Investigations

Collection of models submitted to PLaSMo by Robert Muetzelfeldt and automatically transferred to FAIRDOM Hub.

Integrated systems biology approach including transcriptome, metabolome, proteome analyses and modelling to elucidate amino acid degradation in S. solfataricus P2.

Click on Snapshot 2 to download data, models and analysis for Daniel Seaton et al. biorXiv 2017 https://doi.org/10.1101/182071 and Molecular Systems Biology, accepted Jan 2018, https://doi.org/10.15252/msb.20177962. Note that the published paper cannot be fully linked into this record as the DOI above was not live when we made the Research Object from this Investigation on FAIRDOMHub.

Data, models and simulations for the Chew et al. 2014 paper (PNAS, https://doi.org/10.1073/pnas.1410238111), using wild-type Arabidopsis ecotype Col-0 in standard 12hL:12hD growth conditions, compared to La(er) or Fei-0 accessions, or to plants overexpressing a micro RNA (miR156).

Biphasic response as a mechanism against mutant takeover in tissue homeostasis circuits

Frequency doubling in the cyanobacterial circadian clock

The objectives of WP1 within the colosys project are:

1. Produce resources of data and information that will be used for the identification of CC driver genes (WP2) and for the construction and configuration of computational models of cancer-related biological processes (WP2 and WP3)
2. Integrate information from public patient data and cancer cell line data repositories with information from project specific clinical and model data
3. Convert information from public cellular signalling databases ...

Experimental data and all related material for the publication "Multi -omics reveal lifestyle of acidophile, mineral-oxidizing model species Leptospirillum ferriphilumT". changed ID

Experimental data and all related material for the publication "Multi -omics reveal lifestyle of acidophile, mineral-oxidizing model species Leptospirillum ferriphilumT".

Gene co-epxression network analyses are common in the study of large scale biological data sets. In this study, we have developed a methodology for the comparison of pairs of co-expression networks using the s-core network peeling approach. We apply the methodology to gene-expression data for human and mouse.

The gluconeogenic conversion of 3-phosphoglycerate via 1,3-bisphosphoglycerate to glyceraldehyde-3-phosphate was compared at 30 C and at 70 C. At 30 C it was possible to produce 1,3-bisphosphoglycerate from 3-phosphoglycerate with phosphoglycerate kinase, but at 70 C, 1,3- bisphosphoglycerate was dephosphorylated rapidly to 3-phosphoglycerate, effectively turning the phosphoglycerate kinase into a futile cycle. At both temperatures it was possible to convert 3-phosphoglycerate to glyceraldehyde ...

Drug detoxification dynamics explain the postantibiotic effect

Understanding how liver function arises from the complex interaction of morphology, perfusion, and metabolism from single cells up to the entire organ requires systems-levels computational approaches.

Protein abundance of AKT and ERK pathway components governs cell-type- specific regulation of proliferation

Antibiotics are made during the second phase of growth when there is a transition in metabolism from primary to secondary metabolism. Primary metabolism is growth related and involves all the normal cellular activities associated with cell growth and division. Whereas secondary metabolism is non-growth linked and is non-essential but many important activities occur during this phase which help the bacterium survive.

One of these activities is antibiotic production and is widespread in streptomycetes ...

Integrated systems biology approach including transcriptome, metabolome, biochemistry, proteome analyses and modelling to elucidate the catabolic pathway for L-fucose in S. solfataricus P2.