Publications and Preprints

Christian J. Quiles Pérez, Alexandria Olzak, Aminata Fofana, Kamal Deep, Calissa Carlisle, Emily Bradley, Kathryn Kananen, Larry Beaver, Connor Skaggs, Justin A. North, Patrick H. Bradley (2026). Anaerobic riboflavin degradation by human gut Lachnospiraceae. Journal of Bacteriology.

Christoph D. Rau, Patrick H. Bradley (2026). Optimizing strain selection for association studies under hard cost constraints. GENETICS.

Kathryn Kananen, Nghi Tran, Patrick H. Bradley (2026). Phylogenize2: robust phylogenetic methods link genes to phenotypes across host-associated and environmental microbiomes. bioRxiv.

Nghi Tran, Kathryn Kananen, Patrick H. Bradley (2026). A robust, sensitive phylogenetic method enables gene-level metagenomic analyses. bioRxiv.

Matthew Rendina, Peter J. Turnbaugh, Patrick H. Bradley (2025). Human xenobiotic metabolism proteins have full-length and split homologs in the gut microbiome. G3 Genes|Genomes|Genetics.

Stephanie N. Majernik, Larry Beaver, Patrick H. Bradley (2025). Small amounts of misassembly can have disproportionate effects on pangenome-based metagenomic analyses. mSphere.

Kathryn Kananen, Iva Veseli, Christian J. Quiles Pérez, Samuel Miller, A. Murat Eren, Patrick H. Bradley (2025). Adaptive adjustment of significance thresholds produces large gains in microbial gene annotations and metabolic insights. Bioinformatics Advances.

Shiva Jahanbahkshi, Amna Bibi, Rebecca Hoyd, Caroline Dravillas, Nyelia Williams, Shiqi Zhang, Aaditya Pallerla, Shankar Suman, Joseph Amann, Mounika Goruganthu, Tamio Okimoto, Yangyang Liu, Marisa A. Bittoni, Ni Shi, Alvin Anand, Bailey Conrad, Lane Nevers, Kristen Heitman, Maxine Webb, Elizabeth M Grainger, Madison Grogan, Christian Quiles, Tong Chen, Carolyn J. Presley, Lang Li, Patrick Bradley, Yael Vodovotz, David P. Carbone, Steven K. Clinton, Jiangjiang Zhu, Daniel Spakowicz (2025). Berry Supplement-Modified Human Microbiome Improves Immunotherapy Response in Mouse Models. medRxiv.

Patricia A. Ross, Wenhao Xu, Ekaterina Jalomo-Khayrova, Gert Bange, Vadim M. Gumerov, Patrick H. Bradley, Victor Sourjik, Igor B. Zhulin (2024). Framework for exploring the sensory repertoire of the human gut microbiota. mBio.

Patrick H. Bradley (2023). Four-part harmony between diet, drugs, microbes, and host. Cell Host & Microbe.

Patrick H. Bradley, Katherine S. Pollard (2020). Building a chemical blueprint for human blood. Nature.

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

Patrick H. Bradley, Patrick A. Gibney, David Botstein, Olga G. Troyanskaya, Joshua D. Rabinowitz (2019). Minor isozymes tailor yeast metabolism to carbon availability. mSystems.

Patrick H. Bradley, Stephen Nayfach, Katherine S. Pollard (2018). Phylogeny-corrected identification of microbial gene families relevant to human gut colonization. PLOS Computational Biology.

Patrick H. Bradley, Katherine S. Pollard (2017). Proteobacteria explain significant functional variability in the human gut microbiome. Microbiome.

Stephen Nayfach, Patrick H. Bradley, Stacia K. Wyman, Timothy J. Laurent, Alex Williams, Jonathan A. Eisen, Katherine S. Pollard, Thomas J. Sharpton (2015). Automated and accurate estimation of gene family abundance from shotgun metagenomes. PLoS Computational Biology.

Amy a Caudy, Yuanfang Guan, Yue Jia, Christina Hansen, Chris DeSevo, Alicia P Hayes, Joy Agee, Juan R Alvarez-Dominguez, Hugo Arellano, Daniel Barrett, Cynthia Bauerle, Namita Bisaria, Patrick H Bradley, J Scott Breunig, Erin Bush, David Cappel, Emily Capra, Walter Chen, John Clore, Peter a Combs, Christopher Doucette, Olukunle Demuren, Peter Fellowes, Sam Freeman, Evgeni Frenkel, Daniel Gadala-Maria, Richa Gawande, David Glass, Samuel Grossberg, Anita Gupta, Latanya Hammonds-Odie, Aaron Hoisos, Jenny Hsi, Yu-Han Huang Hsu, Sachi Inukai, Konrad J Karczewski, Xiaobo Ke, Mina Kojima, Samuel Leachman, Danny Lieber, Anna Liebowitz, Julia Liu, Yufei Liu, Trevor Martin, Jose Mena, Rosa Mendoza, Cameron Myhrvold, Christian Millian, Sarah Pfau, Sandeep Raj, Matt Rich, Joe Rokicki, William Rounds, Michael Salazar, Matthew Salesi, Rajani Sharma, Sanford Silverman, Cara Singer, Sandhya Sinha, Max Staller, Philip Stern, Hanlin Tang, Sharon Weeks, Maxwell Weidmann, Ashley Wolf, Carmen Young, Jie Yuan, Christopher Crutchfield, Megan McClean, Coleen T Murphy, Manuel Llinás, David Botstein, Olga G Troyanskaya, Maitreya J Dunham (2013). A new system for comparative functional genomics of *Saccharomyces* yeasts. Genetics.

Patrick A. Gibney, Mark J. Hickman, Patrick H. Bradley, John C. Matese, David Botstein (2013). Phylogenetic portrait of the *Saccharomyces cerevisiae* functional genome. G3 (Bethesda, MD).

Maja M Klosinska, Christopher a Crutchfield, Patrick H Bradley, Joshua D Rabinowitz, James R Broach (2011). Yeast cells can access distinct quiescent states. Genes & Development.

Viktor M. Boer, Christopher A. Crutchfield, Patrick H. Bradley, David Botstein, Joshua D. Rabinowitz (2010). Growth-limiting intracellular metabolites in yeast growing under diverse nutrient limitations. Molecular Biology of the Cell.

Patrick H Bradley, Matthew J Brauer, Joshua D Rabinowitz, Olga G Troyanskaya (2009). Coordinated concentration changes of transcripts and metabolites in *Saccharomyces cerevisiae*. PLoS Comput Biol.