Web-based kinetic modelling using JWS Online

The control of flux.

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Biochemistry by numbers: simulation of biochemical pathways with Gepasi 3

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Roles of triosephosphate isomerase and aerobic metabolism in Trypanosoma brucei

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Metabolic control analysis in a nutshell

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The Human Physiome: how standards, software and innovative service infrastructures are providing the building blocks to make it achievable

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Parameter estimate of signal transduction pathways

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Ranked retrieval of Computational Biology models

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Reverse engineering of metabolic networks, a critical assessment

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Control, responses and modularity of cellular regulatory networks: a control analysis perspective

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SYCAMORE—a systems biology computational analysis and modeling research environment

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Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)

Waltemath, D., Bergmann, F., Chaouiya, C., Czauderna, T., Gleeson, P., Goble, C., Golebiewski, M., Hucka, M., Juty, N., Krebs, O., et al. (2014) · Standards in Genomic Sciences · doi:10.4056/sigs.5279417 · Cited by 30

Understanding drugs and diseases by systems biology?

Schneider, H.-C., & Klabunde, T. (2012) · Bioorganic & Medicinal Chemistry Letters · doi:10.1016/j.bmcl.2012.12.031 · Cited by 31

Identifying and characterising regulatory metabolites with generalised supply–demand analysis

Rohwer, J. M., & Hofmeyr, J. S. (2007) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2007.10.032 · Cited by 28

From Top-Down to Bottom-Up: Computational Modeling Approaches for Cellular Redoxin Networks

Pillay, C. S., Hofmeyr, J. S., Mashamaite, L. N., & Rohwer, J. M. (2012) · Antioxidants and Redox Signaling · doi:10.1089/ars.2012.4771 · Cited by 28

Drug target identification through systems biology

Haanstra, J. R., & Bakker, B. M. (2015) · Drug Discovery Today Technologies · doi:10.1016/j.ddtec.2015.06.002 · Cited by 28

D‐Lactate production as a function of glucose metabolism in Saccharomyces cerevisiae

Stewart, B. J., Navid, A., Kulp, K. S., Knaack, J. S., & Bench, G. (2013) · Yeast · doi:10.1002/yea.2942 · Cited by 26

Creating interactive, web-based and data-enriched maps with the Systems Biology Graphical Notation

Junker, A., Rohn, H., Czauderna, T., Klukas, C., Hartmann, A., & Schreiber, F. (2012) · Nature Protocols · doi:10.1038/nprot.2012.002 · Cited by 26

Supply–Demand Analysis

Hofmeyr, J. S., & Rohwer, J. M. (2011) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/b978-0-12-385118-5.00025-6 · Cited by 26

A data integration approach for cell cycle analysis oriented to model simulation in systems biology

Alfieri, R. R., Ivan Merelli, A., Mosca, E., & Milanesi, L. (2007) · BMC Systems Biology · doi:10.1186/1752-0509-1-35 · Cited by 26

BASICO: A simplified Python interface to COPASI

Bergmann, F. (2023) · The Journal of Open Source Software · doi:10.21105/joss.05553 · Cited by 28

A Systems Biology Approach to Deciphering the Etiology of Steatosis Employing Patient-Derived Dermal Fibroblasts and iPS Cells

Józefczuk, J., Kashofer, K., Ummanni, R., Henjes, F., Rehman, S., Geenen, S., Wruck, W., Regenbrecht, C. R. A., Daskalaki, A., Wierling, C., et al. (2012) · Frontiers in Physiology · doi:10.3389/fphys.2012.00339 · Cited by 26

Elucidating the Sources of β-Catenin Dynamics in Human Neural Progenitor Cells

Mazemondet, O., John, M., Leye, S., Rolfs, A., & Uhrmacher, A. M. (2012) · PLoS ONE · doi:10.1371/journal.pone.0042792 · Cited by 25

A comparative analysis of kinetic models of erythrocyte glycolysis

du Preez, F. B., Conradie, R., Penkler, G. P., Holm, K., van Dooren, F. L. J., & Snoep, J. L. (2007) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2007.10.006 · Cited by 25

Ki MoSys: a web-based repository of experimental data for KInetic MOdels of biological SYStems

Costa, R. S., Veríssimo, A., & Vinga, S. (2014) · BMC Systems Biology · doi:10.1186/s12918-014-0085-3 · Cited by 24

