Recent advances in constraint and machine learning-based metabolic modeling by leveraging stoichiometric balances, thermodynamic feasibility and kinetic law formalisms.
Sign Up to like & getrecommendations! Published in 2020 at "Metabolic engineering"
DOI: 10.1016/j.ymben.2020.11.013
Abstract: Understanding the governing principles behind organisms' metabolism and growth underpins their effective deployment as bioproduction chassis. A central objective of metabolic modeling is predicting how metabolism and growth are affected by both external environmental factors… read more here.
Keywords: metabolic modeling; machine learning; constraint machine; recent advances ... See more keywords
Multiscale Multiobjective Systems Analysis (MiMoSA): an advanced metabolic modeling framework for complex systems
Sign Up to like & getrecommendations! Published in 2019 at "Scientific Reports"
DOI: 10.1038/s41598-019-53188-0
Abstract: In natural environments, cells live in complex communities and experience a high degree of heterogeneity internally and in the environment. Even in ‘ideal’ laboratory environments, cells can experience a high degree of heterogeneity in their… read more here.
Keywords: metabolic modeling; analysis mimosa; multiobjective systems; systems analysis ... See more keywords
System-level metabolic modeling facilitates unveiling metabolic signature in exceptional longevity.
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DOI: 10.1111/acel.13595
Abstract: Although it is well known that metabolic control plays a crucial role in regulating the health span and life span of various organisms, little is known for the systems metabolic profile of centenarians, the paradigm… read more here.
Keywords: level metabolic; system level; longevity; signature ... See more keywords
Erratum to: The JBEI quantitative metabolic modeling library (jQMM): a python library for modeling microbial metabolism
Sign Up to like & getrecommendations! Published in 2017 at "BMC Bioinformatics"
DOI: 10.1186/s12859-017-1631-y
Abstract: Author details Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. Joint BioEnergy Institute, Emeryville, CA, USA. Department of Chemical and Biomolecular Engineering, University of California, Berkeley, CA, USA. Department of Bioengineering,… read more here.
Keywords: erratum jbei; metabolic modeling; berkeley usa; jbei quantitative ... See more keywords
BacArena: Individual-based metabolic modeling of heterogeneous microbes in complex communities
Sign Up to like & getrecommendations! Published in 2017 at "PLoS Computational Biology"
DOI: 10.1371/journal.pcbi.1005544
Abstract: Recent advances focusing on the metabolic interactions within and between cellular populations have emphasized the importance of microbial communities for human health. Constraint-based modeling, with flux balance analysis in particular, has been established as a… read more here.
Keywords: metabolic modeling; bacarena individual; modeling heterogeneous; based metabolic ... See more keywords
Genome-scale metabolic modeling reveals metabolic trade-offs associated with lipid production in Rhodotorula toruloides
Sign Up to like & getrecommendations! Published in 2023 at "PLOS Computational Biology"
DOI: 10.1371/journal.pcbi.1011009
Abstract: Rhodotorula toruloides is a non-conventional, oleaginous yeast able to naturally accumulate high amounts of microbial lipids. Constraint-based modeling of R. toruloides has been mainly focused on the comparison of experimentally measured and model predicted growth… read more here.
Keywords: offs associated; metabolic modeling; rhodotorula toruloides; metabolic trade ... See more keywords
Genome‐scale metabolic modeling reveals SARS‐CoV‐2‐induced metabolic changes and antiviral targets
Sign Up to like & getrecommendations! Published in 2021 at "Molecular Systems Biology"
DOI: 10.15252/msb.202110260
Abstract: Tremendous progress has been made to control the COVID‐19 pandemic caused by the SARS‐CoV‐2 virus. However, effective therapeutic options are still rare. Drug repurposing and combination represent practical strategies to address this urgent unmet medical… read more here.
Keywords: metabolic modeling; host metabolism; genome scale; sars cov ... See more keywords
Understanding Antimicrobial Resistance Using Genome-Scale Metabolic Modeling
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DOI: 10.3390/antibiotics12050896
Abstract: The urgent necessity to fight antimicrobial resistance is universally recognized. In the search of new targets and strategies to face this global challenge, a promising approach resides in the study of the cellular response to… read more here.
Keywords: scale metabolic; antimicrobial resistance; metabolic modeling; genome scale ... See more keywords
New Insights on Metabolic Features of Bacillus subtilis Based on Multistrain Genome-Scale Metabolic Modeling
Sign Up to like & getrecommendations! Published in 2023 at "International Journal of Molecular Sciences"
DOI: 10.3390/ijms24087091
Abstract: Bacillus subtilis is an effective workhorse for the production of many industrial products. The high interest aroused by B. subtilis has guided a large metabolic modeling effort of this species. Genome-scale metabolic models (GEMs) are… read more here.
Keywords: scale metabolic; scale; bacillus subtilis; multistrain genome ... See more keywords
Genome-Scale Metabolic Modeling Reveals Sequential Dysregulation of Glutathione Metabolism in Livers from Patients with Alcoholic Hepatitis
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DOI: 10.3390/metabo12121157
Abstract: Alcoholic hepatitis (AH) is the most severe form of alcoholic liver disease for which there is no efficacious treatment aiding most patients. AH manifests differently in individuals, with some patients showing debilitating symptoms more so… read more here.
Keywords: scale metabolic; sequential dysregulation; metabolic modeling; dysregulation ... See more keywords