Publications

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64 Publications visible to you, out of a total of 64
Stealthy annotation of experimental biology by spreadsheets

Abstract

Not specified

Authors: Katherine Wolstencroft, Stuart Owen, Matthew Horridge, Simon Jupp, Olga Krebs, Jacky Snoep, Franco du Preez, Wolfgang Mueller, Robert Stevens, Carole Goble

Date Published: 1st Feb 2013

Publication Type: Not specified

A Mechanistic, Model-Based Approach to Safety Assessment in Clinical Development

Abstract

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Editor:

Date Published: 2013

Publication Type: Not specified

Semantic Data and Models Sharing in Systems Biology: The Just Enough Results Model and the SEEK Platform

Abstract

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Editor:

Date Published: 2013

Publication Type: Not specified

Semantic Data and Models Sharing in Systems Biology: The Just Enough Results Model and the SEEK Platform

Abstract

Not specified

Authors: Katherine Wolstencroft, Stuart Owen, Olga Krebs, Wolfgang Mueller, Quyen Nguyen, Jacky L. Snoep, Carole Goble

Date Published: 2013

Publication Type: Not specified

Semantic Data and Models Sharing in Systems Biology: The Just Enough Results Model and the SEEK Platform

Abstract

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Authors: Katherine Wolstencroft, Stuart Owen, Olga Krebs, Wolfgang Mueller, Quyen Nguyen, Jacky L. Snoep, Carole Goble

Date Published: 2013

Publication Type: Not specified

From steady-state to synchronized yeast glycolytic oscillations II: model validation.

Abstract (Expand)

UNLABELLED: In an accompanying paper [du Preez et al., (2012) FEBS J279, 2810-2822], we adapt an existing kinetic model for steady-state yeast glycolysis to simulate limit-cycle oscillations. Here we … validate the model by testing its capacity to simulate a wide range of experiments on dynamics of yeast glycolysis. In addition to its description of the oscillations of glycolytic intermediates in intact cells and the rapid synchronization observed when mixing out-of-phase oscillatory cell populations (see accompanying paper), the model was able to predict the Hopf bifurcation diagram with glucose as the bifurcation parameter (and one of the bifurcation points with cyanide as the bifurcation parameter), the glucose- and acetaldehyde-driven forced oscillations, glucose and acetaldehyde quenching, and cell-free extract oscillations (including complex oscillations and mixed-mode oscillations). Thus, the model was compliant, at least qualitatively, with the majority of available experimental data for glycolytic oscillations in yeast. To our knowledge, this is the first time that a model for yeast glycolysis has been tested against such a wide variety of independent data sets. DATABASE: The mathematical models described here have been submitted to the JWS Online Cellular Systems Modelling Database and can be accessed at http://jjj.biochem.sun.ac.za/database/dupreez/index.html.

Authors: F. B. du Preez, D. D. van Niekerk, J. L. Snoep

Date Published: 13th Jun 2012

Publication Type: Not specified

SABIO-RK: Access to Biochemical Reaction Kinetics Data

Abstract

Not specified

Authors: Martin Golebiewski, Martin Golebiewski

Date Published: 7th Oct 2011

Publication Type: Not specified

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