Synthetic Biology in Plants, a Boon for Coming Decades

Gupta, D., Sharma, G., Saraswat, P., & Ranjan, R. (2021) · Molecular Biotechnology · doi:10.1007/s12033-021-00386-9 · Cited by 26

A General Hybrid Modeling Framework for Systems Biology Applications: Combining Mechanistic Knowledge with Deep Neural Networks under the SBML Standard

Pinto, J., Ramos, J. R. C., Costa, R. S., & Oliveira, R. (2023) · AI · doi:10.3390/ai4010014 · Cited by 25

Modeling and Simulation Tools: From Systems Biology to Systems Medicine

Olivier, B. G., Swat, M. J., & Moné, M. J. (2015) · Methods in molecular biology · doi:10.1007/978-1-4939-3283-2_19 · Cited by 27

Article Commentary: Predictive Modeling of Drug Treatment in the Area of Personalized Medicine

Ogilvie, L. A., Wierling, C., Kessler, T., Lehrach, H., & Lange, B. M. H. (2015) · Cancer Informatics · doi:10.4137/cin.s19330 · Cited by 24

Challenges for an enzymatic reaction kinetics database

Wittig, U., Rey, M., Kania, R., Bittkowski, M., Shi, L., Golebiewski, M., Weidemann, A., Müller, W., & Rojas, I. (2014) · The FEBS Journal · doi:10.1111/febs.12562 · Cited by 22

Simplification of biochemical models: a general approach based on the analysis of the impact of individual species and reactions on the systems dynamics

Surovtsova, I., Simus, N., Hübner, K., Sahle, S., & Kummer, U. (2012) · BMC Systems Biology · doi:10.1186/1752-0509-6-14 · Cited by 23

A mathematical modelling approach to assessing the reliability of biomarkers of glutathione metabolism

Geenen, S., du Preez, F. B., Reed, M. C., Nijhout, H. F., Kenna, J. G., Wilson, I. D., Westerhoff, H. V., & Snoep, J. L. (2011) · European Journal of Pharmaceutical Sciences · doi:10.1016/j.ejps.2011.08.017 · Cited by 23

Web-based applications for building, managing and analysing kinetic models of biological systems

Lee, D., Saha, R., Yusufi, F.-N.-K., Park, W., & Karimi, I. A. (2008) · Briefings in Bioinformatics · doi:10.1093/bib/bbn039 · Cited by 23

Standards, Databases, and Modeling Tools in Systems Biology

Kohl, M. (2010) · Methods in molecular biology · doi:10.1007/978-1-60761-987-1_26 · Cited by 23

“Reproducible” Research in Mathematical Sciences Requires Changes in our Peer Review Culture and Modernization of our Current Publication Approach

Schnell, S. D. (2018) · Bulletin of Mathematical Biology · doi:10.1007/s11538-018-0500-9 · Cited by 25

Relating simulation studies by provenance—Developing a family of Wnt signaling models

Budde, K., Smith, J., Wilsdorf, P., Haack, F., & Uhrmacher, A. M. (2021) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1009227 · Cited by 23

The Development of Computational Biology in South Africa: Successes Achieved and Lessons Learnt

Mulder, N., Christoffels, A. G., de Oliveira, T., Gamieldien, J., Hazelhurst, S., Joubert, F., Kumuthini, J., Pillay, C. S., Snoep, J. L., Bishop, Ö. T., et al. (2016) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004395 · Cited by 21

Standard-GEM supports reproducible development of genome-scale metabolic modelsPreprint

Anton, M., Almaas, E., Bäuerle, F., Beber, M. E., Benfeitas, R., Benito-Vaquerizo, S., Blank, L. M., Clasen, F., de Buck, C., Dräger, A., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.03.21.512712 · Cited by 24

MAMMOTh: A new database for curated mathematical models of biomolecular systems

Владимирович, К. Ф., Akberdin, I. R., Lashin, S. A., Ree, N., Timonov, V., Ratushny, A. V., Khlebodarova, T. M., & Likhoshvai, V. A. (2017) · Journal of Bioinformatics and Computational Biology · doi:10.1142/s0219720017400108 · Cited by 19

