Publications

Abstract:

Not specified

Authors: Matthias König, David Nickerson, Padraig Gleeson, Martin Golebiewski, Mike Hucka, Jacky Snoep, Vasundra Toure, Olaf Wolkenhauer, Dagmar Waltemath, Neal Maxwell Lewis,Mısırlı Göksel,Kalbasi Reza,Dräger Andreas,Atalag Koray,Chelliah Vijayalakshmi,Cooling Michael T,Cook Daniel L,Crook Sharon,de Alba Miguel,Friedman Samuel H,Garny Alan,Gennari John H,Juty Nick,Myers Chris,Olivier Brett G,Sauro Herbert M,Scharm Martin,Wipat Anil

Date Published: 21st Nov 2018

Journal: Not specified

Abstract (Expand)

Tissues use feedback circuits in which cells send signals to each other to control their growth and survival. We show that such feed- back circuits are inherently unstable to mutants that misread the ...

Author: Karin Omer,Alon Uri

Date Published: 26th Jun 2017

Journal: Mol Syst Biol

Abstract (Expand)

Organisms use circadian clocks to generate 24-h rhythms in gene expression. However, the clock can interact with other pathways to generate shorter period oscillations. It remains unclear how these ...

Author: Martins Bruno MC,Das Arijit K,Antunes Liliana,Locke James CW

Date Published: 22nd Dec 2016

Journal: Mol Syst Biol

Abstract (Expand)

The FAIRDOMHub is a repository for publishing FAIR (Findable, Accessible, Interoperable and Reusable) Data, Operating procedures and Models (https://fairdomhub.org/) for the Systems Biology community. ...

Authors: Katy Wolstencroft, Olga Krebs, Jacky Snoep, Natalie Stanford, Finn Bacall, Martin Golebiewski, Rostyslav Kuzyakiv, Quyen Nguyen, Stuart Owen, Jakub Straszewski, Alan Williams, Bernd Rinn, Wolfgang Müller, Carole Goble, Soiland-Reyes S.,van Niekerk D. D.,Malmstrom L.

Date Published: 3rd Dec 2016

Journal: Nucleic Acids Res

Abstract (Expand)

Glycolysis is the main pathway for ATP production in the malaria parasite Plasmodium falciparum and essential for its survival. Following a sensitivity analysis of a detailed kinetic model for glycolysis ...

Authors: Dawie Van Niekerk, Jacky Snoep, Penkler Gerald P.,du Toit Francois

Date Published: 1st Feb 2016

Journal: FEBS J

Abstract (Expand)

We propose a hierarchical modelling approach to construct models for disease states at the whole-body level. Such models can simulate effects of drug-induced inhibition of reaction steps on the whole-body ...

Authors: Jacky Snoep, Kathleen Green, Dawie Van Niekerk, Eicher J.,Palm D. C.,Penkler G.,du Toit F.,Walters N.,Burger R.,Westerhoff H. V.

Date Published: 27th Nov 2015

Journal: Biochemical Society Transactions

Abstract (Expand)

The enzymes in the Embden–Meyerhof–Parnas pathway of Plasmodium falciparum trophozoites were kinetically characterized and their integrated activities analyzed in a mathematical model. For validation ...

Authors: Dawie Van Niekerk, Jacky Snoep, Penkler Gerald,du Toit Francois,Adams Waldo,Rautenbach Marina,Palm Daniel C.

Date Published: 1st Apr 2015

Journal: FEBS J

Abstract:

Not specified

Authors: Dawie Van Niekerk, Jacky Snoep, Gustavsson Anna-Karin,Adiels Caroline B.,Kooi Bob,Goksör Mattias

Date Published: 1st Jun 2014

Journal: FEBS J

Abstract:

Not specified

Authors: Dawie Van Niekerk, Jacky Snoep, Gustavsson Anna-Karin,Adiels Caroline B.,Goksör Mattias

Date Published: 3rd Jan 2014

Journal: Not specified

Abstract (Expand)

Four enzymes of the gluconeogenic pathway in Sulfolobus solfataricus were purified and kinetically characterized. The enzymes were reconstituted in vitro to quantify the contribution of temperature ...

Authors: Theresa Kouril, Hans Westerhoff, Bettina Siebers, Jacky Snoep, Esser Dominik,Kort Julia

Date Published: 20th Jul 2013

Journal: FEBS J.

Abstract (Expand)

Research in Systems Biology involves integrating data and knowledge about the dynamic processes in biological systems in order to understand and model them. Semantic web technologies should be ideal ...

Authors: None

Date Published: 2013

Journal: The Semantic Web – ISWC 2013

Abstract (Expand)

The increase in volume and complexity of biological data has led to increased requirements to reuse that data. Consistent and accurate metadata is essential for this task, creating new challenges in ...

Authors: Katy Wolstencroft, Stuart Owen, Olga Krebs, Jacky Snoep, Franco Du Preez, Wolfgang Müller, Carole Goble, Horridge Matthew,Jupp Simon,Stevens Robert

Date Published: 1st Oct 2012

Journal: Concurrency Computat.: Pract. Exper.

