[HTML][HTML] From bag-of-genes to bag-of-genomes: metabolic modelling of communities in the era of metagenome-assembled genomes
Metagenomic sequencing of complete microbial communities has greatly enhanced our
understanding of the taxonomic composition of microbiotas. This has led to breakthrough …
understanding of the taxonomic composition of microbiotas. This has led to breakthrough …
Large-scale bioprocess competitiveness: the potential of dynamic metabolic control in two-stage fermentations
Highlights•Comparison of biocatalysts/bioprocesses with traditional chemical
catalysts/processes.•Turnover rates of biocatalysts can exceed those of chemical catalysts.•2 …
catalysts/processes.•Turnover rates of biocatalysts can exceed those of chemical catalysts.•2 …
Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v. 3.0
Constraint-based reconstruction and analysis (COBRA) provides a molecular mechanistic
framework for integrative analysis of experimental molecular systems biology data and …
framework for integrative analysis of experimental molecular systems biology data and …
Nonlinear programming reformulation of dynamic flux balance analysis models
RD de Oliveira, GAC Le Roux, R Mahadevan - Computers & Chemical …, 2023 - Elsevier
Dynamic flux balance analysis (dFBA) models are very popular in systems biology because
of the many possible applications. dFBA consists of dynamic mass balance equations that …
of the many possible applications. dFBA consists of dynamic mass balance equations that …
An extended and generalized framework for the calculation of metabolic intervention strategies based on minimal cut sets
P Schneider, A von Kamp, S Klamt - PLoS computational biology, 2020 - journals.plos.org
The concept of minimal cut sets (MCS) provides a flexible framework for analyzing
properties of metabolic networks and for computing metabolic intervention strategies. In …
properties of metabolic networks and for computing metabolic intervention strategies. In …
[HTML][HTML] A mathematical framework for yield (vs. rate) optimization in constraint-based modeling and applications in metabolic engineering
Background: The optimization of metabolic rates (as linear objective functions) represents
the methodical core of flux-balance analysis techniques which have become a standard tool …
the methodical core of flux-balance analysis techniques which have become a standard tool …
Kinetic modeling of metabolism: Present and future
Kinetic models of metabolism are predictors of temporal metabolic behavior of living
organisms that integrate multi-omics data sets with reaction network models to interpret …
organisms that integrate multi-omics data sets with reaction network models to interpret …
BoostGAPFILL: improving the fidelity of metabolic network reconstructions through integrated constraint and pattern-based methods
Motivation Metabolic network reconstructions are often incomplete. Constraint-based and
pattern-based methodologies have been used for automated gap filling of these networks …
pattern-based methodologies have been used for automated gap filling of these networks …
Development of a Genome-Scale Metabolic Model of Clostridium thermocellum and Its Applications for Integration of Multi-Omics Datasets and Computational Strain …
Solving environmental and social challenges such as climate change requires a shift from
our current non-renewable manufacturing model to a sustainable bioeconomy. To lower …
our current non-renewable manufacturing model to a sustainable bioeconomy. To lower …
Improving the accuracy of flux balance analysis through the implementation of carbon availability constraints for intracellular reactions
M Lularevic, AJ Racher, C Jaques… - Biotechnology and …, 2019 - Wiley Online Library
Constraint‐based modeling methods, such as Flux Balance Analysis (FBA), have been
extensively used to decipher complex, information rich‐omics datasets to elicit system‐wide …
extensively used to decipher complex, information rich‐omics datasets to elicit system‐wide …