Kinetic Modeling of Saccharomyces cerevisiae Central Carbon Metabolism: Achievements, Limitations, and Opportunities

Lao‐Martil, D., Verhagen, K. J. A., Schmitz, J. P. J., Teusink, B., Wahl, A., & van Riel, N. A. W. (2022) · Metabolites · doi:10.3390/metabo12010074 · Cited by 20

Data extraction for the reaction kinetics database SABIO-RK

Wittig, U., Kania, R., Bittkowski, M., Wetsch, E., Shi, L., Jong, L. M., Golebiewski, M., Rey, M., Weidemann, A., Rojas, I., et al. (2014) · Perspectives in Science · doi:10.1016/j.pisc.2014.02.004 · Cited by 19

Heterogeneity of glycolytic oscillatory behaviour in individual yeast cells

Gustavsson, A., van Niekerk, D. D., Adiels, C. B., Goksör, M., & Snoep, J. L. (2013) · FEBS Letters · doi:10.1016/j.febslet.2013.11.028 · Cited by 19

Streamlining the construction of large-scale dynamic models using generic kinetic equations

Adiamah, D. A., Handl, J., & Schwartz, J. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq136 · Cited by 20

Structured cell simulator coupled with a fluidized bed bioreactor model to predict the adaptive mercury uptake by E. coli cells

Maria, G. C., & Luta, I. (2013) · Computers & Chemical Engineering · doi:10.1016/j.compchemeng.2013.06.004 · Cited by 18

TIde: a software for the systematic scanning of drug targets in kinetic network models

Schulz, M., Bakker, B. M., & Klipp, E. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-344 · Cited by 18

Approaches to Biosimulation of Cellular Processes

Bruggeman, F. J., & Westerhoff, H. V. (2006) · Journal of Biological Physics · doi:10.1007/s10867-006-9016-x · Cited by 17

Annotation-based feature extraction from sets of SBML models

Alm, R., Waltemath, D., Wolfien, M., Wolkenhauer, O., & Henkel, R. (2015) · Journal of Biomedical Semantics · doi:10.1186/s13326-015-0014-4 · Cited by 22

Trade‐off of dynamic fragility but not of robustness in metabolic pathways in silico

Quinton-Tulloch, M. J., Bruggeman, F. J., Snoep, J. L., & Westerhoff, H. V. (2012) · FEBS Journal · doi:10.1111/febs.12057 · Cited by 17

Flux Control in Glycolysis Varies Across the Tree of Life

Orlenko, A., Hermansen, R. A., & Liberles, D. A. (2016) · Journal of Molecular Evolution · doi:10.1007/s00239-016-9731-2 · Cited by 17

COMODI: an ontology to characterise differences in versions of computational models in biology

Scharm, M., Waltemath, D., Mendes, P., & Wolkenhauer, O. (2016) · Journal of Biomedical Semantics · doi:10.1186/s13326-016-0080-2 · Cited by 14

A detailed kinetic model of glycolysis in Plasmodium falciparum-infected red blood cells for antimalarial drug target identification

van Niekerk, D. D., du Toit, F., Green, K., Palm, D., & Snoep, J. L. (2023) · Journal of Biological Chemistry · doi:10.1016/j.jbc.2023.105111 · Cited by 16

Graphical Modeling Tools for Systems Biology

Gostner, R., Baldacci, B., Morine, M. J., & Priami, C. (2014) · ACM Computing Surveys · doi:10.1145/2633461 · Cited by 17

Optimality Principles in the Regulation of Metabolic Networks

Berkhout, J., Bruggeman, F. J., & Teusink, B. (2012) · Metabolites · doi:10.3390/metabo2030529 · Cited by 17

Tracing regulatory routes in metabolism using generalised supply-demand analysis

Christensen, C. D., Hofmeyr, J. S., & Rohwer, J. M. (2015) · BMC Systems Biology · doi:10.1186/s12918-015-0236-1 · Cited by 16

MOSBIE: a tool for comparison and analysis of rule-based biochemical models

Wenskovitch, J. E., Harris, L. A., Tapia, J.-J., Faeder, J. R., & Marai, G. E. (2014) · BMC Bioinformatics · doi:10.1186/1471-2105-15-316 · Cited by 15

Integrating Bioinformatics and Computational Biology: Perspectives and Possibilities for In Silico Network Reconstruction in Molecular Systems Biology

