Manimaran S, Selby HM, Okrah K, Ruberman C, Leek JT, Quackenbush J, Haibe-Kains B, Corrada Bravo H, Johnson WE (2016) BatchQC: Interactive software for evaluating sample and batch effects in genomic data Bioinformatics doi: 10.1093/bioinformatics/btw538 [link]

  • Nellore A, Collado-Torres L, Jaffe AE, Morton J, Pritt J, Alquicera-Hernandez J, Leek JT, Langmead B (2015) Rail-RNA: Scalable analysis of RNA-seq splicing and coverage bioRxiv doi:10.1101/019067 [link] [software] (accepted at Bioinformatics)

  • Collado Torres L, Frazee AC, Love MI, Irizarry RA, Jaffe AE, Leek JT derfinder: Software for annotation-agnostic RNA-seq differential expression analysis bioRxiv doi:10.1101/015370 [link] [software] (accepted at Nucleic Acids Research)

  • Darby MM, Leek JT, Langmead B, Yolken RB, Sabunciyan S (2016) Widespread Splicing of Repetitive Element Loci into Coding Regions of Gene Transcripts Hum. Mol. Genet. doi: 10.1093/hmg/ddw321

  • Pertea M, Kim D, Pertea GM, Leek JT, Salzberg SL (2016) Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown Nature Protocols 11, 1650–1667

  • Nellore A, Wilks C, Hansen KD, Leek JT, Langmead B (2016) Rail-dbGaP: a protocol and tool for analyzing protected genomic data in a commercial cloud Bioinformatics [link] [software] [dbgap docs]

  • Leek JT, Patil P and Peng RD (2016) What should researchers expect when they replicate studies? A statistical view of replicability in psychological science Perspectives in Psychological Science [preprint] [code] [compliled code]

  • Patil, P, Colantuoni, E, Leek, JT, Rosenblum, M (2016) Measuring the contribution of genomic predictors to improving estimator precision in randomized trials Contemporary Clinical Trials Communications. [preprint] [analysis code]

2015

  • 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. (Accepted) Evolution of cellular morpho-phenotypes in cancer metastasis Scientific Reports.

  • Jaffe AE, Hyde T, Kleinman J, Weinberger D, Chenoweth JG, McKay RD, Leek JT, and Colantuoni C. (2015) Practical impacts of genomic data “cleaning” on biological discovery using surrogate variable analysis BMC Bioinformatics 16:372 [link] [software]

  • Patil P and Leek JT (2015) Discussion of “visualizing statistical models: Removing the blindfold” Statistical Analysis and Data Mining. doi 10.1002/sam.11275 [link]

  • Collado Torres L, Jaffe AE, and Leek JT (2015) regionReport: Interactive reports for region-based analyses F1000Research 4:105 [link] [preprint] [software]

  • Frazee AC, Jaffe AE, Langmead B, Leek JT (2015) Polyester: simulating RNA-seq datasets with differential expression Bioinformatics doi:10.1093/bioinformatics/btv272 [link][preprint] [software devel][software release] [analysis code]

  • Leek JT, Peng RD (2015) P-values are just the tip of the iceberg Nature [link]

  • Patil P, Bachant-Winner PO, Haibe-Kains B, Leek JT (2014) Avoiding test set bias with rank-based predictors Bioinformatics doi: 10.1093/bioinformatics/btv157 [link] [preprint] [analysis code]

  • Frazee AC, Pertea G, Jaffe AE, Langmead B, Salzberg SL, Leek JT (2015) Ballgown bridges the gap between transcriptome assembly and expression analysis Nature Biotechnology 33, 243–246 (2015) [link] [supplement] [preprint] [software devel] [software release] [analysis code] [geuvadis data]

  • Leek JT and Peng RD (2015) What is the question? Science DOI: 10.1126/science.aaa6146 [link]

  • Leek JT and Peng RD (2015) Opinion: Reproducible research can still be wrong: Adopting a prevention approach PNAS 112 (6) 1645-1645 [link] [preprint]

2014

  • 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 (2014) Developmental regulation of human cortex transcription and its clinical relevance at single base resolution Nature Neuroscience doi:10.1038/nn.3898 [link]

