msHOT: modifying Hudson's ms simulator to incorporate crossover and gene conversion hotspots. - Garrett Hellenthal; Matthew Stephens (Bioinform., 2007)

Variance adaptive shrinkage (vash): flexible empirical Bayes estimation of variances. - Mengyin Lu; Matthew Stephens (Bioinform., 2016)

A new sequence logo plot to highlight enrichment and depletion. - Kushal K. Dey; Dongyue Xie; Matthew Stephens (BMC Bioinform., 2018)

Inference and visualization of DNA damage patterns using a grade of membership model. - Hussein Al-Asadi; Kushal K. Dey; John Novembre; Matthew Stephens (Bioinform., 2019)

Creating and sharing reproducible research code the workflowr way. - John D. Blischak; Peter Carbonetto; Matthew Stephens (F1000Research, 2019)

Non-negative matrix factorization algorithms greatly improve topic model fits. - Peter Carbonetto; Abhishek Sarkar; Zihao Wang; Matthew Stephens (CoRR, 2021)

Empirical Bayes Matrix Factorization. - Wei Wang; Matthew Stephens (J. Mach. Learn. Res., 2021)

Flexible Signal Denoising via Flexible Empirical Bayes Shrinkage. - Zhengrong Xing; Peter Carbonetto; Matthew Stephens (J. Mach. Learn. Res., 2021)

A flexible empirical Bayes approach to multiple linear regression and connections with penalized regression. - Youngseok Kim; Wei Wang; Peter Carbonetto; Matthew Stephens (J. Mach. Learn. Res., 2024)