Web-based kinetic modelling using JWS Online

The control of flux.

KACSER, H., & Ja, B. (1973) · PubMed · Cited by 1,455

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 574

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

Metabolic control analysis in a nutshell

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

Cell-signalling dynamics in time and space

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

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

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 662

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

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

Li, C., Donizelli, M., Rodríguez, N., Dharuri, H. K., 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 561

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

Orton, R. J., Sturm, O. E., Vyshemirsky, V., Calder, M., Gilbert, D., & Kölch, W. (2005) · Biochemical Journal · doi:10.1042/bj20050908 · Cited by 368

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

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

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

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

Waltemath, D., Adams, R. R., Bergmann, F., Hucka, M., Kolpakov, F., Miller, A. K., Moraru, I. I., Nickerson, D. P., Sahle, S., Snoep, J. L., et al. (2011) · BMC Systems Biology · doi:10.1186/1752-0509-5-198 · Cited by 259

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 245

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

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

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

Mathematical modeling of intracellular signaling pathways

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

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

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 147

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

Thermodynamically Feasible Kinetic Models of Reaction Networks

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

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

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

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

Smallbone, K., Simeonidis, E., Broomhead, D. S., & Kell, D. B. (2007) · FEBS Journal · doi:10.1111/j.1742-4658.2007.06076.x · Cited by 103

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

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

Model storage, exchange and integration

Novère, N. G. L. (2006) · BMC Neuroscience · doi:10.1186/1471-2202-7-s1-s11 · Cited by 101

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 99

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 90

Plant systems biology: insights, advances and challenges

Sheth, B. P., & Thaker, V. S. (2014) · Planta · doi:10.1007/s00425-014-2059-5 · Cited by 89

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 87

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

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 86

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

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

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

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 78

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

Computational systems biology of the cell cycle

Csikász‐Nagy, A. (2009) · Briefings in Bioinformatics · doi:10.1093/bib/bbp005 · Cited by 76

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 75

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

Simulating Plant Metabolic Pathways with Enzyme-Kinetic Models

Schallau, K., & Junker, B. H. (2010) · PLANT PHYSIOLOGY · doi:10.1104/pp.109.149237 · Cited by 71

Reproducibility in Computational Neuroscience Models and Simulations

McDougal, R. A., Bulanova, A., & Lytton, W. W. (2016) · IEEE Transactions on Biomedical Engineering · doi:10.1109/tbme.2016.2539602 · Cited by 73

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

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 67

Resources, standards and tools for systems biology

Wierling, C., Herwig, R., & Lehrach, H. (2007) · Briefings in Functional Genomics and Proteomics · doi:10.1093/bfgp/elm027 · Cited by 69

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

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

Dada, J. O., Spasić, ‪., Paton, N. W., & Mendes, P. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq069 · Cited by 64

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

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

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

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 58

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

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 60

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 57

“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

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

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

Medley, K., Choi, K., König, M., Smith, L. P., Gu, S., Hellerstein, J. L., Sealfon, S. C., & Sauro, H. M. (2018) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1006220 · Cited by 57

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 58

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 56

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

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

Henkel, R., Wolkenhauer, O., & Waltemath, D. (2015) · Database · doi:10.1093/database/bau130 · Cited by 50

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

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 55

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

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

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 50

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 47

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 47

What mRNA Abundances Can Tell us about Metabolism

Hoppe, A. (2012) · Metabolites · doi:10.3390/metabo2030614 · Cited by 49

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 48

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

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 45

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 47

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 43

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 44

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 44

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

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

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 41

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 38

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 40

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 41

Mathematical modeling of cancer metabolism

Medina, M. Á. (2018) · Critical Reviews in Oncology/Hematology · doi:10.1016/j.critrevonc.2018.02.004 · Cited by 36

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

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

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

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 37

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

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

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

Functional ingredient production: application of global metabolic models

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

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 36

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

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

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

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

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

Kinetic and Thermodynamic Aspects of Enzyme Control and Regulation

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

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