  • Fisher A, Anderson GB, Leek JT (2014) A randomized trial in a massive online open course shows people don't know what a statistically significant relationship looks like, but they can learn PeerJ 2:e589 DOI 10.7717/peerj.589 [paper] [preprint] [p-value shiny app]

  • Leek JT (2014) svaseq: removing batch effects and other unwanted noise from sequencing data Nucl. Acids Res. doi: 10.1093/nar/gku864 [paper] [preprint] [software] [analysis code]

  • Parker HS, Corrada Bravo H, Leek JT. (2014) Removing batch effects for prediction problems with frozen surrogate variable analysis. PeerJ 2:e561 DOI 10.7717/peerj.561 [paper] [preprint] [software]

  • Parker HS, Leek JT, Favorov AV, Considine M, Xia X, Chavan S, Chung CH, Fertig EJ (2014) Preserving biological heterogeneity with a permuted surrogate variable analysis for genomics batch correction [link] [analysis code] [software]

  • Hayes LN, Severance EG, Leek JT, Gressitt KL, Rohleder C, Coughlin JM, Leweke FM, Yolken RH, Sawa A. (2014) Inflammatory molecular signature associated with infectious agents in psychosis. Scizhophrenia Bulletin doi: 10.1093/schbul/sbu052 [link]

  • Frazee AC, Sabunciyan S, Hansen KD, Irizarry RA, Leek JT (2014) Differential expression analysis of RNA-seq data at single-base resolution Biostatistics 10.1093/biostatistics/kxt053 [link][software] [newer software]

  • Jager LR, Leek JT (2014) An estimate of the science-wise false discovery rate and application to the top medical literature Biostatistics 15(1) 1-12 [link][blog post] [code] data [preprint]

  • Jager LR, Leek JT (2014) Rejoinder: An estimate of the science-wise false discovery rate and application to the top medical literature Biostatistics 15(1) 39-45 [link]

2013

  • Jaffe AE, Storey JD, Ji H, Leek JT (2013) Gene set bagging for estimating the probability a statistically significant result will replicate BMC Bioinformatics 14 (1), 360 [link] code

  • Marchionni L, Afsari B, Geman D, Leek JT (2013) A simple and reproducible breast cancer prognostic test BMC Genomics 14 (1) 336[link] data and code

  • Leek JT, Salzberg SL (2013) Sequestration: inadvertently killing biomedical research to score political points Genome Biology 14 (3), 109 [link]

  • Pirooznia M, Seifuddin F, Goes FS, Leek JT, Zandi PP (2013) SVAw - a web-based application tool for automated surrogate variable analysis of gene expression studies Source Code for Biology and Medicine 2013, 8:8 [link] [web app]

  • Boca SM, Corrada Bravo H, Caffo B, Leek JT, and Parmigiani G. (2013) A decision-theory approach to interpretable set analysis for high-dimensional data. Biometrics 69(3) 614-623. [pdf] [preprint]

2012

  • Corrada Bravo H, Pihur V, McCall M, Irizarry RA, Leek JT (2012). Gene expression anti-profiles as a basis for accurate universal cancer signatures BMC Bioinformatics 13:272 [link] data [code]

  • Leek JT, Rasgon JL, Taub MA. (2012) A statistical approach to selecting and confirming validation targets in -omics experiments BMC Bioinformatics 13:150 [link] [software]

  • Leek JT, Peng RD, and Anderson RR. (2012) Personalized medicine: Keep a way open for tailored treatments Nature 484: 318. [submitted version] [link] [on the blog]

  • Parker HS and Leek JT. (2012) The practical effect of batch on genomic prediction SAGMB 11: 3 [preprint] [link] [data]

  • Jaffe AE, Murakami P, Lee H, Leek JT, Fallin MD, Feinberg AP, Irizarry RA. (2012) Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies International Journal of Epidemiology 41:200-209. [link]

  • Leek JT, Johnson WE, Parker HS, Jaffe AE, and Storey JD. (2012) The sva package for removing batch effects and other unwanted variation in high-throughput experiments. Bioinformatics DOI:10.1093/bioinformatics/bts034 [link] [software]

