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2020 – today
- 2023
[j19]Theresa Kouril, Craig October, Stephanie Hollocks, Christoff Odendaal
, David D. van Niekerk, Jacky L. Snoep:
Inhibitor titrations reveal low control of glyceraldehyde 3-phosphate dehydrogenase and high control of hexokinase on glycolytic flux in an aggressive triple-negative breast cancer cell line. Biosyst. 231: 104969 (2023)- [j18]David D. van Niekerk, Erik Rust, Frank J. Bruggeman, Hans V. Westerhoff, Jacky L. Snoep:
Is distance from equilibrium a good indicator for a reaction's flux control? Biosyst. 232: 104988 (2023) - 2022
- [j17]Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz E. Beber, Frank T. Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary B. Haiman, Jan Hasenauer, Joseph L. Hellerstein, Henning Hermjakob, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, Rahuman S. Malik-Sheriff, Synchon Mandal, Robert A. McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali Sinan Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David D. van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, James C. Schaff, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr:
BioSimulators: a central registry of simulation engines and services for recommending specific tools. Nucleic Acids Res. 50(W1): 108-114 (2022) - [i1]Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz E. Beber, Frank T. Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Fröhlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary B. Haiman, Joseph L. Hellerstein, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matús Kalas, Matthias König, Wolfram Liebermeister, Synchon Mandal, Robert A. McDougal, J. Kyle Medley, Pedro Mendes, Robert Müller, Chris J. Myers, Aurélien Naldi, Tung V. N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loïc Paulevé, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali Sinan Saglam, Dilawar Singh, Ankur Sinha, Jacky L. Snoep, Hugh Sorby, Ryan K. Spangler, Jörn Starruß, Payton J. Thomas, David D. van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, Jonathan R. Karr:
BioSimulators: a central registry of simulation engines and services for recommending specific tools. CoRR abs/2203.06732 (2022) - 2021
- [j16]Shade Horn, Jacky L. Snoep, David D. van Niekerk:
Uncovering the effects of heterogeneity and parameter sensitivity on within-host dynamics of disease: malaria as a case study. BMC Bioinform. 22(1): 384 (2021)
2010 – 2019
- 2019
- [j15]Maxwell Lewis Neal, Matthias König, David P. Nickerson, Goksel Misirli, Reza Kalbasi, Andreas Dräger, Koray Atalag, Vijayalakshmi Chelliah, Michael T. Cooling, Daniel L. Cook, Sharon M. Crook, Miguel de Alba, Samuel H. Friedman, Alan Garny, John H. Gennari, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nick S. Juty, Chris J. Myers, Brett G. Olivier, Herbert M. Sauro, Martin Scharm, Jacky L. Snoep, Vasundra Touré, Anil Wipat, Olaf Wolkenhauer, Dagmar Waltemath:
Harmonizing semantic annotations for computational models in biology. Briefings Bioinform. 20(2): 540-550 (2019) - 2017
- [j14]Martin Peters, Johann J. Eicher, David D. van Niekerk, Dagmar Waltemath, Jacky L. Snoep:
The JWS online simulation database. Bioinform. 33(10): 1589-1590 (2017) - [j13]Katherine Wolstencroft, Olga Krebs, Jacky L. Snoep, Natalie J. Stanford, Finn Bacall, Martin Golebiewski, Rostyk Kuzyakiv, Quyen Nguyen, Stuart Owen, Stian Soiland-Reyes, Jakub Straszewski, David D. van Niekerk, Alan R. Williams, Lars Malmström, Bernd Rinn, Wolfgang Müller, Carole A. Goble:
FAIRDOMHub: a repository and collaboration environment for sharing systems biology research. Nucleic Acids Res. 45(Database-Issue): D404-D407 (2017) - 2016
- [j12]Nicola J. Mulder, Alan Christoffels, Tulio de Oliveira, Junaid Gamieldien, Scott Hazelhurst, Fourie Joubert, Judit Kumuthini, Ché S. Pillay, Jacky L. Snoep, Özlem Tastan Bishop, Nicki Tiffin:
The Development of Computational Biology in South Africa: Successes Achieved and Lessons Learnt. PLoS Comput. Biol. 12(2) (2016) - [c6]Olga Krebs, Katy Wolstencroft, Natalie J. Stanford, Norman Morrison, Martin Golebiewski, Rostyk Kuzyakiv, Stuart Owen, Quyen Nguyen, Jacky L. Snoep, Wolfgang Müller, Carole A. Goble:
FAIRDOM approach for semantic interoperability of systems biology data and models. ODLS 2016: 1-2 - 2015
