The Bradley Lab

Our long-term aim is to understand the gut microbiome as well as we currently understand model microbes, using both computational and high-throughput experimental tools. This understanding will allow us to interpret and eventually to modulate human microbiomes more precisely. We are part of Ohio State’s Department of Microbiology, Infectious Diseases Institute, and Center of Microbiome Science.

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The Bradley Lab

Latest News

Apr 7, 2025 1 min read
Kananen et al. published; Majernik et al. accepted

Big congratulations to Kat and Stephanie on their papers being published and accepted, respectively!
Nov 30, 2024 1 min read
Congrats Stephanie!

Congrats to Stephanie for successfully passing her candidacy and submitting her new paper developing a tool (PanSweep) to help identify contamination in pangenomes!
Sep 26, 2024 1 min read
New Paper Submission

Congrats to both Kat and Patrick for their paper submission about functional annotation improvements using adaptive thresholds!
Aug 25, 2024 1 min read
Goodbye Larry!

Congrats to Larry Beaver for his new position at the Energy Advancement and Innovation Center here on West Campus. We are sad to see you go, but are extremely grateful for everything you have done for the group.
Jul 25, 2024 1 min read
ISMB 2024
ISMB 2024

We have returned from ISMB with many a new idea. Patrick Bradley gave a fantastic talk on his tool Phylogenize2. In addition, both Stephanie Majernik and Kathryn Kananen gave talks on some of the work they have been doing on pangenome contamination and genome annotation.
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Recent Publications

Adaptive adjustment of significance thresholds produces large gains in microbial gene annotations and metabolic insights
Gene function annotations enable microbial ecologists to make inferences about metabolic potential from genomes and metagenomes. …
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Framework for exploring the sensory repertoire of the human gut microbiota
Bacteria sense changes in their environment and transduce signals to adjust their cellular functions accordingly. For this purpose, …
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Host and gut bacteria share metabolic pathways for anti-cancer drug metabolism
Pharmaceuticals have extensive reciprocal interactions with the microbiome, but whether bacterial drug sensitivity and metabolism is …
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phylogenize: correcting for phylogeny reveals genes associated with microbial distributions
Phylogenetic comparative methods are powerful but presently under-utilized ways to identify microbial genes underlying differences in …
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Minor isozymes tailor yeast metabolism to carbon availability
Isozymes are enzymes that differ in sequence but catalyze the same chemical reactions. Despite their apparent redundancy, isozymes are …
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Recent Preprints (in review)

Human xenobiotic metabolism proteins have full-length and split homologs in the gut microbiome
Xenobiotics, including pharmaceutical drugs, can be metabolized by both host and microbiota, in some cases by homologous enzymes. We …
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Small amounts of misassembly can have disproportionate effects on pangenome-based metagenomic analyses
Individual genes from microbiomes can drive host-level phenotypes. To help identify such candidate genes, several recent tools estimate …
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Featured Projects

PanSweep
Find potential pangenome contaminants
PanSweep
phylogenize
Find genes underlying microbial environment associations with phylogenize
phylogenize

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