Patrick H. Bradley

Anaerobic riboflavin degradation by human gut Lachnospiraceae

This study identifies C. scindens as the first anaerobe to catabolize riboflavin into lumichrome, revealing a novel gene neighborhood for anaerobic flavin degradation in Lachnospiraceae.

Phylogenize2: robust phylogenetic methods link genes to phenotypes across host-associated and environmental microbiomes

Phylogenize2 links microbial gene families to abundance phenotypes across diverse environments, identifying genes associated with specific ecological roles.

A robust, sensitive phylogenetic method enables gene-level metagenomic analyses

The paper develops a new statistical method for metagenomic gene-level analysis that reduces false positives and identifies a novel transcription factor linked to liver cirrhosis.

Optimizing Strain Selection for Association Studies Under Hard Cost Constraints

The paper evaluates strain selection methods under cost constraints for association studies, finding that cost-based approaches often outperform diversity-focused ones.

Human xenobiotic metabolism proteins have full-length and split homologs in the gut microbiome

The paper identifies full-length and split homologs of human xenobiotic metabolism proteins in the gut microbiome, revealing their roles in drug metabolism and highlighting potential implications for microbial contributions to xenobiotic processing.

Small amounts of misassembly can have disproportionate effects on pangenome-based metagenomic analyses

The paper shows that contamination in metagenome assemblies can lead to false positive gene associations in pangenome-based analyses, but provides a method to identify and remove these contaminants.

Adaptive adjustment of significance thresholds produces large gains in microbial gene annotations and metabolic insights

The paper improves microbial gene annotations by adaptively adjusting significance thresholds, enhancing sensitivity without sacrificing accuracy, especially for non-model organisms and underrepresented protein families.

phylogenize: correcting for phylogeny reveals genes associated with microbial distributions

phylogenize corrects for phylogeny to identify microbial genes associated with community composition differences using 16S and shotgun sequencing data.

Minor isozymes tailor yeast metabolism to carbon availability

The paper identifies two minor yeast isozymes, ACO2 and PYK2, that have distinct roles in adapting to carbon availability through differential expression and functional advantages under specific metabolic conditions.

Phylogeny-corrected identification of microbial gene families relevant to human gut colonization

The paper identifies microbial genes associated with gut colonization and disease by using phylogenetic correction in metagenomic data analysis.

Proteobacteria drive significant functional variability in the human gut microbiome

The paper identifies genes with significant variability across healthy human gut microbiomes, revealing functional differences driven by Proteobacteria.

Automated and accurate estimation of gene family abundance from shotgun metagenomes

This paper develops ShotMAP, a metagenome annotation pipeline, and evaluates its performance on marine and gut microbiome data, finding functional differences in Crohn's disease patients.