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60 Publications visible to you, out of a total of 60
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

Inferring statin-induced gene regulatory relationships in primary human hepatocytes

Abstract (Expand)

MOTIVATION: Statins are the most widely used cholesterol-lowering drugs. The primary target of statins is HMG-CoA reductase, a key enzyme in cholesterol synthesis. However, statins elicit pleitropic … responses including beneficial as well as adverse effects in the liver or other organs. Today, the regulatory mechanisms that cause these pleiotropic effects are not sufficiently understood. RESULTS: In this work, genome-wide RNA expression changes in primary human hepatocytes of six individuals were measured at up to six time points upon atorvastatin treatment. A computational analysis workflow was applied to reconstruct regulatory mechanisms based on these drug-response data and available knowledge about transcription factor (TF) binding specificities and protein-drug interactions. Several previously unknown TFs were predicted to be involved in atorvastatin-responsive gene expression. The novel relationships of nuclear receptors NR2C2 and PPARA on CYP3A4 were successfully validated in wet-lab experiments. AVAILABILITY: Microarray data are available at the Gene Expression Omnibus (GEO) database at www.ncbi.nlm.nih.gov/geo/, under accession number GSE29868. CONTACT: andreas.zell@uni-tuebingen.de; adrian.schroeder@uni-tuebingen.de SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Authors: A. Schroder, J. Wollnik, C. Wrzodek, A. Drager, M. Bonin, O. Burk, M. Thomas, W. E. Thasler, U. M. Zanger, A. Zell

Date Published: 14th Jul 2011

Publication Type: Not specified

Inferring statin-induced gene regulatory relationships in primary human hepatocytes

Abstract

Not specified

Authors: A. Schroder, J. Wollnik, C. Wrzodek, A. Drager, M. Bonin, O. Burk, M. Thomas, W. E. Thasler, U. M. Zanger, A. Zell

Date Published: 14th Jul 2011

Publication Type: Not specified

Data archiving is a good investment.

Abstract

Not specified

Authors: H. A. Piwowar, T. J. Vision, M. C. Whitlock

Date Published: 20th May 2011

Publication Type: Not specified

Identification and characterization of the PhhR regulon in Pseudomonas putida

Abstract

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Authors: M. Carmen Herrera, Estrella Duque, José J. Rodríguez-Herva, Ana M. Fernández-Escamilla, Juan L. Ramos

Date Published: 2010

Publication Type: Not specified

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