Web-based kinetic modelling using JWS Online

The control of flux.

KACSER, H., & Ja, B. (1973) · PubMed · Cited by 1,452 · see citing works

Biochemistry by numbers: simulation of biochemical pathways with Gepasi 3

Mendes, P. (1997) · Trends in Biochemical Sciences · doi:10.1016/s0968-0004(97)01103-1 · Cited by 573 · see citing works

Roles of triosephosphate isomerase and aerobic metabolism in Trypanosoma brucei

Helfert, S., Estévez, A. M., Bakker, B. M., Michels, P. A. M., & CLAYTON, C. E. (2001) · Biochemical Journal · doi:10.1042/0264-6021:3570117 · Cited by 148 · see citing works

Metabolic control analysis in a nutshell

Hofmeyr, J. S., Hucka, M., Morohashi, M., & Kitano, H. (2001) · Cited by 65 · see citing works

Cell-signalling dynamics in time and space

Kholodenko, B. N. (2006) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1838 · Cited by 1,347 · see citing works

Biomodels database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems

Le Novere, N. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkj092 · Cited by 762 · see citing works

Reactome: a knowledge base of biologic pathways and processes

Västrik, I., D’Eustachio, P., Schmidt, E., Geeta, J.-T., Gopinath, G., Croft, D. W., de Bono, B., Gillespie, M. E., Jassal, B., Lewis, S., et al. (2007) · Genome biology · doi:10.1186/gb-2007-8-3-r39 · Cited by 656 · see citing works

Minimum information requested in the annotation of biochemical models (MIRIAM)

Novère, N. L., Finney, A., Hucka, M., Bhalla, U. S., Campagne, F., Collado-Vides, J., Crampin, E. J., Halstead, M., Klipp, E., Mendes, P., et al. (2005) · Nature Biotechnology · doi:10.1038/nbt1156 · Cited by 622 · see citing works

BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models

Li, C., Donizelli, M., Rodriguez, N., Dharuri, H., Endler, L., Chelliah, V., Li, L., He, E., Henry, A., Stefan, M. I., et al. (2010) · BMC Systems Biology · doi:10.1186/1752-0509-4-92 · Cited by 597 · see citing works

Computational modelling of the receptor-tyrosine-kinase-activated MAPK pathway

Orton, R. J., Sturm, O. E., Vyshemirsky, V., Muffy Calder, A., Gilbert, D., & Kölch, W. (2005) · Biochemical Journal · doi:10.1042/bj20050908 · Cited by 355 · see citing works

BioModels: ten-year anniversary

Chelliah, V., Juty, N., Ajmera, I., Ali, R., Dumousseau, M., Glont, M., Hucka, M., Jalowicki, G., Keating, S., Knight-Schrijver, V., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gku1181 · Cited by 281 · see citing works

The CellML Model Repository

Lloyd, C. M., Lawson, J. R., Hunter, P. J., & Nielsen, P. F. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn390 · Cited by 276 · see citing works

SABIO-RK--database for biochemical reaction kinetics

Wittig, U., Kania, R., Golebiewski, M., Rey, M., Shi, L., Jong, L. M., Algaa, E., Weidemann, A., Sauer‐Danzwith, H., Mir, S., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr1046 · Cited by 260 · see citing works

Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language

Waltemath, D., Adams, R., Bergmann, F. T., Hucka, M., Kolpakov, F., Miller, A. K., Moraru, I., Nickerson, D., Sahle, S., Snoep, J., et al. (2011) · BMC Systems Biology · doi:10.1186/1752-0509-5-198 · Cited by 269 · see citing works

DIZZY: STOCHASTIC SIMULATION OF LARGE-SCALE GENETIC REGULATORY NETWORKS

Ramsey, S. A., Orrell, D., & Bolouri, H. (2005) · Journal of Bioinformatics and Computational Biology · doi:10.1142/s0219720005001132 · Cited by 253 · see citing works

Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project

Hucka, M., Finney, A., Doyle, J. C., Kitano, H., Kovitz, B., Shapiro, B. E., Funahashi, A., Matthews, J., Bornstein, B., Keating, S., et al. (2004) · Systems Biology · doi:10.1049/sb:20045008 · Cited by 232 · see citing works

The Physiome Model Repository 2

Yu, T., Lloyd, C. M., Nickerson, D. P., Cooling, M. T., Miller, A. K., Garny, A., Terkildsen, J. R., Lawson, J., Britten, R. D., Hunter, P. J., et al. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btq723 · Cited by 169 · see citing works

