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RedCom: A strategy for reduced metabolic modeling of complex microbial communities and its application for analyzing experimental datasets from anaerobic digestion
2019
PLoS Computational Biology
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Constraint-based modeling (CBM) is increasingly used to analyze the metabolism of complex microbial communities involved in ecology, biomedicine, and various biotechnological processes. ...
We employed the RedCom approach for modeling communities of up to nine organisms involved in typical degradation steps of anaerobic digestion in biogas plants. ...
Reduced metabolic modeling of microbial communities and application for the biogas process in (B) ). ...
doi:10.1371/journal.pcbi.1006759
pmid:30707687
pmcid:PMC6373973
fatcat:ngorerlqtbc5xdhhmrk7mrgaoi
gapseq: Informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models
[article]
2020
bioRxiv
pre-print
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A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
Here, we present gapseq: a novel tool for automated pathway prediction and metabolic network reconstruction from microbial genome sequences. gapseq combines databases of reference protein sequences (UniProt ...
Furthermore, we illustrate the application of gapseq-reconstructed models to simulate biochemical interactions between microorganisms in multi-species communities. ...
for analyzing 862 experimental datasets from anaerobic digestion. ...
doi:10.1101/2020.03.20.000737
fatcat:ns7g4rei6nbzzkxonhhybynlt4