Publications

Abstract (Expand)

The Computational Modeling in Biology Network (COMBINE) is an initiative to coordinate the development of community standards and formats in computational systems biology and related fields. This report ...

Authors: Carole Goble, Olga Krebs, Waltemath Dagmar,Bergmann Frank T.,Chaouiya Claudine,Czauderna Tobias,Gleeson Padraig,Golebiewski Martin,Hucka Michael,Juty Nick,Le Novère Nicolas,Mi Huaiyu,Moraru Ion I.,Myers Chris J.,Nickerson David,Olivier Brett G.,Rodriguez Nicolas,Schreiber Falk,Smith Lucian,Zhang Fengkai,Bonnet Eric

Date Published: 15th Mar 2014

Journal: Stand. Genomic Sci.

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 (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)

Encouraging more broad and inclusive data sharing in today's world will involve concerted community efforts to overcome technical barriers and human foibles. Vivien Marx investigates. (includes ...

Author: Marx Vivien

Date Published: 7th Jun 2012

Journal: Nat Biotechnol

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)

To make full use of research data, the bioscience community needs to adopt technologies and reward mechanisms that support interoperability and promote the growth of an open 'data commoning' ...

Authors: Carole Goble, Katy Wolstencroft, Sansone Susanna-Assunta,Rocca-Serra Philippe,Field Dawn,Maguire Eamonn,Taylor Chris,Hofmann Oliver,Fang Hong,Neumann Steffen,Tong Weida,Amaral-Zettler Linda,Begley Kimberly,Booth Tim,Bougueleret Lydie,Burns Gully,Chapman Brad,Clark Tim,Coleman Lee-Ann,Copeland Jay,Das Sudeshna,de Daruvar Antoine,de Matos Paula,Dix Ian,Edmunds Scott,Evelo Chris T,Forster Mark J,Gaudet Pascale,Gilbert Jack,Griffin Julian L,Jacob Daniel,Kleinjans Jos,Harland Lee,Haug Kenneth,Hermjakob Henning,Ho Sui Shannan J,Laederach Alain,Liang Shaoguang,Marshall Stephen,McGrath Annette,Merrill Emily,Reilly Dorothy,Roux Magali,Shamu Caroline E,Shang Catherine A,Steinbeck Christoph,Trefethen Anne,Williams-Jones Bryn,Xenarios Ioannis,Hide Winston

Date Published: 28th Jan 2012

Journal: Nat. Genet.

Abstract (Expand)

BACKGROUND: Ontologies are being developed for the life sciences to standardise the way we describe and interpret the wealth of data currently being generated. As more ontology based applications begin ...

Authors: Stuart Owen, Katy Wolstencroft, Jupp Simon,Horridge Matthew,Iannone Luigi,Klein Julie,Schanstra Joost,Stevens Robert

Date Published: 25th Jan 2012

Journal: BMC bioinformatics

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)

This paper briefly describes the SABIO-RK database model for the storage of reaction kinetics information and the guidelines followed within the SABIO-RK project to annotate the kinetic data. Such ...

Authors: Isabel Rojas, Renate Kania, Olga Krebs, Golebiewski Martin,Mir Saqib,Weidemann Andreas,Wittig Ulrike

Date Published: 14th Sep 2007

Journal: In Silico Biol. (Gedrukt)

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