Formulation, construction and analysis of kinetic models of metabolism: A review of modelling frameworks

Saa, P. A., & Nielsen, L. K. (2017) · Biotechnology Advances · doi:10.1016/j.biotechadv.2017.09.005 · Cited by 166 · see citing works

Mathematical modeling of intracellular signaling pathways

Klipp, E., & Liebermeister, W. (2006) · BMC Neuroscience · doi:10.1186/1471-2202-7-s1-s10 · Cited by 158 · see citing works

A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes

Smallbone, K., Messiha, H. L., Carroll, K. M., Winder, C. L., Malys, N., Dunn, W. B., Murabito, E., Swainston, N., Dada, J. O., Khan, F., et al. (2013) · FEBS Letters · doi:10.1016/j.febslet.2013.06.043 · Cited by 147 · see citing works

A protocol for dynamic model calibration

Villaverde, A. F., Pathirana, D., Fröhlich, F., Hasenauer, J., & Banga, J. R. (2021) · Briefings in Bioinformatics · doi:10.1093/bib/bbab387 · Cited by 140 · see citing works

FAIRDOMHub: a repository and collaboration environment for sharing systems biology research

Wolstencroft, K., Krebs, O., Snoep, J. L., Stanford, N., Bacall, F., Golebiewski, M., Kuzyakiv, R., Nguyen, Q., Owen, S., Soiland‐Reyes, S., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw1032 · Cited by 132 · see citing works

Thermodynamically Feasible Kinetic Models of Reaction Networks

Ederer, M., & Gilles, E. D. (2007) · Biophysical Journal · doi:10.1529/biophysj.106.094094 · Cited by 123 · see citing works

Towards building the silicon cell: A modular approach

Snoep, J. L., Bruggeman, F. J., Olivier, B. G., & Westerhoff, H. V. (2005) · Biosystems · doi:10.1016/j.biosystems.2005.07.006 · Cited by 121 · see citing works

SEEK: a systems biology data and model management platform

Wolstencroft, K., Owen, S., Krebs, O., Nguyen, Q., Stanford, N., Golebiewski, M., Weidemann, A., Bittkowski, M., An, L., Shockley, D., et al. (2015) · BMC Systems Biology · doi:10.1186/s12918-015-0174-y · Cited by 113 · see citing works

Something from nothing − bridging the gap between constraint‐based and kinetic modelling

B, K. S. A., Simeonidis, E., Broomhead, D. S., & Kell, D. B. (2007) · FEBS Journal · doi:10.1111/j.1742-4658.2007.06076.x · Cited by 98 · see citing works

Annotation and merging of SBML models with semanticSBML

Krause, F., Uhlendorf, J., Lubitz, T., Schulz, M., Klipp, E., & Liebermeister, W. (2010) · Bioinform. · doi:10.1093/bioinformatics/btp642 · Cited by 108 · see citing works

The role of low-grade inflammation and metabolic flexibility in aging and nutritional modulation thereof: a systems biology approach

Calçada, D., Vianello, D., Giampieri, E., Sala, C., Castellani, G., de Graaf, A., Kremer, B., van Ommen, B., Feskens, E., Santoro, A., et al. (2014) · Mechanisms of Ageing and Development · doi:10.1016/j.mad.2014.01.004 · Cited by 97 · see citing works

Model storage, exchange and integration

Novère, N. G. L. (2006) · BMC Neuroscience · doi:10.1186/1471-2202-7-s1-s11 · Cited by 97 · see citing works

Experimental and mathematical approaches to modeling plant metabolic networks

Ríos‐Estepa, R., & Lange, B. M. (2007) · Phytochemistry · doi:10.1016/j.phytochem.2007.04.021 · Cited by 94 · see citing works

Computational approaches to the topology, stability and dynamics of metabolic networks

Steuer, R. (2007) · Phytochemistry · doi:10.1016/j.phytochem.2007.04.041 · Cited by 88 · see citing works

Plant systems biology: insights, advances and challenges

Sheth, B. P., & Thaker, V. S. (2014) · Planta · doi:10.1007/s00425-014-2059-5 · Cited by 88 · see citing works

Open Source Brain: A Collaborative Resource for Visualizing, Analyzing, Simulating, and Developing Standardized Models of Neurons and Circuits

