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ProteomicsMulti-Functional Enzymes and Metabolic Cross-Feeding Constrain Implementation of Genome Scale Metabolic Model Based Designs
Genome scale metabolic models (GSMM) are commonly used to identify gene deletion sets that result in growth coupling, pairing product formation with substrate utilization. While such approaches can improve strain performance beyond levels typically accessible using targeted strain engineering approa...
ORGANISM(S): Pseudomonas putida KT2440 
2025-03-08 | PXD050285 | Pride
Omics Gsmm Strain engineering 
ProteomicsVibrio natriegens genome-scale metabolic modelling (GSMM) reveals insights into halophilic adaptations and resource allocation
Proteome profiles of Vibrio natriegens used for genome-scale metabolic modeling (GSMM). Profiling was performed across cell cultures grown aerobically on minimal medium. Cultures profiles were acquired across a range of salinities.
ORGANISM(S): Vibrio Natriegens Nbrc 15636 (ncbitaxon:1219067) 
2023-02-07 | MSV000091219 | MassIVE
ModelsTorres2019 - Contextualized P. pastoris GSMM under glucose growth and various oxygenation levels
This SBML file contains a contextualized GSMM of P. pastoris metabolism based on the most recent metabolic reconstruction iMT1026v3. The model has been adjusted to accurately describe glucose growth under various oxygenation levels (Low: 4% DO; Medium: 30% DO; Excess: 56% DO). The GAME and NGAME par...
2019-10-16 | MODEL1910040001 | BioModels
MetabolomicsGenome-scale metabolic modelling of responses to polymyxins in Pseudomonas aeruginosa
Background: Pseudomonas aeruginosa often causes multidrug-resistant infections in immunocompromised patients and polymyxins are often used as the last-line therapy. Alarmingly, resistance to polymyxins has been increasingly reported worldwide recently. To rescue this last-resort class of antibiotics...
2018-02-28 | MTBLS630 | MetaboLights
ModelsBordel2018 - GSMM for Human Metabolic Reactions (HMR database)
Bordel2018 - GSMM for Human Metabolic Reactions (HMR database) This model is described in the article: Constraint based modeling of metabolism allows finding metabolic cancer hallmarks and identifying personalized therapeutic windows Sergio Bordel Oncotarget. 2018; 9:19716-1...
MODEL1707250000 | BioModels
TranscriptomicsReduced glutathione levels in Enterococcus faecalis trigger metabolic and transcriptional compensatory adjustments during iron exposure.
Enterococcus faecalis, a facultative anaerobic pathogen and common constituent of the gastrointestinal microbiota, must navigate varying iron levels within the host. This study investigates the bacterium's response to elevated iron levels in the context of glutathione deficiency, a critical low mole...
ORGANISM(S): Enterococcus faecalis V583 Enterococcus faecalis OG1RF 
2026-09-17 | GSE275402 | GEO
UnknownComputational analysis of reciprocal association of metabolism and epigenetics in the budding yeast: a genome-scale metabolic model (GSMM) approach.
Not available
S-EPMC4218804 | biostudies-literature
UnknownIntegration of enzyme constraints in a genome-scale metabolic model of Aspergillus niger improves phenotype predictions.
Not available
S-EPMC8247156 | biostudies-literature
UnknownEnhancing Genome-Scale Model by Integrative Exometabolome and Transcriptome: Unveiling Carbon Assimilation towards Sphingolipid Biosynthetic Capability of Cordyceps militaris.
Not available
S-EPMC9409897 | biostudies-literature
UnknownBiomimetic manganese-based theranostic nanoplatform for cancer multimodal imaging and twofold immunotherapy.
Not available
S-EPMC9048124 | biostudies-literature
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