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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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Phylogeny-corrected identification of microbial gene families relevant to human gut colonization
The mechanisms by which different microbes colonize the healthy human gut versus other body sites, the gut in disease states, or other …
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Proteobacteria explain significant functional variability in the human gut microbiome
BACKGROUND While human gut microbiomes vary significantly in taxonomic composition, biological pathway abundance is surprisingly …
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Automated and accurate estimation of gene family abundance from shotgun metagenomes
Shotgun metagenomic DNA sequencing is a widely applicable tool for characterizing the functions that are encoded by microbial …
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A new system for comparative functional genomics of *Saccharomyces* yeasts
Whole-genome sequencing, particularly in fungi, has progressed at a tremendous rate. More difficult, however, is experimental testing …
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
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Phylogenetic portrait of the *Saccharomyces cerevisiae* functional genome
The genome of budding yeast (Saccharomyces cerevisiae) contains approximately 5800 protein-encoding genes, the majority of which are …
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Yeast cells can access distinct quiescent states
We conducted a phenotypic, transcriptional, metabolic, and genetic analysis of quiescence in yeast induced by starvation of …
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Growth-limiting intracellular metabolites in yeast growing under diverse nutrient limitations
Microbes tailor their growth rate to nutrient availability. Here, we measured, using liquid chromatography-mass spectrometry, …
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Coordinated concentration changes of transcripts and metabolites in *Saccharomyces cerevisiae*
Metabolite concentrations can regulate gene expression, which can in turn regulate metabolic activity. The extent to which functionally …
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