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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
MetabolomicsModel-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation
Macrophages are central players in immune response, manifesting divergent phenotypes to control inflammation and innate immunity through release of cytokines and other signaling factors. Recently, the focus on metabolism has been reemphasized as critical signaling and regulatory pathways of human pa...
2012-09-05 | MTBLS23 | MetaboLights
MetabolomicsSalmonella Modulates Metabolism during Growth under Conditions that Induce Expression of Virulence Genes
Salmonella enterica serovar Typhimurium (S. Typhimurium) is a facultative pathogen that uses complex mechanisms to invade and proliferate within mammalian host cells. To investigate possible contributions of metabolic processes to virulence in S. Typhimurium grown under conditions known to induce ex...
2013-05-02 | MTBLS35 | MetaboLights
ProteomicsGenome-scale metabolic modeling reveals metabolic trade-offs associated with lipid production in Rhodotorula toruloides
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 rates, while the analysis of intrac...
ORGANISM(S): Rhodotorula toruloides 
2023-03-13 | PXD037281 | Pride
Proteomics Rhodotorula toruloides Metabolic fluxes Multiple substrates Genome-scale model 
TranscriptomicsModel-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation
We used genome-scale modeling and multi-omics (transcriptomics, proteomics, and metabolomics) analysis to assess metabolic features that are critical for macrophage activation. We constructed a genome-scale metabolic network for the RAW 264.7 cell line to determine metabolic modulators of activation...
ORGANISM(S): Mus musculus 
2012-08-02 | E-GEOD-39785 | biostudies-arrayexpress
TranscriptomicsInterrogation of global mutagenesis data with a genome scale model of Neisseria meningitidis to assess gene fitness in vitro and in sera.
Background Neisseria meningitidis is an important human commensal and pathogen that causes several thousand deaths each year, mostly in young children. How the pathogen replicates and causes disease in the host is largely unknown, particularly the role of metabolism in colonization and disease. Com...
ORGANISM(S): Neisseria meningitidis 
2012-01-23 | E-BUGS-129 | biostudies-arrayexpress
ModelsMetabolic Interactions in the Gut Microbiome
We present a novel methodology to construct a Boolean dynamic model from time series metagenomic information and integrate this modeling with genome-scale metabolic network reconstructions to identify metabolic underpinnings for microbial interactions. We apply this in the context of a critical heal...
5731 | Cell Collective
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
ProteomicsEnterococcus faecalis V583, Part 1
Genome-scale models represent the link between an organism's genetic information and experimentally observable biological phenotypes. They facilitate metabolic engineering and the discovery of network properties such as the identification of novel drug targets. Most commonly, metabolite consumption ...
ORGANISM(S): Enterococcus faecalis (Streptococcus faecalis) 
2016-12-06 | PXD001576 | Pride
Swath Ph_shift Efv583 
ProteomicsEnterococcus faecalis V583 - data analysis
Genome-scale models represent the link between an organism's genetic information and experimentally observable biological phenotypes. They facilitate metabolic engineering and the discovery of network properties such as the identification of novel drug targets. Most commonly, metabolite consumption ...
ORGANISM(S): Enterococcus faecalis (Streptococcus faecalis) 
2016-12-06 | PXD002869 | Pride
Swath Ph_shift Efv583 
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