Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0
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- Type
- article
- Published
- 2007-03-01
- Cited by
- 1,779
- References
- 88
- Access
- Open access
- OpenAlex
- https://openalex.org/W2147472054
- Semantic Scholar
- https://api.semanticscholar.org/CorpusID:54559873
Keywords
Toolbox, Computer science, Cobra, SBML, In silico
References
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- Metabolic capabilities of Escherichia coli: I. synthesis of biosynthetic precursors and cofactors.
- Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli
- The JAK-STAT signaling network in the human B-cell: an extreme signaling pathway analysis.
- Integrating high-throughput and computational data elucidates bacterial networks
- Genome-scale thermodynamic analysis of Escherichia coli metabolism.
- Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions
- The genome sequence of the capnophilic rumen bacterium Mannheimia succiniciproducens
- Two-dimensional annotation of genomes
- Genome-scale models of microbial cells: evaluating the consequences of constraints
- Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis
- Identification of Potential Pathway Mediation Targets in Toll-like Receptor Signaling
- Metabolic gene–deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes
- In silico design and adaptive evolution of Escherichia coli for production of lactic acid.
- Towards multidimensional genome annotation
- Genome-scale in silico models of E. coli have multiple equivalent phenotypic states: assessment of correlated reaction subsets that comprise network states.
- Elementary metabolite units (EMU): a novel framework for modeling isotopic distributions.
- Global organization of metabolic fluxes in the bacterium Escherichia coli
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- Synthetic biology triggers new era of antibiotics development.
- A Systems-Level Approach for Investigating Pseudomonas aeruginosa Biofilm Formation
- Multi‐scale modeling for sustainable chemical production
- Exploration and comparison of inborn capacity of aerobic and anaerobic metabolisms of Saccharomyces cerevisiae for microbial electrical current production
- Genome-scale metabolic model for Lactococcus lactis MG1363 and its application to the analysis of flavor formation
- In silico assessment of the metabolic capabilities of an engineered functional reversal of the β-oxidation cycle for the synthesis of longer-chain (C≥4) products.
- CBFA: phenotype prediction integrating metabolic models with constraints derived from experimental data
- Regulatory effects on central carbon metabolism from poly-3-hydroxybutryate synthesis.
- Reconstruction and in silico analysis of an Actinoplanes sp. SE50/110 genome-scale metabolic model for acarbose production
- Xylose-induced dynamic effects on metabolism and gene expression in engineered Saccharomyces cerevisiae in anaerobic glucose-xylose cultures
- Assessment of nitric oxide (NO) redox reactions contribution to nitrous oxide (N2O) formation during nitrification using a multispecies metabolic network model
- Plant sulfur and Big Data.
- Advances and perspectives in computational prediction of microbial gene essentiality.
- Unique attributes of cyanobacterial metabolism revealed by improved genome-scale metabolic modeling and essential gene analysis
- Metabolic engineering strategies to bio-adipic acid production.
- Population FBA predicts metabolic phenotypes in yeast
- Structural and functional analyses of microbial metabolic networks reveal novel insights into genome-scale metabolic fluxes
- Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow
- Environmental systems biology of temperature adaptation in yeast
- Multi agent genome-scale metabolic reconstruction modeling software schema.
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