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MetabolomicsGrowth control of the eukaryote cell: a systems biology study in yeast
Metabolic control analysis is being exploited in a systems biology study of the eukaryotic cell. Using chemostat culture, we have measured the impact of changes in flux (growth rate) on the transcriptome, proteome, endometabolome and exometabolome of the yeast Saccharomyces cerevisiae. Each function...
2012-04-19 | MTBLS8 | MetaboLights
MetabolomicsEnergy-translation coupling limits yeast anaerobic growth

This study employs yeast as a model system to thoroughly investigate the differences in regulatory mechanisms under various nutrient limitation conditions, utilizing a systems biology approach integrated with techniques such as multi-omics analysis.To obtain a comprehensive quantitative landscap...

2026-05-24 | MTBLS14573 | MetaboLights
TranscriptomicsMulti-layer omics dataset for cross-species translational systems biology
Inferring in humans biological responses to external cues such as drugs, chemicals, viruses and hormones, is an essential question in biomedicine and cannot be easily studied in humans. Thus, biomedical research has continuously relied on animal models for studying the impact of these compounds and ...
ORGANISM(S): Rattus norvegicus 
2014-06-10 | E-MTAB-2091 | biostudies-arrayexpress
MetabolomicsMetabolic Profiling of Escherichia coli-Based Cell-Free Expression Systems for Process Optimization
Biotechnology has transformed the production of various chemicals and pharmaceuticals due to its efficient and selective processes, but it is inherently limited by its use of live cells as 'biocatalysts.' Cell-free expression (CFE) systems, which use a protein lysate isolated from whole cells, have ...
2020-06-02 | MTBLS1079 | MetaboLights
TranscriptomicsSystem level characterization of galactose mutants of yeast
Adaptively evolved mutants of yeast on galactose were characterized by feremtation physiology and tools from systems biology. Three evolved mutants of yeast grown on aerobic batch with galactose as carbon source
ORGANISM(S): Saccharomyces cerevisiae 
2011-03-31 | E-GEOD-27185 | biostudies-arrayexpress
ProteomicsSystem Biology approach to protein stability regulation in yeast
Cellular protein levels depend upon their synthesis and degradation rates (i.e protein turnover). Characterizing protein turnover is thus essential for determining cell response to different stimuli but the main determinants of this process are poorly understood. We comprehensively addressed this by...
ORGANISM(S): Saccharomyces Cerevisiae (ncbitaxon:4932) 
2016-04-21 | MSV000079673 | MassIVE
TranscriptomicsSystems Biology Analysis of Zymomonas mobilis ZM4 Ethanol Stress Responses
Background Zymomonas mobilis ZM4 is a capable ethanologenic bacterium with high ethanol productivity and ethanol tolerance. Previous studies indicated that several stress-related proteins and changes in the ZM4 membrane lipid composition may contribute to ethanol tolerance. However, the molecular m...
ORGANISM(S): Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821 
2013-09-04 | E-GEOD-21165 | biostudies-arrayexpress
TranscriptomicsSystems biology approaches reveal low-dose effects of nanoparticles
Here, we show that systems biology approaches can uncover mechanisms underlying cellular responses to nanomaterials. Using RNA Seq, we found that cationic nanoparticles are capable of triggering down-regulation of cell cycle-related genes in primary human bronchial epithelial cells at doses that do ...
ORGANISM(S): Homo sapiens 
2015-01-17 | E-MTAB-2397 | biostudies-arrayexpress
ProteomicsDIA-based systems biology approach unveils novel E3-dependent responses to a metabolic shift
Yeast Saccharomyces cerevisiae is a powerful model system for systems-wide biology screens and large-scale proteomics methods. The proteomics community has achieved nearly complete coverage for this organism owing to advances in mass spectrometry. However, it remains challenging to scale the technol...
ORGANISM(S): Saccharomyces cerevisiae (Baker's yeast) 
2020-11-26 | PXD021559 | Pride
Proteomics Dia Gid e3 ligase Mass spectrometry Systems biology Yeast Lc-ms/ms 
TranscriptomicsStructural systems biology evaluation of metabolic thermotolerance in Escherichia coli
Investigation of whole genome gene expression level in E. coli K-12 MG1655 in glucose M9 minimal media with/without heatshock A six chip study using total RNA recovered from E. coli K-12 MG1655 grown up to OD600nm 0.6 (mid-exponential phase) in M9 minimal media supplemented with 0.2% glucose with/wi...
ORGANISM(S): Escherichia coli str. K-12 substr. MG1655 
2013-06-20 | E-GEOD-42675 | biostudies-arrayexpress
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