Publications


    2012

  • Corrada Bravo H*, Pihur V*, McCall M*, Irizarry RA and Leek JT (2012). Gene expression anti-profiles as a basis for accurate universal cancer signatures BMC Bioinformatics 13:272 [link] [data]
  • Leek JT+, Rasgon JL, Taub MA*. (2012) "A statistical approach to selecting and confirming validation targets in -omics experiments" BMC Bioinformatics 13:150 [pdf] [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 [pdf] [supplemental materials] [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]

    • 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] [link] [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]
  • Boca SM*, Corrada Bravo H*, Brian Caffo, Leek JT+, and Parmigiani G. (2010) "A decision-theory approach to interpretable set analysis for high-dimensional data." JHU Biostat Working Paper 211. [link]
  • 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. [pdf] [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]
* = Hopkins Student/Postdoctoral Fellow; + = J. Leek a corresponding author