Patrick Bradley

Publications

• Phylogenetic portrait of the Saccharomyces cerevisiae functional genome.
• A new system for comparative functional genomics of Saccharomyces yeasts.
• Yeast cells can access distinct quiescent states.
• Growth-limiting intracellular metabolites in yeast growing under diverse nutrient limitations.
• Coordinated concentration changes of transcripts and metabolites in Saccharomyces cerevisiae.
• Proteobacteria explain significant functional variability in the human gut microbiome
• Phylogeny-corrected identification of microbial gene families relevant to human gut colonization
• Minor Isozymes Tailor Yeast Metabolism to Carbon Availability
• Host and gut bacteria share metabolic pathways for anti-cancer drug metabolism
• Framework for exploring the sensory repertoire of the human gut microbiota
• Adaptive adjustment of significance thresholds produces large gains in microbial gene annotations and metabolic insights
• Small amounts of misassembly can have disproportionate effects on pangenome-based metagenomic analyses
• Human xenobiotic metabolism proteins have full-length and split homologs in the gut microbiome
• Adaptive adjustment of profile HMM significance thresholds improves functional and metabolic insights into microbial genomes