  • Jaffe AE, Feinberg AP, Irizarry IR, and Leek JT.(2011) Significance analysis and statistical dissection of variably methylated regions Biostatistics 13: 166-178 [link] [pdf] [code]

2011

  • Frazee AC, Langmead B, and Leek JT. (2011) ReCount: A multi-experiment resource of analysis-ready RNA-seq gene count datasets BMC Bioinformatics 12:449 [link] [data]

  • Leek JT, Taub MA, Pineda FJ. (2011) Cooperation between referees and authors increases peer review accuracy PLoS One 6:e26895 [link] [data]

  • Colantuoni C, Lipska BK, Hyde TM, Tao R, Leek JT , Colantuoni EA, Elkahlhoun AG, Herman MM, Weinberger DR, Kleinman JE.(2011) Temporal dynamics and genetic control of transcription in the human prefrontal cortex Nature 478: 519-523. [pdf] [data]

  • Desai KH, Tan CS, Leek JT , Maier RV, Tompkins RG, Storey JD, and IHGRI.(2011) Dissecting inflammatory complications in critically injured patients by within-patient gene expression changes: A longitudinal clinical genomics study PLoS Medicine 8:e1001093 [link] [data]

  • Hansen KD, Wu Z, Irizarry RI, and Leek JT. (2011) Sequencing technology does not eliminate biological variability. Nature Biotechnology, 29:572–573 [pdf]

  • Leek JT, Storey JD (2011) The joint null criterion for multiple hypothesis tests. Statistical Applications in Genetics and Molecular Biology 10:28 [pdf] [code]

  • Woo S, Leek JT, Storey JD (2011) A computationally efficient modular optimal discovery procedure. Bioinformatics 27:509-515 [link] [pdf]

  • Leek JT. (2011) Asymptotic conditional singular value decomposition for high-dimensional genomic data. Biometrics 67:344-352 [pdf] [code]

2010

  • Leek JT , Scharpf RB, Corrada Bravo H, Simcha D, Langmead B, Johnson WE, Geman D, Baggerly K, Irizarry RA (2010), Tackling the widespread and critical impact of batch effects in high-throughput data. Nature Reviews Genetics 11:733-739 [link] [pdf] [data]

  • Langmead B, Hansen KD, Leek JT (2010), Cloud-scale RNA-sequencing differential expression analysis with Myrna. Genome Biology 11:R83. [link] [pdf] [code]

  • Lu R, Markowetz F, Unwin RD, Leek JT , Airoldi EM, MacArthur BD, Lachmann A, Rozov R, Ma'ayan A, Boyer LA, Troyanskaya OG, Whetton AD, and Lemischka IR. (2010) Systems-level dynamic analyses of fate change in murine embryonic stem cells. Nature 462: 358:362. [pdf]

2009 and Earlier

  • Leek JT. (2009) The tspair package for finding top scoring pair classifiers in R. Bioinformatics 25:1203-1204. [pdf] [software]

  • Leek JT and Storey JD. (2008) A general framework for multiple testing dependence. Proceedings of the National Academy of Sciences , 105: 18718-18723. [pdf] [software]

  • Leek JT and Storey JD. (2007) Capturing heterogeneity in gene expression studies by `Surrogate Variable Analysis'. PLoS Genetics, 3: e161. [link] [software]

  • Akey JM, Biswas S, Leek JT, and Storey JD. (2007) On the design and analysis of expression studies in human populations. Nature Genetics, 39: 807-808. [pdf]

  • Storey JD, Dai JY, and Leek JT. (2006), The optimal discovery procedure for large-scale significance testing, with applications to comparative microarray experiments. Biostatistics, 8: 414-432. [pdf] [software]

  • Leek JT, Monsen E, Dabney AR, and Storey JD. (2006), EDGE: Extraction and analysis of differential gene expression. Bioinformatics, 22: 507-508. [pdf] [software]

  • Storey JD, Xiao W, Leek JT, Tompkins RG, and Davis RW. (2005), Significance analysis of timecourse microarray experiments. Proceedings of the National Academy of Sciences, 102: 12837-12842. [pdf] [software]