Alves, R., Vilaprinyó, E., & Albert Sorribas, B. (2008) · Current Bioinformatics · doi:10.2174/157489308784340694 · Cited by 16

E-photosynthesis: Web-based platform for modeling of complex photosynthetic processes

Šafránek, D., Červený, J., Klement, M., Pospíšilová, J., Brim, L., Lazár, D., & Nedbal, L. (2010) · Biosystems · doi:10.1016/j.biosystems.2010.10.013 · Cited by 15

Zooming in on Yeast Osmoadaptation

Kühn, C., & Klipp, E. (2011) · Advances in experimental medicine and biology · doi:10.1007/978-1-4419-7210-1_17 · Cited by 15

SABIO-RK: A data warehouse for biochemical reactions and their kinetics

Krebs, O., Golebiewski, M., Kania, R., Mir, S., Šarić, J., Weidemann, A., Wittig, U., & Rojas, I. (2007) · Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics · doi:10.1515/jib-2007-49 · Cited by 14

Bagged K-Means Clustering of Metabolome Data

Hageman, J. A., van den Berg, R. A., Westerhuis, J. A., Hoefsloot, H. C. J., & Smilde, A. K. (2006) · Critical Reviews in Analytical Chemistry · doi:10.1080/10408340600969916 · Cited by 14

Escalating model sizes and complexities call for standardized forms of representation

Hucka, M., & Finney, A. (2005) · Molecular Systems Biology · doi:10.1038/msb4100015 · Cited by 14

Enzyme characterisation and kinetic modelling of the pentose phosphate pathway in yeastPreprint

Messiha, H. L., Kent, E., Malys, N., Carroll, K. M., Swainston, N., Mendes, P., & Smallbone, K. (2014) · doi:10.7287/peerj.preprints.146v4 · Cited by 15

Workflow for Data Analysis in Experimental and Computational Systems Biology: Using Python as ‘Glue’

Badenhorst, M., Barry, C. J., Swanepoel, C. J., van Staden, C. T., Wissing, J., & Rohwer, J. M. (2019) · Processes · doi:10.3390/pr7070460 · Cited by 13

Sustainable Model Building

Krause, F., Schulz, M., Swainston, N., & Liebermeister, W. (2011) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/b978-0-12-385118-5.00019-0 · Cited by 13

Clinical Applications of Metabolic Models in SBML Format

Renz, A., Mostolizadeh, R., & Dräger, A. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-801238-3.11524-7 · Cited by 13

Mathematical Models of Mitochondrial Aging and Dynamics

Kowald, A., & Klipp, E. (2014) · Progress in molecular biology and translational science · doi:10.1016/b978-0-12-394625-6.00003-9 · Cited by 12

Software Tools for Systems Biology

Sauro, H. M., & Bergmann, F. (2010) · Elsevier eBooks · doi:10.1016/b978-0-12-372550-9.00012-2 · Cited by 14

Identifying frequent patterns in biochemical reaction networks: a workflow

Lambusch, F., Waltemath, D., Wolkenhauer, O., Sandkuhl, K., Rosenke, C., & Henkel, R. (2018) · Database · doi:10.1093/database/bay051 · Cited by 13

Systems biology model databases and resources

van Gend, C. H. D. R., & Snoep, J. L. (2008) · Essays in Biochemistry · doi:10.1042/bse0450223 · Cited by 13

An online model composition tool for system biology models

Coskun, S. A., Çiçek, A. E., Lai, N., Dash, R. K., Ozsoyoglu, Z. M., & Özsoyoğlu, G. (2013) · BMC Systems Biology · doi:10.1186/1752-0509-7-88 · Cited by 12

Publishing reproducible dynamic kinetic models

Porubsky, V. L., Smith, L. P., & Sauro, H. M. (2020) · Briefings in Bioinformatics · doi:10.1093/bib/bbaa152 · Cited by 13

Documenting, storing, and executing models in Ecology: A conceptual framework and real implementation in a global change monitoring program

Bonet, F. J., Pérez‐Pérez, R., Benito, B. M., de Albuquerque, F. S., & Zamora, R. (2013) · Environmental Modelling & Software · doi:10.1016/j.envsoft.2013.10.027 · Cited by 11