Abstract:

Not specified

Authors: Dawie Van Niekerk, Jacky Snoep, Gustavsson Anna-Karin,Adiels Caroline B.,du Preez Franco B.,Goksör Mattias

Date Published: 1st Aug 2012

Journal: Not specified

Abstract (Expand)

An existing detailed kinetic model for the steady-state behavior of yeast glycolysis was tested for its ability to simulate dynamic behavior. Using a small subset of experimental data, the original ...

Authors: Franco Du Preez, Jacky Snoep, van Niekerk David D,Kooi Bob,Rohwer Johann M

Date Published: 21st Jun 2012

Journal: The FEBS journal

Abstract (Expand)

In an accompanying paper [du Preez et al., (2012) FEBS J doi: 10.1111/j.1742-4658.2012.08665.x], we adapt an existing kinetic model for steady-state yeast glycolysis to simulate limit-cycle oscillations. ...

Authors: Franco Du Preez, Jacky Snoep, van Niekerk David D

Date Published: 13th Jun 2012

Journal: The FEBS journal

Abstract (Expand)

Yeast glycolytic oscillations have been studied since the 1950s in cell-free extracts and intact cells. For intact cells, sustained oscillations have so far only been observed at the population level, ...

Authors: Franco Du Preez, Jacky Snoep, Gustavsson Anna-Karin,van Niekerk David D,Adiels Caroline B,Goksör Mattias

Date Published: 23rd May 2012

Journal: The FEBS journal

Abstract (Expand)

RightField is a Java application that provides a mechanism for embedding ontology annotation support for scientific data in Microsoft Excel or Open Office spreadsheets. The result is semantic annotation ...

Authors: Katy Wolstencroft, Stuart Owen, Wolfgang Müller, Finn Bacall, Jacky Snoep, Quyen Nguyen, Olga Krebs, Carole Goble, Horridge Matthew,du Preez Franco

Date Published: 2012

Journal: Knowledge Engineering and Knowledge Management

Abstract (Expand)

The increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such experiments. The recently published ...

Authors: Jacky Snoep, Waltemath Dagmar,Adams Richard,Bergmann Frank T,Hucka Michael,Kolpakov Fedor,Miller Andrew K,Moraru Ion I,Nickerson David,Sahle Sven,Le Novère Nicolas

Date Published: 15th Dec 2011

Journal: BMC Syst Biol

Abstract (Expand)

Systems biology research is typically performed by multidisciplinary groups of scientists, often in large consortia and in distributed locations. The data generated in these projects tend to be ...

Authors: None

Date Published: 29th Sep 2011

Journal: Meth. Enzymol.

Abstract (Expand)

One of the main pathways for the detoxification of reactive metabolites in the liver involves glutathione conjugation. Metabolic profiling studies have shown paradoxical responses in glutathione-related ...

Authors: Franco Du Preez, Hans Westerhoff, Jacky Snoep, Geenen Suzanne,Reed Michael,Nijhout H Frederik,Kenna J Gerry,Wilson Ian D

Date Published: 24th Aug 2011

Journal: Eur J Pharm Sci

Abstract (Expand)

The development of disease may be characterized as a pathological shift of homeostasis; the main goal of contemporary drug treatment is, therefore, to return the pathological homeostasis back to the ...

Authors: Jacky Snoep, Hans Westerhoff, Kolodkin Alexey,Boogerd Fred C,Plant Nick,Bruggeman Frank J,Goncharuk Valeri,Lunshof Jeantine,Moreno-Sanchez Rafael,Yilmaz Nilgun,Bakker Barbara M,Balling Rudi

Date Published: 16th Jun 2011

Journal: Eur J Pharm Sci

Abstract (Expand)

MOTIVATION: In the Life Sciences, guidelines, checklists and ontologies describing what metadata is required for the interpretation and reuse of experimental data are emerging. Data producers, however, ...

Authors: Katy Wolstencroft, Stuart Owen, Olga Krebs, Wolfgang Müller, Jacky Snoep, Franco Du Preez, Carole Goble, Horridge Matthew

Date Published: 26th May 2011

Journal: Bioinformatics

Abstract (Expand)

The topology of nuclear receptor (NR) signaling is captured in a systems biological graphical notation. This enables us to identify a number of ‘design’ aspects of the topology of these networks that ...

Authors: Jacky Snoep, Kolodkin Alexey N,Bruggeman Frank J,Plant Nick,Moné Martijn J,Bakker Barbara M,Campbell Moray J,van Leeuwen Johannes P T M,Carlberg Carsten,Westerhoff Hans V

Date Published: 21st Dec 2010

Journal: Mol Syst Biol

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 ...

Authors: Dawie Van Niekerk, Jacky Snoep, du Preez F. B.

Date Published: No date defined

Journal: FEBS J

Abstract (Expand)

UNLABELLED: An existing detailed kinetic model for the steady-state behavior of yeast glycolysis was tested for its ability to simulate dynamic behavior. Using a small subset of experimental data, the ...

Authors: Dawie Van Niekerk, Jacky Snoep, du Preez F. B.,Kooi B.,Rohwer J. M.

Date Published: No date defined

Journal: FEBS J

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