Gleeson, P., Cantarelli, M., Marin, B., Quintana, A., Earnshaw, M., Sadeh, S., Piasini, E., Birgiolas, J., Cannon, R. C., Cayco-Gajic, N. A., et al. (2019) · Neuron · doi:10.1016/j.neuron.2019.05.019 · Cited by 85 · see citing works

Systems biology towards life in silico: mathematics of the control of living cells

Westerhoff, H. V., Kolodkin, A. N., Conradie, R., Wilkinson, S. J., Bruggeman, F. J., Krab, K., van Schuppen, J. H., Härdin, H. M., Bakker, B. M., Moné, M. J., et al. (2008) · Journal of Mathematical Biology · doi:10.1007/s00285-008-0160-8 · Cited by 85 · see citing works

Quantitative elementary mode analysis of metabolic pathways: the example of yeast glycolysis

Schwartz, J., & Kanehisa, M. I. (2006) · BMC Bioinformatics · doi:10.1186/1471-2105-7-186 · Cited by 85 · see citing works

Bringing metabolic networks to life: integration of kinetic, metabolic, and proteomic data

Liebermeister, W., & Klipp, E. (2006) · Theoretical Biology and Medical Modelling · doi:10.1186/1742-4682-3-42 · Cited by 82 · see citing works

Resources for integrative systems biology: from data through databases to networks and dynamic system models

Ng, A., Bursteinas, B., Gao, Q., Mollison, E., & Zvelebil, M. (2006) · Briefings in Bioinformatics · doi:10.1093/bib/bbl036 · Cited by 82 · see citing works

Sustained glycolytic oscillations in individual isolated yeast cells

Gustavsson, A., van Niekerk, D. D., Adiels, C. B., du Preez, F. B., Goksör, M., & Snoep, J. L. (2012) · FEBS Journal · doi:10.1111/j.1742-4658.2012.08639.x · Cited by 78 · see citing works

Computational Models of Metabolism: Stability and Regulation in Metabolic Networks

Steuer, R., & Junker, B. H. (2008) · Advances in chemical physics · doi:10.1002/9780470475935.ch3 · Cited by 76 · see citing works

Harmonizing semantic annotations for computational models in biology

Neal, M. L., König, M., Nickerson, D., Mısırlı, G., Kalbasi, R., Dräger, A., Atalag, K., Chelliah, V., Cooling, M. T., Cook, D. L., et al. (2019) · Briefings in Bioinformatics · doi:10.1093/bib/bby087 · Cited by 74 · see citing works

Computational systems biology of the cell cycle

Csikász‐Nagy, A. (2009) · Briefings in Bioinformatics · doi:10.1093/bib/bbp005 · Cited by 74 · see citing works

Modeling and Simulation Using CellDesigner

Matsuoka, Y., Funahashi, A., Ghosh, S., & Kitano, H. (2014) · Methods in molecular biology · doi:10.1007/978-1-4939-0805-9_11 · Cited by 74 · see citing works

A combined experimental and modelling approach for the Weimberg pathway optimisation

Shen, L., Kohlhaas, M., Enoki, J., Meier, R., Schönenberger, B., Wohlgemuth, R., Kourist, R., Niemeyer, F. C., van Niekerk, D. D., Bräsen, C., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-14830-y · Cited by 71 · see citing works

Simulating Plant Metabolic Pathways with Enzyme-Kinetic Models

Schallau, K., & Junker, B. H. (2010) · PLANT PHYSIOLOGY · doi:10.1104/pp.109.149237 · Cited by 70 · see citing works

Reproducibility in Computational Neuroscience Models and Simulations

McDougal, R., Bulanova, A. S., & Lytton, W. (2016) · IEEE Transactions on Biomedical Engineering · doi:10.1109/tbme.2016.2539602 · Cited by 64 · see citing works

A quadratic programming approach for decomposing steady-state metabolic flux distributions onto elementary modes

Schwartz, J., & Kanehisa, M. I. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti1132 · Cited by 68 · see citing works

BioModels: Content, Features, Functionality, and Use

Juty, N., Ali, R., Glont, M., Keating, S., Rodríguez, N., Swat, M. J., Wimalaratne, S., Hermjakob, H., Novère, N. G. L., Laibe, C., et al. (2015) · CPT Pharmacometrics & Systems Pharmacology · doi:10.1002/psp4.3 · Cited by 66 · see citing works