Plant Systems Biology: Insights and Advancements

Bhardwaj, T., & Somvanshi, P. (2015) · Springer eBooks · doi:10.1007/978-81-322-2172-2_28 · Cited by 11

Tryptophan Production Maximization in a Fed-Batch Bioreactor with Modified E. coli Cells, by Optimizing Its Operating Policy Based on an Extended Structured Cell Kinetic Model

Maria, G. C., & Renea, L. (2021) · Bioengineering · doi:10.3390/bioengineering8120210 · Cited by 11

Modeling biochemical transformation processes and information processing with Narrator

Mandel, J. J., Fuß, H., Palfreyman, N., & Dubitzky, W. (2007) · BMC Bioinformatics · doi:10.1186/1471-2105-8-103 · Cited by 13

Response to temporal parameter fluctuations in biochemical networks

Liebermeister, W. (2005) · Journal of Theoretical Biology · doi:10.1016/j.jtbi.2004.12.010 · Cited by 11

Analysis of positive descriptor systems

Virnik, E. (2008) · DepositOnce · doi:10.14279/depositonce-1879 · Cited by 11

Reproducibility of Model-Based Results in Systems Biology

Waltemath, D., Henkel, R., Winter, F., & Wolkenhauer, O. (2013) · Springer eBooks · doi:10.1007/978-94-007-6803-1_10 · Cited by 9

unIn silico Derivation of a Reduced Kinetic Model for Stationary or Oscillating Glycolysis in Escherichia coli Bacterium

Maria, G. C. (2015) · Chemical and Biochemical Engineering Quarterly · doi:10.15255/cabeq.2014.2002 · Cited by 10

Sensitivity analysis in systems biology modelling and its application to a multi-scale model of blood glucose homeostasis

Sumner, T. (2010) · UCL Discovery (University College London) · Cited by 10

PharmML in Action: an Interoperable Language for Modeling and Simulation

Bizzotto, R., Comets, E., Smith, G., Yvon, F., Kristensen, N., & Swat, M. (2017) · CPT: Pharmacometrics & Systems Pharmacology · doi:10.1002/psp4.12213 · Cited by 9

Information Retrieval in Life Sciences: A Programmatic Survey

Lange, M., Henkel, R., Müller, W., Waltemath, D., & Weise, S. F. (2013) · Springer eBooks · doi:10.1007/978-3-642-41281-3_3 · Cited by 8

SED-ML web tools: generate, modify and export standard-compliant simulation studies

Bergmann, F., Nickerson, D. P., Waltemath, D., & Scharm, M. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw812 · Cited by 9

A Comparative Analysis of Dynamic Models of the Central Carbon Metabolism of Escherichia coli

Lima, A., Baixinho, V., Machado, D., & Rocha, I. (2016) · IFAC-PapersOnLine · doi:10.1016/j.ifacol.2016.12.137 · Cited by 9

Executable biochemical space for specification and analysis of biochemical systems

Troják, M., Šafránek, D., Mertová, L., & Brim, L. (2020) · PLoS ONE · doi:10.1371/journal.pone.0238838 · Cited by 9

What it takes to understand and cure a living system: computational systems biology and a systems biology-driven pharmacokinetics–pharmacodynamics platform

Swat, M. J., Kiełbasa, S. M., Polak, S., Olivier, B. G., Bruggeman, F. J., Quinton-Tulloch, M. J., Snoep, J. L., Verhoeven, A. J., & Westerhoff, H. V. (2010) · Interface Focus · doi:10.1098/rsfs.2010.0011 · Cited by 9

From regulation of cell fate decisions towards patient-specific treatments, insights from mechanistic models of signalling pathways

Simon, M., Konrath, F., & Wolf, J. (2024) · Current Opinion in Systems Biology · doi:10.1016/j.coisb.2024.100533 · Cited by 8

Systems‐based understanding of pharmacological responses with combinations of multidisciplinary methodologies

Kariya, Y., Honma, M., & Suzuki, H. (2013) · Biopharmaceutics & Drug Disposition · doi:10.1002/bdd.1865 · Cited by 8

Data Integration and Semantic Enrichment of Systems Biology Models and Simulations

