Jeffrey T. Leek

36 papers Journal 36
YearRankTypeTitle / Venue / Authors
2026 J jnl
PanCanBench: A Comprehensive Benchmark for Evaluating Large Language Models in Pancreatic Oncology.
CoRR
Yimin Zhao, Sheela R. Damle, Simone E. Dekker, Scott Geng, Karly Williams Silva, Jesse J. Hubbard, Manuel F. Fernandez, Fatima Zelada-Arenas, Alejandra Alvarez, Brianne Flores, Alexis Rodriguez, Stephen Salerno, Carrie Wright, Zihao Wang, Pang Wei Koh, Jeffrey T. Leek
2025 J jnl
Do We Really Even Need Data? A Modern Look at Drawing Inference with Predicted Data.
CoRR
Stephen Salerno, Kentaro Hoffman, Awan Afiaz, Anna Neufeld, Tyler H. McCormick, Jeffrey T. Leek
2025 J jnl
ipd: an R package for conducting inference on predicted data.
Bioinform.
Stephen Salerno, Jiacheng Miao, Awan Afiaz, Kentaro Hoffman, Anna Neufeld, Qiongshi Lu, Tyler H. McCormick, Jeffrey T. Leek
2024 J jnl
Best practices to evaluate the impact of biomedical research software - metric collection beyond citations.
Bioinform.
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, Paul C. Boutros, Spyridon Bakas, J. Gregory Caporaso, Guilherme Del Fiol, Harry Hochheiser, Brian Haas, Patrick D. Schloss, James A. Eddy, Jake Albrecht, Andrey Fedorov, Levi Waldron, Ava M. Hoffman, Richard L. Bradshaw, Jeffrey T. Leek, Carrie Wright
2024 J jnl
Do We Really Even Need Data?
CoRR
Kentaro Hoffman, Stephen Salerno, Awan Afiaz, Jeffrey T. Leek, Tyler H. McCormick
2024 J jnl
From Narratives to Numbers: Valid Inference Using Language Model Predictions from Verbal Autopsy Narratives.
CoRR
Shuxian Fan, Adam Visokay, Kentaro Hoffman, Stephen Salerno, Li Liu, Jeffrey T. Leek, Tyler H. McCormick
2023 J jnl
Evaluation of software impact designed for biomedical research: Are we measuring what's meaningful?
CoRR
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, Paul C. Boutros, Spyridon Bakas, J. Gregory Caporaso, Guilherme Del Fiol, Harry Hochheiser, Brian Haas, Patrick D. Schloss, James A. Eddy, Jake Albrecht, Andrey Fedorov, Levi Waldron, Ava M. Hoffman, Richard L. Bradshaw, Jeffrey T. Leek, Carrie Wright
2023 J jnl
Motivation, inclusivity, and realism should drive data science education.
CoRR
Candace Savonen, Carrie Wright, Ava M. Hoffman, Elizabeth M. Humphries, Katherine E. L. Cox, Frederick J. Tan, Jeffrey T. Leek
2022 J jnl
Diversifying the Genomic Data Science Research Community.
CoRR
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, Shazia Tabassum Hakim, Ava M. Hoffman, Natalie Kucher, Andrew Lee, Joslynn Lee, Jeffrey T. Leek, Robert Meller, Loyda B. Méndez, Miguel P. Méndez-González, Stephen Mosher, Michele Nishiguchi, Siddharth Pratap, Tiffany Rolle, Sourav Roy, Rachel Saidi, Michael C. Schatz, Shurjo Sen, James Sniezek, Edu Suarez Martinez, Frederick Tan, Jennifer Vessio, Karriem Watson, Wendy Westbroek, Joseph Wilcox, Xianfa Xie
2022 J jnl
Open-source Tools for Training Resources - OTTR.
CoRR
Candace Savonen, Carrie Wright, Ava M. Hoffman, John Muschelli, Katherine E. L. Cox, Frederick J. Tan, Jeffrey T. Leek
2021 J jnl
Linking open-source code commits and MOOC grades to evaluate massive online open peer review.
CoRR
Siruo Wang, Leah R. Jager, Kai Kammers, Aboozar Hadavand, Jeffrey T. Leek
2020 J jnl
Ari: The Automated R Instructor.
CoRR
Sean Kross, Jeffrey T. Leek, John Muschelli
2020 J jnl
Tools for Analyzing R Code the Tidy Way.
R J.
Lucy D'Agostino McGowan, Sean Kross, Jeffrey T. Leek
2020 J jnl
ari: The Automated R Instructor.
R J.
Sean Kross, Jeffrey T. Leek, John Muschelli
2019 J jnl
Analysis of Student Behavior Using the R Package crsra.
J. Learn. Anal.
Aboozar Hadavand, John Muschelli, Jeffrey T. Leek
2017 J jnl
Rail-RNA: scalable analysis of RNA-seq splicing and coverage.
