Ajmera I, Swat M, Laibe C, Le Novère N, Chelliah V. (2013). The impact of mathematical modeling on the understanding of diabetes and related complications. CPT: pharmacometrics & systems pharmacology. 2 [PubMed]

Alm R, Waltemath D, Wolfien M, Wolkenhauer O, Henkel R. (2015). Annotation-based feature extraction from sets of SBML models. Journal of biomedical semantics. 6 [PubMed]

Bergmann FT et al. (2014). COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. BMC bioinformatics. 15 [PubMed]

Bergmann FT et al. (2018). Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3). Journal of integrative bioinformatics. 15 [PubMed]

Büchel F et al. (2013). Path2Models: large-scale generation of computational models from biochemical pathway maps. BMC systems biology. 7 [PubMed]

Chelliah V et al. (2015). BioModels: ten-year anniversary. Nucleic acids research. 43 [PubMed]

Coskun SA et al. (2013). An online model composition tool for system biology models. BMC systems biology. 7 [PubMed]

Gleeson P et al. (2019). Open Source Brain: A Collaborative Resource for Visualizing, Analyzing, Simulating, and Developing Standardized Models of Neurons and Circuits. Neuron. 103 [PubMed]

Glont M et al. (2018). BioModels: expanding horizons to include more modelling approaches and formats. Nucleic acids research. 46 [PubMed]

Hoops S et al. (2006). COPASI--a COmplex PAthway SImulator. Bioinformatics (Oxford, England). 22 [PubMed]

Hucka M et al. (2003). The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics (Oxford, England). 19 [PubMed]

King ZA et al. (2016). BiGG Models: A platform for integrating, standardizing and sharing genome-scale models. Nucleic acids research. 44 [PubMed]

Kitano H et al. (2008). CellDesigner 3.5: a versatile modeling tool for biochemical networks Proc. IEEE. 96

König M, Dräger A, Holzhütter HG. (2012). CySBML: a Cytoscape plugin for SBML. Bioinformatics (Oxford, England). 28 [PubMed]

Lambusch F et al. (2018). Identifying frequent patterns in biochemical reaction networks: a workflow. Database : the journal of biological databases and curation. 2018 [PubMed]

Le Novère N. (2015). Quantitative and logic modelling of molecular and gene networks. Nature reviews. Genetics. 16 [PubMed]

Le Novère N et al. (2006). BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic acids research. 34 [PubMed]

Le Novère N et al. (2005). Minimum information requested in the annotation of biochemical models (MIRIAM). Nature biotechnology. 23 [PubMed]

Li D, Gao J. (2019). Towards perturbation prediction of biological networks using deep learning. Scientific reports. 9 [PubMed]

Lloret-Villas A et al. (2017). The Impact of Mathematical Modeling in Understanding the Mechanisms Underlying Neurodegeneration: Evolving Dimensions and Future Directions. CPT: pharmacometrics & systems pharmacology. 6 [PubMed]

Lloyd CM, Halstead MD, Nielsen PF. (2004). CellML: its future, present and past. Progress in biophysics and molecular biology. 85 [PubMed]

Mardinoglu A et al. (2014). Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease. Nature communications. 5 [PubMed]

McDougal RA et al. (2017). Twenty years of ModelDB and beyond: building essential modeling tools for the future of neuroscience. Journal of computational neuroscience. 42 [PubMed]

McLaughlin JA et al. (2018). SynBioHub: A Standards-Enabled Design Repository for Synthetic Biology. ACS synthetic biology. 7 [PubMed]

Medley JK et al. (2018). Tellurium notebooks-An environment for reproducible dynamical modeling in systems biology. PLoS computational biology. 14 [PubMed]

Neal ML et al. (2019). SemGen: a tool for semantics-based annotation and composition of biosimulation models. Bioinformatics (Oxford, England). 35 [PubMed]

Perez-Riverol Y et al. (2019). Quantifying the impact of public omics data. Nature communications. 10 [PubMed]

Peters M, Eicher JJ, van Niekerk DD, Waltemath D, Snoep JL. (2017). The JWS online simulation database. Bioinformatics (Oxford, England). 33 [PubMed]

Resasco DC et al. (2012). Virtual Cell: computational tools for modeling in cell biology. Wiley interdisciplinary reviews. Systems biology and medicine. 4 [PubMed]

Schulz M, Krause F, Le Novère N, Klipp E, Liebermeister W. (2011). Retrieval, alignment, and clustering of computational models based on semantic annotations. Molecular systems biology. 7 [PubMed]

Somogyi ET et al. (2015). libRoadRunner: a high performance SBML simulation and analysis library. Bioinformatics (Oxford, England). 31 [PubMed]

Stanford NJ et al. (2015). The evolution of standards and data management practices in systems biology. Molecular systems biology. 11 [PubMed]

Swat MJ et al. (2015). Pharmacometrics Markup Language (PharmML): Opening New Perspectives for Model Exchange in Drug Development. CPT: pharmacometrics & systems pharmacology. 4 [PubMed]

Szigeti B et al. (2018). A blueprint for human whole-cell modeling. Current opinion in systems biology. 7 [PubMed]

Uhlen M et al. (2017). A pathology atlas of the human cancer transcriptome. Science (New York, N.Y.). 357 [PubMed]

Waltemath D et al. (2011). Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language. BMC systems biology. 5 [PubMed]

Watanabe L et al. (2019). iBioSim 3: A Tool for Model-Based Genetic Circuit Design. ACS synthetic biology. 8 [PubMed]

Wilkinson MD et al. (2016). The FAIR Guiding Principles for scientific data management and stewardship. Scientific data. 3 [PubMed]

Yu T et al. (2011). The Physiome Model Repository 2. Bioinformatics (Oxford, England). 27 [PubMed]