Chelliah, V., Endler, L., Juty, N., Laibe, C., Li, C., Rodríguez, N., & Novère, N. G. L. (2009) · Lecture notes in computer science · doi:10.1007/978-3-642-02879-3_2 · Cited by 8

E-Cyanobacterium.org: A Web-Based Platform for Systems Biology of Cyanobacteria

Troják, M., Šafránek, D., Hrabec, J., Šalagovič, J., Romanovská, F., & Červený, J. (2016) · Lecture notes in computer science · doi:10.1007/978-3-319-45177-0_20 · Cited by 8

Population-Based Parameter Identification for Dynamical Models of Biological Networks with an Application to Saccharomyces cerevisiae

Węglarz‐Tomczak, E., Tomczak, J. M., Eiben, A. E., & Brul, S. (2021) · Processes · doi:10.3390/pr9010098 · Cited by 8

The Model Repository of the Models of Infectious Disease Agent Study

Cooley, P. C., Roberts, D. J., Bakalov, V., Bikmal, S., Cantor, S., Costandine, T., Ganapathi, L., Golla, B. J., Grubbs, G., Hollingsworth, C. R., et al. (2008) · IEEE Transactions on Information Technology in Biomedicine · doi:10.1109/titb.2007.910354 · Cited by 8

Exploring the Dynamics of Large-Scale Biochemical Networks: A Computational Perspective

Steuer, R. (2011) · The Open Bioinformatics Journal · doi:10.2174/1875036201105010004 · Cited by 8

In Silico Cell: Challenges and Perspectives

Akberdin, I. R. (2013) · Mathematical Biology and Bioinformatics · doi:10.17537/2013.8.295 · Cited by 8

Advancement in Sustainable Agriculture: Computational and Bioinformatics Tools

Parray, J. A., Mir, M. Y., & Shameem, N. (2019) · Springer eBooks · doi:10.1007/978-981-13-8840-8_10 · Cited by 8

Validity and combination of biochemical models

Liebermeister, W. (2008) · Cited by 8

OREMPdb: a semantic dictionary of computational pathway models

Umeton, R., Nicosia, G., & Dewey, C. F. (2012) · BMC Bioinformatics · doi:10.1186/1471-2105-13-s4-s6 · Cited by 7

Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices

Stanford, N., Scharm, M., Dobson, P. D., Golebiewski, M., Hucka, M., Kothamachu, V. B., Nickerson, D. P., Owen, S., Pahle, J., Wittig, U., et al. (2019) · Methods in molecular biology · doi:10.1007/978-1-4939-9736-7_17 · Cited by 7

A CCM-based modular and hybrid kinetic model to simulate the tryptophan synthesis in a fed-batch bioreactor using modified E. coli cells

Maria, G. C. (2021) · Computers & Chemical Engineering · doi:10.1016/j.compchemeng.2021.107450 · Cited by 7

An Automatic Translation of SBML into Beta-Binders

Ciocchetta, F., Priami, C., & Quaglia, P. (2008) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2007.70219 · Cited by 6

Modeling Approaches in Systems Biology, Including Silicon Cell Models

Kolodkin, A. N., Boogerd, F. C., Bruggeman, F. J., & Westerhoff, H. V. (2011) · Wiley eBooks · doi:10.1002/9780470963012.ch2 · Cited by 7

A Comprehensive Web-based Platform For Domain-Specific Biological Models

Klement, M., Šafránek, D., Děd, T., Pejznoch, A., Nedbal, L., Steuer, R., Červený, J., & Müller, S. (2013) · Electronic Notes in Theoretical Computer Science · doi:10.1016/j.entcs.2013.11.006 · Cited by 6

Applications of Kinetic Modeling to Plant Metabolism

Rohwer, J. M. (2013) · Methods in molecular biology · doi:10.1007/978-1-62703-661-0_16 · Cited by 6

Deciphering signal transduction networks in the liver by mechanistic mathematical modelling

D’Alessandro, L. A., Klingmüller, U., & Schilling, M. (2022) · Biochemical Journal · doi:10.1042/bcj20210548 · Cited by 6

Towards Enhanced Retrieval of Biological Models through Annotation-Based Ranking

Köhn, D., Maus, C., Henkel, R., & Kolbe, M. (2009) · Lecture notes in computer science · doi:10.1007/978-3-642-02879-3_17 · Cited by 6

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 27

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)