EDGE: extraction and analysis of differential gene expression. - Jeffrey T. Leek; Eva Monsen; Alan R. Dabney; John D. Storey (Bioinform., 2006)

The tspair package for finding top scoring pair classifiers in R. - Jeffrey T. Leek (Bioinform., 2009)

A computationally efficient modular optimal discovery procedure. - Sangsoon Woo; Jeffrey T. Leek; John D. Storey (Bioinform., 2011)

ReCount: A multi-experiment resource of analysis-ready RNA-seq gene count datasets. - Alyssa C. Frazee; Ben Langmead; Jeffrey T. Leek (BMC Bioinform., 2011)

The sva package for removing batch effects and other unwanted variation in high-throughput experiments. - Jeffrey T. Leek; W. Evan Johnson; Hilary S. Parker; Andrew E. Jaffe; John D. Storey (Bioinform., 2012)

Gene expression anti-profiles as a basis for accurate universal cancer signatures. - Héctor Corrada Bravo; Vasyl Pihur; Matthew N. McCall; Rafael A. Irizarry; Jeffrey T. Leek (BMC Bioinform., 2012)

A statistical approach to selecting and confirming validation targets in -omics experiments. - Jeffrey T. Leek; Margaret Taub; Jason L. Rasgon (BMC Bioinform., 2012)

Gene set bagging for estimating the probability a statistically significant result will replicate. - Andrew E. Jaffe; John D. Storey; Hongkai Ji; Jeffrey T. Leek (BMC Bioinform., 2013)

SVAw - a web-based application tool for automated surrogate variable analysis of gene expression studies. - Mehdi Pirooznia; Fayaz Seifuddin; Fernando S. Goes; Jeffrey T. Leek; Peter P. Zandi (Source Code Biol. Medicine, 2013)

Preserving biological heterogeneity with a permuted surrogate variable analysis for genomics batch correction. - Hilary S. Parker; Jeffrey T. Leek; Alexander V. Favorov; Michael Considine; Xiaoxin Xia; Sameer Chavan; Christine H. Chung; Elana J. Fertig (Bioinform., 2014)

Polyester: simulating RNA-seq datasets with differential transcript expression. - Alyssa C. Frazee; Andrew E. Jaffe; Ben Langmead; Jeffrey T. Leek (Bioinform., 2015)

Test set bias affects reproducibility of gene signatures. - Prasad Patil; Pierre-Olivier Bachant-Winner; Benjamin Haibe-Kains; Jeffrey T. Leek (Bioinform., 2015)

Practical impacts of genomic data "cleaning" on biological discovery using surrogate variable analysis. - Andrew E. Jaffe; Thomas Hyde; Joel Kleinman; Daniel Weinbergern; Joshua Chenoweth; Ronald McKay; Jeffrey T. Leek; Carlo Colantuoni (BMC Bioinform., 2015)

Reproducible Research Can Still Be Wrong: Adopting a Prevention Approach. - Jeffrey T. Leek; Roger D. Peng (CoRR, 2015)

regionReport: Interactive reports for region-based analyses. - Leonardo Collado-Torres; Andrew E. Jaffe; Jeffrey T. Leek (F1000Research, 2015)

Statistics: P values are just the tip of the iceberg. - Jeffrey T. Leek; Roger D. Peng (Nat., 2015)

Discussion of "visualizing statistical models: Removing the blindfold". - Prasad Patil; Jeffrey T. Leek (Stat. Anal. Data Min., 2015)

BatchQC: interactive software for evaluating sample and batch effects in genomic data. - Solaiappan Manimaran; Heather Marie Selby; Kwame Okrah; Claire Ruberman; Jeffrey T. Leek; John Quackenbush; Benjamin Haibe-Kains; Héctor Corrada Bravo; W. Evan Johnson (Bioinform., 2016)

Rail-dbGaP: analyzing dbGaP-protected data in the cloud with Amazon Elastic MapReduce. - Abhinav Nellore; Christopher Wilks; Kasper D. Hansen; Jeffrey T. Leek; Ben Langmead (Bioinform., 2016)

Erratum to: Practical impacts of genomic data "cleaning" on biological discovery using surrogate variable analysis. - Andrew E. Jaffe; Thomas Hyde; Joel Kleinman; Daniel R. Weinberger; Joshua Chenoweth; Ronald McKay; Jeffrey T. Leek; Carlo Colantuoni (BMC Bioinform., 2016)

Rail-RNA: scalable analysis of RNA-seq splicing and coverage. - Abhinav Nellore; Leonardo Collado-Torres; Andrew E. Jaffe; José Alquicira-Hernández; Christopher Wilks; Jacob Pritt; James Morton; Jeffrey T. Leek; Ben Langmead (Bioinform., 2017)

Analysis of Student Behavior Using the R Package crsra. - Aboozar Hadavand; John Muschelli; Jeffrey T. Leek (J. Learn. Anal., 2019)

ari: The Automated R Instructor. - Sean Kross; Jeffrey T. Leek; John Muschelli (R J., 2020)

Tools for Analyzing R Code the Tidy Way. - Lucy D'Agostino McGowan; Sean Kross; Jeffrey T. Leek (R J., 2020)

Linking open-source code commits and MOOC grades to evaluate massive online open peer review. - Siruo Wang; Leah R. Jager; Kai Kammers; Aboozar Hadavand; Jeffrey T. Leek (CoRR, 2021)

Diversifying the Genomic Data Science Research Community. - Rosa Alcazar; Maria Alvarez; Rachel Arnold; Mentewab Ayalew; Lyle G. Best; Michael C. Campbell; Kamal Chowdhury; Katherine E. L. Cox; Christina Daulton; Youping Deng; Carla Easter; Karla Fuller; et al. (CoRR, 2022)

Open-source Tools for Training Resources - OTTR. - Candace Savonen; Carrie Wright; Ava M. Hoffman; John Muschelli; Katherine E. L. Cox; Frederick J. Tan; Jeffrey T. Leek (CoRR, 2022)

Motivation, inclusivity, and realism should drive data science education. - Candace Savonen; Carrie Wright; Ava M. Hoffman; Elizabeth M. Humphries; Katherine E. L. Cox; Frederick J. Tan; Jeffrey T. Leek (CoRR, 2023)

Evaluation of software impact designed for biomedical research: Are we measuring what's meaningful? - Awan Afiaz; Andrey Ivanov; John Chamberlin; David Hanauer; Candace Savonen; Mary J. Goldman; Martin Morgan; Michael Reich; Alexander Getka; Aaron Holmes; Sarthak Pati; Dan Knight; et al. (CoRR, 2023)

Do We Really Even Need Data? - Kentaro Hoffman; Stephen Salerno; Awan Afiaz; Jeffrey T. Leek; Tyler H. McCormick (CoRR, 2024)

From Narratives to Numbers: Valid Inference Using Language Model Predictions from Verbal Autopsy Narratives. - Shuxian Fan; Adam Visokay; Kentaro Hoffman; Stephen Salerno; Li Liu; Jeffrey T. Leek; Tyler H. McCormick (CoRR, 2024)