The Systems Biology Graphical Notation (2009)
Le Novère, Nicolas, Hucka, Michael, Mi, Huaiyu, Moodie, Stuart, Schreiber, Falk, Sorokin, Anatoly, ...
Circuit diagrams and Unified Modeling Language diagrams are just two examples of standard visual languages that help accelerate work by promoting regularity, removing ambiguity and enabling software...
Jacky L. Snoep, Carel Van Gend, Cor Stoof, Brett G. Olivier, Riaan Conradie, Franco B. Du, ...
In this contribution we report on the JWS Online project and the progress that has been made since the first ESCEC meeting. Whilst maintaining the same user interface, we have completely redesigned...
Biochemistry Private Bag X1 (2007)
De Boelelaan A, Catholijn M. Jonker, Jacky L. Snoep, Hans V. Westerhoff
Existing chemical models of bacteria are complicated, due to the thousands of interacting chemical reactions within the cell. To gain models are needed. In this paper an intentional dynamic modelling...
Le Novère, Nicolas, Bornstein, Benjamin, Broicher, Alexander, Courtot, Mélanie, Donizelli, Marco, Dharuri, Harish, ...
BioModels Database (http://www.ebi.ac.uk/biomodels/), part of the international initiative BioModels.net, provides access to published, peer-reviewed, quantitative models of biochemical and cellular...
Le Novère, Nicolas, Bornstein, Benjamin, Broicher, Alexander, Courtot, Mélanie, Donizelli, Marco, Dharuri, Harish, ...
BioModels Database (http://www.ebi.ac.uk/biomodels/), part of the international initiative BioModels.net, provides access to published, peer-reviewed, quantitative models of biochemical and cellular...
Minimum information requested in the annotation of biochemical models (MIRIAM) (2005)
Le Novère, Nicolas, Finney, Andrew, Hucka, Michael, Bhalla, Upinder S., Campagne, Fabien, Collado-Vides, Julio, ...
Most of the published quantitative models in biology are lost for the community because they are either not made available or they are insufficiently characterized to allow them to be reused. The...
The eFramework: an Overview (2005)
Brett G. Olivier, Jacky L. Snoep
Summary: JWS Online is a repository of kinetic models, describing biological systems, which can be interactively run and interrogated over the internet. It is implemented using a client-server...
Web-based kinetic modelling using JWS Online (2004)
Olivier, Brett G., Snoep, Jacky L.
Summary: JWS Online is a repository of kinetic models, describing biological systems, which can be interactively run and interrogated over the Internet. It is implemented using a client–server...
Web-based kinetic modelling using JWS online (2004)
Olivier, Brett G., Snoep, Jacky L.
Summary: JWS Online is a repository of kinetic models, describing biological systems, which can be interactively run and interrogated over the internet. It is implemented using a client-server...
Web-based kinetic modelling using JWS online (2004)
Olivier, Brett G., Snoep, Jacky L.
Summary: JWS Online is a repository of kinetic models, describing biological systems, which can be interactively run and interrogated over the internet. It is implemented using a client-server...
Embodied Intentional Dynamics of Bacterial Behaviour (2001)
Catholijn M. Jonker, Jacky L. Snoep, Hans V. Westerhoff
Existing (embodied) chemical models of bacteria are rather complex, due to the thousands of interacting chemical reactions within the cell. To gain a higher level of understanding, more transparent...
De Graef, Mark R., Alexeeva, Svetlana, Snoep, Jacky L., Teixeira De Mattos, M. Joost
Escherichia coli MC4100 was grown in anaerobic glucose-limited chemostat cultures, either in the presence of an electron acceptor (fumarate, nitrate, or oxygen) or fully fermentatively. The...
Ward, Donald E., Ross, R. Paul, Van Der Weijden, Coen C., Snoep, Jacky L., Claiborne, Al
Genes encoding a branched-chain α-keto acid dehydrogenase from Enterococcus faecalis 10C1, E1α (bkdA), E1β (bkdB), E2 (bkdC), and E3 (bkdD), were found to reside in the gene cluster...
Ward, Donald E., Van Der Weijden, Coen C., Van Der Merwe, Marthinus J., Westerhoff, Hans V., Claiborne, Al, Snoep, Jacky L.
