Investigations
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Aim: To provide quantitative data that will allow modeling of gene expression for all enzymes of redox metabolism and the pentose phosphate pathway. Modeling will be used to predict enzyme levels based on the integration of an RNA degradation model with translation and protein degradation rates.
Plan: The amounts of a protein in a cell can be determined by the rates of transcription, mRNA processing, translation, mRNA turnover and protein degradation. In trypanosomes analysis is simpler because ...
methods developed during COSMIC
Genome-wide association studies with ampicillin resistance as phenotype were conducted on based on variant-call data. A linear regression was performed for MICs and logistic regression was performed based on clinical breakpoint concentrations.
Submitter: Lennart Bartels
Studies: Genome-wide association study on ampicillin resistance in Haemophilus in...
Assays: DNA Sequencing
The investigation entails the construction and validation of a detailed mathematical model for glycolysis erythrocytes infected with the malaria parasite Plasmodium falciparum in the blood stage form.
Submitter: Dawie van Niekerk
Studies: Analysis of model for malaria-infected erythrocytes, Intra-erythrocytic malaria parasite volumes, Validation of model for malaria-infected erythrocytes
Assays: Flux vs external glucose, Flux vs parasitaemia, GLC incubation, Inhibition of glycolytic flux, Malaria parasite volume determinations, Metabolic control analysis, Stage specific fluxes, Steady-state
The investigation entails the construction and validation of a detailed mathematical model for glycolysis of the malaria parasite Plasmodium falciparum in the blood stage trophozoite form.
Submitter: Dawie van Niekerk
Studies: Model analysis, Model construction, Model validation
Assays: ALD, ATPASE, Culturing and synchronisation of P. falciparum, ENO, G3PDH, GAPDH, GLC incubation, GLCtr, GLYtr, HK, Inhibition of glucose transport, Inhibition of lactate flux, LACtr, LDH, PFK, PGI, PGK, PGM, PK, PYRtr, Steady state, Supply-demand analysis, TPI, Trophozoite Isolation and Lysate Preparation
Submitter: Dawie van Niekerk
Studies: Allosteric regulation of phosphofructokinase controls the emergence of g..., Heterogeneity of glycolytic oscillatory behaviour in individual yeast cells, Sustained glycolytic oscillations in individual isolated yeast cells
Assays: gustavsson1-4 models, gustavsson5 model
Collection of models submitted to PLaSMo by Alexandra Graf and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: TiMet 2011 PP interaction network - PLM_56, TiMet 2011 Pollen network - PLM_54, TiMet 2011 Root network - PLM_55, TiMet 2011 flower specific protein detection network - PLM_57, TiMet 2011 seed network - PLM_53, TiMet 2011 shoot specific diurnal transcript oscillation network - PLM_58, TiMet 2011 silqueue specific protein detection network - PLM_59
Assays: TiMet 2011 PP interaction network - PLM_56, version 1, TiMet 2011 Pollen network - PLM_54, version 1, TiMet 2011 Pollen network - PLM_54, version 2, TiMet 2011 Root network - PLM_55, version 1, TiMet 2011 flower specific protein detection network - PLM_57, version 1, TiMet 2011 seed network - PLM_53, version 1, TiMet 2011 seed network - PLM_53, version 2, TiMet 2011 shoot specific diurnal transcript oscillation network - PLM_5..., TiMet 2011 silqueue specific protein detection network - PLM_59, version 1
We performed topological analysis on pathways from a harmonised dataset containing pathways from the COVID-19 Disease Map, WikiPathways, and Reactome. The analysis was done using Vanted, SBGN-ED, and LMME which support the import and export of several standard formats (such as SBML, and SBGN-ML).
Submitter: Felicia Burtscher
Studies: Topological analysis of individual pathway networks and aggregated netwo...
Assays: No Assays
Collection of models submitted to PLaSMo by Maria-Luisa Guerriero and automatically transferred to FAIRDOM Hub.
Submitter: BioData SynthSys
Studies: arabidopsis_clock_biopepa - PLM_47