Bioinform.
Abhinav Nellore, Leonardo Collado-Torres, Andrew E. Jaffe, José Alquicira-Hernández, Christopher Wilks, Jacob Pritt, James Morton, Jeffrey T. Leek, Ben Langmead
2016 J jnl
BatchQC: interactive software for evaluating sample and batch effects in genomic data.
Bioinform.
Solaiappan Manimaran, Heather Marie Selby, Kwame Okrah, Claire Ruberman, Jeffrey T. Leek, John Quackenbush, Benjamin Haibe-Kains, Héctor Corrada Bravo, W. Evan Johnson
2016 J jnl
Erratum to: Practical impacts of genomic data "cleaning" on biological discovery using surrogate variable analysis.
BMC Bioinform.
Andrew E. Jaffe, Thomas Hyde, Joel Kleinman, Daniel R. Weinberger, Joshua Chenoweth, Ronald McKay, Jeffrey T. Leek, Carlo Colantuoni
2016 J jnl
Rail-dbGaP: analyzing dbGaP-protected data in the cloud with Amazon Elastic MapReduce.
Bioinform.
Abhinav Nellore, Christopher Wilks, Kasper D. Hansen, Jeffrey T. Leek, Ben Langmead
2015 J jnl
Discussion of "visualizing statistical models: Removing the blindfold".
Stat. Anal. Data Min.
Prasad Patil, Jeffrey T. Leek
2015 J jnl
Practical impacts of genomic data "cleaning" on biological discovery using surrogate variable analysis.
BMC Bioinform.
Andrew E. Jaffe, Thomas Hyde, Joel Kleinman, Daniel Weinbergern, Joshua Chenoweth, Ronald McKay, Jeffrey T. Leek, Carlo Colantuoni
2015 J jnl
Reproducible Research Can Still Be Wrong: Adopting a Prevention Approach.
CoRR
Jeffrey T. Leek, Roger D. Peng
2015 J jnl
Statistics:
Nat.
Jeffrey T. Leek, Roger D. Peng
2015 J jnl
Test set bias affects reproducibility of gene signatures.
Bioinform.
Prasad Patil, Pierre-Olivier Bachant-Winner, Benjamin Haibe-Kains, Jeffrey T. Leek
2015 J jnl
regionReport: Interactive reports for region-based analyses.
F1000Research
Leonardo Collado-Torres, Andrew E. Jaffe, Jeffrey T. Leek
2014 J jnl
Preserving biological heterogeneity with a permuted surrogate variable analysis for genomics batch correction.
Bioinform.
Hilary S. Parker, Jeffrey T. Leek, Alexander V. Favorov, Michael Considine, Xiaoxin Xia, Sameer Chavan, Christine H. Chung, Elana J. Fertig
2013 J jnl
Gene set bagging for estimating the probability a statistically significant result will replicate.
BMC Bioinform.
Andrew E. Jaffe, John D. Storey, Hongkai Ji, Jeffrey T. Leek
2013 J jnl
SVAw - a web-based application tool for automated surrogate variable analysis of gene expression studies.
Source Code Biol. Medicine
Mehdi Pirooznia, Fayaz Seifuddin, Fernando S. Goes, Jeffrey T. Leek, Peter P. Zandi
2012 J jnl
A statistical approach to selecting and confirming validation targets in -omics experiments.
BMC Bioinform.
Jeffrey T. Leek, Margaret Taub, Jason L. Rasgon
2012 J jnl
Gene expression anti-profiles as a basis for accurate universal cancer signatures.
BMC Bioinform.
Héctor Corrada Bravo, Vasyl Pihur, Matthew N. McCall, Rafael A. Irizarry, Jeffrey T. Leek
2012 J jnl
The sva package for removing batch effects and other unwanted variation in high-throughput experiments.
Bioinform.
Jeffrey T. Leek, W. Evan Johnson, Hilary S. Parker, Andrew E. Jaffe, John D. Storey
2011 J jnl
A computationally efficient modular optimal discovery procedure.
Bioinform.
Sangsoon Woo, Jeffrey T. Leek, John D. Storey
2011 J jnl
ReCount: A multi-experiment resource of analysis-ready RNA-seq gene count datasets.
BMC Bioinform.
Alyssa C. Frazee, Ben Langmead, Jeffrey T. Leek
2009 J jnl
The
Bioinform.
Jeffrey T. Leek
2006 J jnl
EDGE: extraction and analysis of differential gene expression.
Bioinform.
Jeffrey T. Leek, Eva Monsen, Alan R. Dabney, John D. Storey
2006 J jnl
EDGE: extraction and analysis of differential gene expression.
Bioinform.
Jeffrey T. Leek, Eva Monsen, Alan R. Dabney, John D. Storey