Coordinated Concentration Changes of Transcripts and Metabolites in Saccharomyces cerevisiae. - Patrick H. Bradley; Matthew J. Brauer; Joshua D. Rabinowitz; Olga G. Troyanskaya (PLoS Comput. Biol., 2009)

Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes. - Stephen Nayfach; Patrick H. Bradley; Stacia K. Wyman; Timothy J. Laurent; Alexander G. Williams; Jonathan A. Eisen; Katherine S. Pollard; Thomas J. Sharpton (PLoS Comput. Biol., 2015)

Phylogeny-corrected identification of microbial gene families relevant to human gut colonization. - Patrick H. Bradley; Stephen Nayfach; Katherine S. Pollard (PLoS Comput. Biol., 2018)

phylogenize: correcting for phylogeny reveals genes associated with microbial distributions. - Patrick H. Bradley; Katherine S. Pollard (Bioinform., 2020)