Recently the bkd gene cluster from Enterococcus faecalis was sequenced, and it was shown that the gene products constitute a pathway for the catabolism of branched-chain α-keto acids. We have now...
The Glycolytic Flux in Escherichia coli Is Controlled by the Demand for ATP
Koebmann, Brian J., Westerhoff, Hans V., Snoep, Jacky L., Nilsson, Dan, Jensen, Peter R.
The nature of the control of glycolytic flux is one of the central, as-yet-uncharacterized issues in cellular metabolism. We developed a molecular genetic tool that specifically induces ATP...
Role of Hexose Transport in Control of Glycolytic Flux in Saccharomyces cerevisiae
Elbing, Karin, Larsson, Christer, Bill, Roslyn M., Albers, Eva, Snoep, Jacky L., Boles, Eckhard, ...
The yeast Saccharomyces cerevisiae predominantly ferments glucose to ethanol at high external glucose concentrations, irrespective of the presence of oxygen. In contrast, at low external glucose...
Control analysis for autonomously oscillating biochemical networks.
Reijenga, Karin A, Westerhoff, Hans V, Kholodenko, Boris N, Snoep, Jacky L
It has hitherto not been possible to analyze the control of oscillatory dynamic cellular processes in other than qualitative ways. The control coefficients, used in metabolic control analyses of...
Le Novère, Nicolas, Bornstein, Benjamin, Broicher, Alexander, Courtot, Mélanie, Donizelli, Marco, Dharuri, Harish, ...
BioModels Database (), part of the international initiative BioModels.net, provides access to published, peer-reviewed, quantitative models of biochemical and cellular systems. Each model is...
De Graef, Mark R., Alexeeva, Svetlana, Snoep, Jacky L., Teixeira De Mattos, M. Joost
Escherichia coli MC4100 was grown in anaerobic glucose-limited chemostat cultures, either in the presence of an electron acceptor (fumarate, nitrate, or oxygen) or fully fermentatively. The...
Ward, Donald E., Ross, R. Paul, Van Der Weijden, Coen C., Snoep, Jacky L., Claiborne, Al
Genes encoding a branched-chain α-keto acid dehydrogenase from Enterococcus faecalis 10C1, E1α (bkdA), E1β (bkdB), E2 (bkdC), and E3 (bkdD), were found to reside in the gene cluster...
Ward, Donald E., Van Der Weijden, Coen C., Van Der Merwe, Marthinus J., Westerhoff, Hans V., Claiborne, Al, Snoep, Jacky L.
Recently the bkd gene cluster from Enterococcus faecalis was sequenced, and it was shown that the gene products constitute a pathway for the catabolism of branched-chain α-keto acids. We have now...
The Glycolytic Flux in Escherichia coli Is Controlled by the Demand for ATP
Koebmann, Brian J., Westerhoff, Hans V., Snoep, Jacky L., Nilsson, Dan, Jensen, Peter R.
The nature of the control of glycolytic flux is one of the central, as-yet-uncharacterized issues in cellular metabolism. We developed a molecular genetic tool that specifically induces ATP...
Role of Hexose Transport in Control of Glycolytic Flux in Saccharomyces cerevisiae
Elbing, Karin, Larsson, Christer, Bill, Roslyn M., Albers, Eva, Snoep, Jacky L., Boles, Eckhard, ...
The yeast Saccharomyces cerevisiae predominantly ferments glucose to ethanol at high external glucose concentrations, irrespective of the presence of oxygen. In contrast, at low external glucose...
Control analysis for autonomously oscillating biochemical networks.
Reijenga, Karin A, Westerhoff, Hans V, Kholodenko, Boris N, Snoep, Jacky L
It has hitherto not been possible to analyze the control of oscillatory dynamic cellular processes in other than qualitative ways. The control coefficients, used in metabolic control analyses of...
Le Novère, Nicolas, Bornstein, Benjamin, Broicher, Alexander, Courtot, Mélanie, Donizelli, Marco, Dharuri, Harish, ...
BioModels Database (), part of the international initiative BioModels.net, provides access to published, peer-reviewed, quantitative models of biochemical and cellular systems. Each model is...