- [j11]Katherine Wolstencroft, Stuart Owen, Olga Krebs, Quyen Nguyen, Natalie J. Stanford, Martin Golebiewski, Andreas Weidemann, Meik Bittkowski, Lihua An, David Shockley, Jacky L. Snoep, Wolfgang Müller, Carole A. Goble:
SEEK: a systems biology data and model management platform. BMC Syst. Biol. 9: 33 (2015) - [j10]Ettore Murabito, Riccardo Colombo, Chengkun Wu, Malkhey Verma, Samrina Rehman, Jacky L. Snoep, Shaoliang Peng, Naiyang Guan, Xiangke Liao, Hans V. Westerhoff:
SupraBiology 2014: Promoting UK-China collaboration on Systems Biology and High Performance Computing. Quant. Biol. 3(1): 46-53 (2015) - [c5]Olga Krebs, Katy Wolstencroft, Natalie J. Stanford, Norman Morrison, Martin Golebiewski, Stuart Owen, Quyen Nguyen, Jacky L. Snoep, Wolfgang Müller, Carole A. Goble:
FAIRDOM approach for semantic interoperability of systems biology data and models. ICBO 2015 - 2013
- [j9]Katherine Wolstencroft, Stuart Owen, Matthew Horridge, Simon Jupp, Olga Krebs, Jacky L. Snoep, Franco B. du Preez, Wolfgang Müller, Robert Stevens, Carole A. Goble:
Stealthy annotation of experimental biology by spreadsheets. Concurr. Comput. Pract. Exp. 25(4): 467-480 (2013) - [c4]Katherine Wolstencroft, Stuart Owen, Olga Krebs, Wolfgang Müller, Quyen Nguyen, Jacky L. Snoep, Carole A. Goble:
Semantic Data and Models Sharing in Systems Biology: The Just Enough Results Model and the SEEK Platform. ISWC (2) 2013: 212-227 - 2012
- [c3]Katy Wolstencroft, Stuart Owen, Matthew Horridge, Wolfgang Müller, Finn Bacall, Jacky L. Snoep, Franco B. du Preez, Quyen Nguyen, Olga Krebs, Carole A. Goble:
RightField: Scientific Knowledge Acquisition by Stealth through Ontology-Enabled Spreadsheets. EKAW 2012: 438-441 - 2011
- [j8]Katy Wolstencroft, Stuart Owen, Matthew Horridge, Olga Krebs, Wolfgang Müller, Jacky L. Snoep, Franco B. du Preez, Carole A. Goble:
RightField: embedding ontology annotation in spreadsheets. Bioinform. 27(14): 2021-2022 (2011) - [j7]Dagmar Waltemath, Richard R. Adams, Frank T. Bergmann, Michael Hucka, Fedor A. Kolpakov, Andrew K. Miller, Ion I. Moraru, David P. Nickerson, Sven Sahle, Jacky L. Snoep, Nicolas Le Novère:
Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language. BMC Syst. Biol. 5: 198 (2011) - [j6]Dagmar Waltemath, Richard R. Adams, Daniel A. Beard, Frank T. Bergmann, Upinder S. Bhalla, Randall Britten, Vijayalakshmi Chelliah, Mike T. Cooling, Jonathan Cooper, Edmund J. Crampin, Alan Garny, Stefan Hoops, Michael Hucka, Peter J. Hunter, Edda Klipp, Camille Laibe, Andrew K. Miller, Ion I. Moraru, David P. Nickerson, Poul M. F. Nielsen, Macha Nikolski, Sven Sahle, Herbert M. Sauro, Henning Schmidt, Jacky L. Snoep, Dominic P. Tolle, Olaf Wolkenhauer, Nicolas Le Novère:
Minimum Information About a Simulation Experiment (MIASE). PLoS Comput. Biol. 7(4) (2011) - 2010
- [j5]Chen Li, Marco Donizelli, Nicolas Rodriguez, Harish Dharuri, Lukas Endler, Vijayalakshmi Chelliah, Lu Li, Enuo He, Arnaud Henry, Melanie I. Stefan, Jacky L. Snoep, Michael Hucka, Nicolas Le Novère, Camille Laibe:
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst. Biol. 4: 92 (2010) - [j4]Catholijn M. Jonker, Jacky L. Snoep, Jan Treur, Hans V. Westerhoff, Wouter C. A. Wijngaards:
The Living Cell as a Multi-agent Organisation: A Compositional Organisation Model of Intracellular Dynamics. Trans. Comput. Collect. Intell. 1: 160-206 (2010) - [c2]Katy Wolstencroft, Matthew Horridge, Stuart Owen, Wolfgang Müller, Finn Bacall, Jacky L. Snoep, Olga Krebs, Carole A. Goble:
Rightfield: Embedding Ontology Term Selection into Spreadsheets for the Annotation of Biological Data. ISWC (Posters & Demos) 2010
2000 – 2009
- 2007
- [j3]Carel van Gend, Riaan Conradie, Franco B. du Preez, Jacky L. Snoep:
Data and Model Integration Using JWS Online. Silico Biol. 7(6): 27-35 (2007) - 2006
- [j2]Nicolas Le Novère, Benjamin J. Bornstein, Alexander Broicher, Mélanie Courtot, Marco Donizelli, Harish Dharuri, Lu Li, Herbert M. Sauro, Maria J. Schilstra, Bruce E. Shapiro, Jacky L. Snoep, Michael Hucka:
BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res. 34(Database-Issue): 689-691 (2006) - 2004
- [j1]Brett G. Olivier, Jacky L. Snoep:
Web-based kinetic modelling using JWS Online. Bioinform. 20(13): 2143-2144 (2004) - 2002
- [c1]Catholijn M. Jonker, Jacky L. Snoep, Jan Treur, Hans V. Westerhoff, Wouter C. A. Wijngaards:
Embodied intentional dynamics of bacterial behaviour. AAMAS 2002: 465-466
Coauthor Index
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