Resources, standards and tools for systems biology

Wierling, C., Herwig, R., & Lehrach, H. R. (2007) · Briefings in Functional Genomics and Proteomics · doi:10.1093/bfgp/elm027 · Cited by 66 · see citing works

Introduction to systems biology

Bruggeman, F. J., Hornberg, J. J., Boogerd, F. C., & Westerhoff, H. V. (2007) · Birkhäuser Basel eBooks · doi:10.1007/978-3-7643-7439-6_1 · Cited by 65 · see citing works

SBRML: a markup language for associating systems biology data with models

Dada, J. O., Spasic, I., Paton, N., & Mendes, P. (2010) · Bioinform. · doi:10.1093/bioinformatics/btq069 · Cited by 66 · see citing works

The Silicon Cell initiative: working towards a detailed kinetic description at the cellular level

Snoep, J. L. (2005) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2005.05.003 · Cited by 59 · see citing works

Metabolic flux analysis: a comprehensive review on sample preparation, analytical techniques, data analysis, computational modelling, and main application areas

de Falco, B., Giannino, F., Cartenì, F., Mazzoleni, S., & Kim, D. (2022) · RSC Advances · doi:10.1039/d2ra03326g · Cited by 57 · see citing works

Metabolic network discovery through reverse engineering of metabolome data

Çakır, T., Hendriks, M. M. W. B., Westerhuis, J. A., & Smilde, A. K. (2009) · Metabolomics · doi:10.1007/s11306-009-0156-4 · Cited by 57 · see citing works

Metabolic control analysis to identify optimal drug targets

Hornberg, J. J., Bruggeman, F. J., Bakker, B. M., & Westerhoff, H. V. (2007) · Birkhäuser Basel eBooks · doi:10.1007/978-3-7643-7567-6_7 · Cited by 56 · see citing works

From isolation to integration, a systems biology approach for building the Silicon Cell

Snoep, J. L., & Westerhoff, H. V. (2005) · Springer eBooks · doi:10.1007/b106456 · Cited by 57 · see citing works

Improving Collaboration by Standardization Efforts in Systems Biology

Dräger, A., & Palsson, B. Ã. (2014) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2014.00061 · Cited by 57 · see citing works

The SEEK

Wolstencroft, K., Owen, S., du Preez, F. B., Krebs, O., Müller, W., Goble, C., & Snoep, J. L. (2011) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/b978-0-12-385118-5.00029-3 · Cited by 56 · see citing works

“Hot standards” for the thermoacidophilic archaeon Sulfolobus solfataricus

Zaparty, M., Esser, D., Gertig, S., Haferkamp, P., Kouril, T., Manica, A., Pham, T. K., Reimann, J., Schreiber, K., Sierocinski, P., et al. (2009) · Extremophiles · doi:10.1007/s00792-009-0280-0 · Cited by 56 · see citing works

Development of an accurate kinetic model for the central carbon metabolism of Escherichia coli

Jahan, N., Maeda, K., Matsuoka, Y., Sugimoto, Y., & Kurata, H. (2016) · Microbial Cell Factories · doi:10.1186/s12934-016-0511-x · Cited by 57 · see citing works

Tellurium notebooks—An environment for reproducible dynamical modeling in systems biology

Medley, J., Choi, K., König, M., Smith, L. P., Gu, S., Hellerstein, J., Sealfon, S., & Sauro, H. (2018) · PLoS Comput. Biol. · doi:10.1371/journal.pcbi.1006220 · Cited by 58 · see citing works

Benchmarking of numerical integration methods for ODE models of biological systems

Städter, P., Schälte, Y., Schmiester, L., Hasenauer, J., & Stapor, P. L. (2021) · Scientific Reports · doi:10.1038/s41598-021-82196-2 · Cited by 55 · see citing works

Computational Strategies for a System-Level Understanding of Metabolism

Cazzaniga, P., Damiani, C., Besozzi, D., Colombo, R., Nobile, M. S., Gaglio, D., Pescini, D., Molinari, S., Mauri, G., Alberghina, L., et al. (2014) · Metabolites · doi:10.3390/metabo4041034 · Cited by 54 · see citing works

Complexity reduction preserving dynamical behavior of biochemical networks

Apri, M., Maarten De Gee, A., & Molenaar, J. (2012) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2012.03.019 · Cited by 53 · see citing works

Combining computational models, semantic annotations and simulation experiments in a graph database

