OntologyTraverser: an R package for GO analysis. - Andrew Young; Nathan Whitehouse; J. Cho; Chad A. Shaw (Bioinform., 2005)

The Hematopoietic Expression Viewer: expanding mobile apps as a scientific tool. - Regis A. James; Mitchell M. Rao; Edward S. Chen; Margaret A. Goodell; Chad A. Shaw (Bioinform., 2012)

NetComm: a network analysis tool based on communicability. - Ian M. Campbell; Regis A. James; Edward S. Chen; Chad A. Shaw (Bioinform., 2014)

An efficient algorithm for accurate computation of the Dirichlet-multinomial log-likelihood function. - Peng Yu; Chad A. Shaw (Bioinform., 2014)

Design tools for MPRA experiments. - Andrew R. Ghazi; Edward S. Chen; David M. Henke; Namrata Madan; Leonard C. Edelstein; Chad A. Shaw (Bioinform., 2018)

Bayesian modelling of high-throughput sequencing assays with malacoda. - Andrew R. Ghazi; Xianguo Kong; Edward S. Chen; Leonard C. Edelstein; Chad A. Shaw (PLoS Comput. Biol., 2020)

A joint modeling approach for longitudinal microbiome data improves ability to detect microbiome associations with disease. - Pamela N. Luna; Jonathan M. Mansbach; Chad A. Shaw (PLoS Comput. Biol., 2020)