Review of the Stata statistical package. - Thomas Lumley (Stat. Comput., 1999)

Environmental Statistics With S-PLUS. - Thomas Lumley (Technometrics, 2001)

An Open Source Environment For The Statistical Evaluation Of Outbreak Detection Methods. - Thomas Lumley; Krisztian Sebestyen; William B. Lober; Ian S. Painter (AMIA, 2005)

GWASTools: an R/Bioconductor package for quality control and analysis of genome-wide association studies. - Stephanie M. Gogarten; Tushar Bhangale; Matthew P. Conomos; Cecelia A. Laurie; Caitlin P. McHugh; Ian S. Painter; Xiuwen Zheng 001; David R. Crosslin; David Levine; Thomas Lumley; Sarah C. Nelson; Ken Rice; et al. (Bioinform., 2012)

Fast computation for genome-wide association studies using boosted one-step statistics. - Arend Voorman; Ken Rice; Thomas Lumley (Bioinform., 2012)

Best of both worlds: relational databases and statistics. - Hannes Mühleisen; Thomas Lumley (SSDBM, 2013)

Time to Diagnosis: Accounting for Differential Endpoint Follow-up in Multi-Cohort Studies. - Petra Buzková; Thomas Lumley (Commun. Stat. Simul. Comput., 2015)

Numerical evaluation of methods approximating the distribution of a large quadratic form in normal variables. - Tong Chen 009; Thomas Lumley (Comput. Stat. Data Anal., 2019)

Privacy with Good Taste - A Case Study in Quantifying Privacy Risks in Genetic Scores. - Raúl Pardo; Willard Rafnsson; Gregor Steinhorn; Denis Lavrov; Thomas Lumley; Christian W. Probst; Ilze Ziedins 001; Andrzej Wasowski (DPM/CBT@ESORICS, 2022)

OrigamiPlot: An R Package and Shiny Web App Enhanced Visualizations for Multivariate Data. - Yiwen Lu; Jiayi Tong; Yuqing Lei; Alex J. Sutton; Haitao Chu; Lisa D. Levine; Thomas Lumley; David A. Asch; Rui Duan 004; Christopher H. Schmid; Yong Chen 016 (CoRR, 2024)

Leveraging error-prone algorithm-derived phenotypes: Enhancing association studies for risk factors in EHR data. - Yiwen Lu; Jiayi Tong; Jessica Chubak; Thomas Lumley; Rebecca A. Hubbard; Hua Xu 001; Yong Chen 016 (J. Biomed. Informatics, 2024)

Multiple Imputation Through XGBoost. - Yongshi Deng; Thomas Lumley (J. Comput. Graph. Stat., 2024)

SAT-Metropolis: Combining Markov Chain Monte Carlo with SAT/SMT Sampling. - Maja Aaslyng Dall; Raúl Pardo; Thomas Lumley; Andrzej Wasowski (SAT, 2025)

COLA-GLM: collaborative one-shot and lossless algorithms of generalized linear models for decentralized observational healthcare data. - Qiong Wu; Jenna Marie Reps; Lu Li; Bingyu Zhang; Yiwen Lu; Jiayi Tong; Dazheng Zhang; Thomas Lumley; Milou T. Brand; Mui Van Zandt; Thomas Falconer; Xing He 003; et al. (npj Digit. Medicine, 2025)