Publications

See also: preprints, filterable list of publications and preprints

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 often retained over evolutionary time, suggesting that they contribute to fitness. We developed an unsupervised …

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 environments remain largely unknown. Identifying microbial genes influencing fitness in the gut could lead to new …

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 invariable across hosts. We hypothesized that healthy microbiomes appear functionally redundant due to factors that …

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 communities. Several bioinformatic tools can be used to functionally annotate metagenomes, allowing researchers to draw …

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 of the inferences about gene function that can be drawn from comparative sequence analysis alone. We present a …

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 associated with some known biological function. Yet the extent of amino acid sequence conservation of these genes …

Yeast cells can access distinct quiescent states

We conducted a phenotypic, transcriptional, metabolic, and genetic analysis of quiescence in yeast induced by starvation of prototrophic cells for one of three essential nutrients (glucose, nitrogen, or phosphate) and compared those results with …

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, textgreater100 intracellular metabolites in steady-state cultures of Saccharomyces cerevisiae growing at five different …

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 related transcripts and metabolites show similar patterns of concentration changes, however, remains …