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Protocol
Comparative Genomic Analysis of Bacterial Data in BV-BRC: An Example Exploring Antimicrobial Resistance
As genomic and related data continue to expand, research biologists are often hampered by the computational hurdles required to analyze their data. The National Institute of Allergy and Infectious Diseases (NI...
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Article
Open AccessKBase: The United States Department of Energy Systems Biology Knowledgebase
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Protocol
Constructing and Analyzing Metabolic Flux Models of Microbial Communities
Here we provide a broad overview of current research in modeling the growth and behavior of microbial communities, while focusing primarily on metabolic flux modeling techniques, including the reconstruction o...
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Article
Open AccessModeling central metabolism and energy biosynthesis across microbial life
Automatically generated bacterial metabolic models, and even some curated models, lack accuracy in predicting energy yields due to poor representation of key pathways in energy biosynthesis and the electron tr...
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Article
Open AccessSystematic identification and analysis of frequent gene fusion events in metabolic pathways
Gene fusions are the most powerful type of in silico-derived functional associations. However, many fusion compilations were made when <100 genomes were available, and algorithms for identifying fusions need upda...
