PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF. - Genevieve L. Stein-O'Brien; Jacob L. Carey; Waishing Lee; Michael Considine; Alexander V. Favorov; Emily Flam; Theresa Guo; Sijia Li; Luigi Marchionni; Thomas Sherman; Shawn Sivy; Daria A. Gaykalova; et al. (Bioinform., 2017)

Detection of rare disease variants in extended pedigrees using RVS. - Thomas Sherman; Jack M. Fu; Robert B. Scharpf; Alexandre Bureau; Ingo Ruczinski (Bioinform., 2019)

CancerInSilico: An R/Bioconductor package for combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer. - Thomas Sherman; Luciane T. Kagohara; Raymon Cao; Raymond Cheng; Matthew Satriano; Michael Considine; Gabriel Krigsfeld; Ruchira Ranaweera; Yong Tang; Sandra A. Jablonski; Genevieve L. Stein-O'Brien; Daria A. Gaykalova; et al. (PLoS Comput. Biol., 2019)

CoGAPS 3: Bayesian non-negative matrix factorization for single-cell analysis with asynchronous updates and sparse data structures. - Thomas Sherman; Tiger Gao; Elana J. Fertig (BMC Bioinform., 2020)