Henkel, R., Wolkenhauer, O., & Waltemath, D. (2015) · Database J. Biol. Databases Curation · doi:10.1093/database/bau130 · Cited by 52 · see citing works

Modelling cyanobacteria: from metabolism to integrative models of phototrophic growth

Steuer, R., Knoop, H., & Machné, R. (2012) · Journal of Experimental Botany · doi:10.1093/jxb/ers018 · Cited by 53 · see citing works

Kinetic modeling of cell metabolism for microbial production

Costa, R. S., Hartmann, A., & Vinga, S. (2015) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2015.12.023 · Cited by 53 · see citing works

Monitoring and Modeling of the Reaction Dynamics in the Valine/Leucine Synthesis Pathway in Corynebacterium glutamicum

Magnus, J. B., Hollwedel, D., Oldiges, M., & Takors, R. (2006) · Biotechnology Progress · doi:10.1021/bp060072f · Cited by 51 · see citing works

How Modeling Standards, Software, and Initiatives Support Reproducibility in Systems Biology and Systems Medicine

Waltemath, D., & Wolkenhauer, O. (2016) · IEEE Transactions on Biomedical Engineering · doi:10.1109/tbme.2016.2555481 · Cited by 49 · see citing works

Systems Biology, Bioinformatics, and Biomarkers in Neuropsychiatry

Alawieh, A. M., Zaraket, F. A., Li, J., Mondello, S., Nokkari, A., Razafsha, M., Fadlallah, B. H., Boustany, R., & Kobeissy, F. H. (2012) · Frontiers in Neuroscience · doi:10.3389/fnins.2012.00187 · Cited by 49 · see citing works

Construction and validation of a detailed kinetic model of glycolysis in Plasmodium falciparum

Penkler, G. P., du Toit, F., Adams, W. W., Rautenbach, M., Palm, D. C., van Niekerk, D. D., & Snoep, J. L. (2015) · FEBS Journal · doi:10.1111/febs.13237 · Cited by 48 · see citing works

Condor-COPASI: high-throughput computing for biochemical networks

Kent, E., Hoops, S., & Mendes, P. (2012) · BMC Systems Biology · doi:10.1186/1752-0509-6-91 · Cited by 48 · see citing works

What mRNA Abundances Can Tell us about Metabolism

Hoppe, A. (2012) · Metabolites · doi:10.3390/metabo2030614 · Cited by 47 · see citing works

Targeting glycolysis in the malaria parasite Plasmodium falciparum

van Niekerk, D. D., Penkler, G. P., du Toit, F., & Snoep, J. L. (2015) · FEBS Journal · doi:10.1111/febs.13615 · Cited by 46 · see citing works

Best Practices for Making Reproducible Biochemical Models

Porubsky, V. L., Goldberg, A. P., Rampadarath, A. K., Nickerson, D. P., Karr, J. R., & Sauro, H. M. (2020) · Cell Systems · doi:10.1016/j.cels.2020.06.012 · Cited by 45 · see citing works

Systems biology tools for toxicology

Geenen, S., Taylor, P. N., Snoep, J. L., Wilson, I. D., Kenna, J. G., & Westerhoff, H. V. (2012) · Archives of Toxicology · doi:10.1007/s00204-012-0857-8 · Cited by 44 · see citing works

Monitoring and modelling the dynamics of the cellular glycolysis pathway: A review and future perspectives

Patil, N., Howe, O. L., Cahill, P. A., & Byrne, H. J. (2022) · Molecular Metabolism · doi:10.1016/j.molmet.2022.101635 · Cited by 42 · see citing works

New types of experimental data shape the use of enzyme kinetics for dynamic network modeling

Tummler, K., Lubitz, T., Schelker, M., & Klipp, E. (2013) · FEBS Journal · doi:10.1111/febs.12525 · Cited by 42 · see citing works

Dupuytren's: a systems biology disease

Rehman, S., Goodacre, R., Day, P. J., Bayat, A., & Westerhoff, H. V. (2011) · Arthritis Research & Therapy · doi:10.1186/ar3438 · Cited by 43 · see citing works

The logic of kinetic regulation in the thioredoxin system

Pillay, C. S., Hofmeyr, J. S., & Rohwer, J. M. (2011) · BMC Systems Biology · doi:10.1186/1752-0509-5-15 · Cited by 41 · see citing works

