Models

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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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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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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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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