Models

The consensus GEM for Saccharomyces cerevisiae, version 8.3.3, maintained on https://github.com/SysBioChalmers/yeast-GEM.

This SBML file uses the RAM extension and contains a minimal genome scaled model for Saccharomyces cerevisiae. The model is based of Yeast 6.06 and was published first in A.-M. Reimers Thesis "Understanding metabolic regulation and cellular resource allocation through optimization".

PGK-GAPDH model yeast kouril7

PGK yeast Fig1a

PGK yeast with/without recycling

Using optical tweezers to position yeast cells in a microfluidic chamber, we were able to observe sustained oscillations in individual isolated cells. Using a detailed kinetic model for the cellular reactions, we simulated the heterogeneity in the response of the individual cells, assuming small differences in a single internal parameter. By operating at two different flow rates per experiment, we observe four of categories of cell behaviour. The present model (gustavsson4) predicts the steady-state ...

The model includes glycolysis, pentosephosphate pathway, purine salvage reactions, purine de novo synthesis, redox balance and biomass growth. The network balances adenylate pool as opened moiety.

Using optical tweezers to position yeast cells in a microfluidic chamber, we were able to observe sustained oscillations in individual isolated cells. Using a detailed kinetic model for the cellular reactions, we simulated the heterogeneity in the response of the individual cells, assuming small differences in a single internal parameter. By operating at two different flow rates per experiment, we observe four of categories of cell behaviour. The present model (gustavsson1) predicts the limit ...

Using optical tweezers to position yeast cells in a microfluidic chamber, we were able to observe sustained oscillations in individual isolated cells. Using a detailed kinetic model for the cellular reactions, we simulated the heterogeneity in the response of the individual cells, assuming small differences in a single internal parameter. By operating at two different flow rates per experiment, we observe four of categories of cell behaviour. The present model (gustavsson2) predicts the damped ...

Using optical tweezers to position yeast cells in a microfluidic chamber, we were able to observe sustained oscillations in individual isolated cells. Using a detailed kinetic model for the cellular reactions, we simulated the heterogeneity in the response of the individual cells, assuming small differences in a single internal parameter. By operating at two different flow rates per experiment, we observe four of categories of cell behaviour. The present model (gustavsson3) predicts the steady-state ...

An existing detailed kinetic model for the steady-state behavior of yeast glycolysis was tested for its ability to simulate dynamic behavior. This model (dupreez1) is the basis kinetic model derived from that published by Teusink et al., 2000 (PMID: 10951190).

An existing detailed kinetic model for the steady-state behavior of yeast glycolysis was tested for its ability to simulate dynamic behavior. This model (dupreez2) is an oscillating version of the basis kinetic model (dupreez1) derived from that published by Teusink et al., 2000 (PMID: 10951190).

An existing detailed kinetic model for the steady-state behavior of yeast glycolysis was tested for its ability to simulate dynamic behavior. This model (dupreez3) is an oscillating version of the model published by Teusink et al., 2000 (PMID: 10951190), which describes data for glycolytic intermediates in oscillating yeast cultures reported by Richard et al., 1996 (PMID: 8813760).

An existing detailed kinetic model for the steady-state behavior of yeast glycolysis was tested for its ability to simulate dynamic behavior. This model (dupreez4) is an oscillating version of the model published by Teusink et al., 2000 (PMID: 10951190), which describes data for glycolytic intermediates in oscillating yeast cultures reported by Richard et al., 1996a (PMID: 8813760) as well as the rapid synchronization following the mixing of two yeast cultures that oscillate 180 degrees out of ...

An existing detailed kinetic model for the steady-state behavior of yeast glycolysis was tested for its ability to simulate dynamic behavior. This model (dupreez5) is an oscillating version of the model published by Teusink et al., 2000 (PMID: 10951190), which describes the amplitude bifurcation of oscillating yeast cultures in a CSTR setup reported by Hynne et al., 2001 (PMID: 11744196).

An existing detailed kinetic model for the steady-state behavior of yeast glycolysis was tested for its ability to simulate dynamic behavior. This model (dupreez6) is an oscillating version of the model published by Teusink et al., 2000 (PMID: 10951190), which describes data for glycolytic intermediates in cell free extracts of oscillating yeast cultures reported by Das and Busse, 1991 (PMCID: 1260073).

An existing detailed kinetic model for the steady-state behavior of yeast glycolysis was tested for its ability to simulate dynamic behavior. This model (dupreez7) is an oscillating version of the model published by Teusink et al., 2000 (PMID: 10951190), which describes the fluorescence signal of NADH in oscillating yeast cultures reported by Nielsen et al., 1998 (PMID: 17029704).