Bridging the gaps in systems biology

Cvijovic, M., Almquist, J., Hagmar, J., Hohmann, S., Kaltenbach, H.-M., Klipp, E., Krantz, M., Mendes, P., Nelander, S., Nielsen, J., et al. (2014) · Molecular Genetics and Genomics · doi:10.1007/s00438-014-0843-3 · Cited by 40 · see citing works

Retrieval, alignment, and clustering of computational models based on semantic annotations

Schulz, M., Krause, F., Novère, N. L., Klipp, E., & Liebermeister, W. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.41 · Cited by 46 · see citing works

Glutathione metabolism modeling: A mechanism for liver drug-robustness and a new biomarker strategy

Geenen, S., du Preez, F. B., Snoep, J. L., Foster, A. J., Sarda, S., Kenna, J. G., Wilson, I. D., & Westerhoff, H. V. (2013) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2013.04.014 · Cited by 39 · see citing works

Closing the gap between formats for storing layout information in systems biology

Hoksza, D., Gawron, P., Ostaszewski, M., Hasenauer, J., & Schneider, R. (2019) · Briefings in Bioinformatics · doi:10.1093/bib/bbz067 · Cited by 32 · see citing works

Control of specific growth rate in Saccharomyces cerevisiae

Snoep, J. L., Mrwebi, M., Schuurmans, J. M., Rohwer, J. M., & de Mattos, M. J. T. (2009) · Microbiology · doi:10.1099/mic.0.023119-0 · Cited by 39 · see citing works

Design principles of nuclear receptor signaling: how complex networking improves signal transduction

Kolodkin, A. N., Bruggeman, F. J., Plant, N. J., Moné, M. J., Bakker, B. M., Campbell, M. J., van Leeuwen, J. P. T. M., Carlberg, C., Snoep, J. L., & Westerhoff, H. V. (2010) · Molecular Systems Biology · doi:10.1038/msb.2010.102 · Cited by 38 · see citing works

Mathematical modeling of cancer metabolism

Medina, M. Á. (2018) · Critical Reviews in Oncology/Hematology · doi:10.1016/j.critrevonc.2018.02.004 · Cited by 38 · see citing works

Representing, storing and accessing molecular interaction data: a review of models and tools

Strömbäck, L., Jakoniené, V., Tan, H., & Lambrix, P. (2006) · Briefings in Bioinformatics · doi:10.1093/bib/bbl039 · Cited by 38 · see citing works

Enzymes or redox couples? The kinetics of thioredoxin and glutaredoxin reactions in a systems biology context

Pillay, C. S., Hofmeyr, J. S., Olivier, B. G., Snoep, J. L., & Rohwer, J. M. (2008) · Biochemical Journal · doi:10.1042/bj20080690 · Cited by 37 · see citing works

Storing and annotating of kinetic data.

Rojas, I., Golebiewski, M., Kania, R., Krebs, O., Mir, S., Weidemann, A., & Wittig, U. (2007) · PubMed · Cited by 37 · see citing works

Systematic integration of experimental data and models in systems biology

Li, P., Dada, J. O., Jameson, D., Spasić, ‪., Swainston, N., Carroll, K. M., Dunn, W. B., Khan, F., Malys, N., Messiha, H. L., et al. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-582 · Cited by 36 · see citing works

Data management strategies for multinational large-scale systems biology projects

Wruck, W., Peuker, M., & Regenbrecht, C. (2012) · Briefings Bioinform. · doi:10.1093/bib/bbs064 · Cited by 36 · see citing works

The JWS online simulation database

Peters, M., Eicher, J. J., van Niekerk, D. D., Waltemath, D., & Snoep, J. L. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btw831 · Cited by 36 · see citing works

Low affinity uniporter carrier proteins can increase net substrate uptake rate by reducing efflux

Bosdriesz, E., Wortel, M. T., Haanstra, J. R., Wagner, M. J., Cortés, P. D. L. T., & Teusink, B. (2018) · Scientific Reports · doi:10.1038/s41598-018-23528-7 · Cited by 37 · see citing works

Functional ingredient production: application of global metabolic models

Smid, E. J., Douwe Molenaar, B., Hugenholtz, J., de Vos, W. M., & Teusink, B. (2005) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2005.03.001 · Cited by 36 · see citing works

Coupled metabolic‐hydrodynamic modeling enabling rational scale‐up of industrial bioprocesses

Wang, G., Haringa, C., Tang, W., Noorman, H. J., Chu, J., Zhuang, Y., & Zhang, S. (2019) · Biotechnology and Bioengineering · doi:10.1002/bit.27243 · Cited by 34 · see citing works

