Microbial Systems Biology
Methods and Protocols
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Protocol
Curating COBRA Models of Microbial Metabolism
Constraint-based reconstruction and analysis (COBRA) methods have been used for over 20 years to generate genome-scale models of metabolism in biological systems. The COBRA models have been utilized to gain ne...
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Book
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Protocol
A Beginner’s Guide to the COBRA Toolbox
COBRA toolbox is one of the most popular tools for systems biology analyses using genome-scale metabolic reconstructions. The toolbox permits the use of many constraint-based analytical methods for examining c...
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Article
Open AccessSystem-level analysis of metabolic trade-offs during anaerobic photoheterotrophic growth in Rhodopseudomonas palustris
Living organisms need to allocate their limited resources in a manner that optimizes their overall fitness by simultaneously achieving several different biological objectives. Examination of these biological t...
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Article
Open AccessCombining multiple functional annotation tools increases coverage of metabolic annotation
Genome-scale metabolic modeling is a cornerstone of systems biology analysis of microbial organisms and communities, yet these genome-scale modeling efforts are invariably based on incomplete functional annota...
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Article
Open AccessQuantitative In Silico analysis of transient metabolism of acetaminophen and associated causes of hepatotoxicity in humans
Although safe at therapeutic levels, excess intake of acetaminophen can lead to hepatic injury or acute liver failure (ALF). A number of different factors influence metabolism and hepatotoxicity of acetaminoph...
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Article
Open AccessGenome-level transcription data of Yersinia pestis analyzed with a New metabolic constraint-based approach
Constraint-based computational approaches, such as flux balance analysis (FBA), have proven successful in modeling genome-level metabolic behavior for conditions where a set of simple cellular objectives can b...
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Book
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Protocol
Development of Constraint-Based System-Level Models of Microbial Metabolism
Genome-scale models of metabolism are valuable tools for using genomic information to predict microbial phenotypes. System-level mathematical models of metabolic networks have been developed for a number of mi...
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Protocol
Systems Biology of Microbial Communities
Microbes exist naturally in a wide range of environments in communities where their interactions are significant, spanning the extremes of high acidity and high temperature environments to soil and the ocean. ...