Deterministic modelling and stochastic simulation of biochemical pathways using MATLAB

Ullah, M., Schmidt, H., Cho, K.-H., & Olaf Wolkenhauer, A. (2006) · Systems Biology · doi:10.1049/ip-syb:20050064 · Cited by 35 · see citing works

SABIO-RK: a database for biochemical reactions and their kinetics

Rojas, I., Golebiewski, M., Kania, R., Krebs, O., Mir, S., Weidemann, A., & Wittig, U. (2007) · BMC Systems Biology · doi:10.1186/1752-0509-1-s1-s6 · Cited by 35 · see citing works

From steady‐state to synchronized yeast glycolytic oscillations I: model construction

du Preez, F. B., van Niekerk, D. D., Kooi, B. W., Rohwer, J. M., & Snoep, J. L. (2012) · FEBS Journal · doi:10.1111/j.1742-4658.2012.08665.x · Cited by 34 · see citing works

When is the Quasi-Steady-State Approximation Admissible in Metabolic Modeling? When Admissible, What Models are Desirable?

Song, H., & Ramkrishna, D. (2009) · Industrial & Engineering Chemistry Research · doi:10.1021/ie900075f · Cited by 33 · see citing works

Cancerous perturbations within the ERK, PI3K/Akt, and Wnt/β-catenin signaling network constitutively activate inter-pathway positive feedback loops

Padala, R. R., Karnawat, R., Viswanathan, S. B., Thakkar, A. V., & Das, A. B. (2017) · Molecular BioSystems · doi:10.1039/c6mb00786d · Cited by 33 · see citing works

Kinetic and Thermodynamic Aspects of Enzyme Control and Regulation

Rohwer, J. M., & Hofmeyr, J. S. (2010) · The Journal of Physical Chemistry B · doi:10.1021/jp108412s · Cited by 33 · see citing works

WebCell: a web-based environment for kinetic modeling and dynamic simulation of cellular networks

Lee, D., Yun, C., Cho, A., Hou, B. K., Park, S., & Lee, S. Y. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl091 · Cited by 33 · see citing works

Emergence of the silicon human and network targeting drugs

Kolodkin, A. N., Boogerd, F. C., Plant, N. J., Bruggeman, F. J., Goncharuk, V. D., Lunshof, J. E., Moreno‐Sánchez, R., Yilmaz, N., Bakker, B. M., Snoep, J. L., et al. (2011) · European Journal of Pharmaceutical Sciences · doi:10.1016/j.ejps.2011.06.006 · Cited by 34 · see citing works

SulfoSYS (Sulfolobus Systems Biology): towards a silicon cell model for the central carbohydrate metabolism of the archaeon Sulfolobus solfataricus under temperature variation

Albers, S., Birkeland, N.-K., Driessen, A. J. M., Gertig, S., Haferkamp, P., Klenk, H., Kouril, T., Manica, A., Pham, T. K., Ruoff, P., et al. (2009) · Biochemical Society Transactions · doi:10.1042/bst0370058 · Cited by 32 · see citing works

JWS online: a web-based tool for curation, review, sotrage and analysis of kinetic models.

Snoep, J. L., van Gend, C. H. D. R., Stoof, C., Oliver, B., Conradie, R., du Preez, F. B., Schaboret, D. T. W. P., Penkler, G. P., & Holm, K. (2007) · VU Research Portal

The eFramework: an Overview

Olivier, B. G., & Snoep, J. L. (2005)

Beilstein-Institut JWS Online: A Web-Based Tool for Curation, Review, Storage and Analysis of Kinetic Models

Snoep, J. L., Gend, C. V., Stoof, C., Olivier, B. G., Conradie, R., Du, F. B., Toit, D., Schabort, W. P. D. T., Penkler, G. P., & Holm, K. (2008)

Java Web Simulation (JWS); A Web Based Database of Kinetic Models

Snoep, J. L., & Olivier, B. G. (2002) · Molecular Biology Reports · doi:10.1023/a:1020350518131 · Cited by 26 · see citing works

JWS Online: A Web-Based Tool for Curation, Review, Storage and Analysis of Kinetic Models

Snoep, J. L., Van Gend, C., Stoof, C., Olivier, B. G., Conradie, R., du Preez, F. B., Schabort, D. T. W. P., Penkler, G. P., & Holm, K. (2007) · SUNScholar (Stellenbosch University)