Sauro, Herbert M.

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models

Hucka, M., Finney, A., Sauro, H. M., Bolouri, H., Doyle, J. C., Kitano, H., Arkin, A. P., Bornstein, B. J., Bray, D., Cornish-Bowden, A., et al. (2003) · Bioinformatics

Gene Regulatory Network AnalysisBioinformatics and Genomic Networks

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The systems biology graphical notation.

Novère, N. L., Hucka, M., Mi, H., Moodie, S., Schreiber, F., Sorokin, A., Demir, E., Wegner, K., Aladjem, M. I., Wimalaratne, S. M., et al. (2009) · Nature Biotechnology

Gene Regulatory Network AnalysisBioinformatics and Genomic Networks

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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

Gene Regulatory Network AnalysisScientific Computing and Data Management

Cited by 622

COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project

Bergmann, F. T., Adams, R., Moodie, S., Cooper, J., Glont, M., Golebiewski, M., Hucka, M., Laibe, C., Miller, A. K., Nickerson, D. P., et al. (2014) · BMC Bioinformatics

Scientific Computing and Data ManagementResearch Data Management Practices

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Minimum Information About a Simulation Experiment (MIASE)

Waltemath, D., Adams, R., Beard, D. A., Bergmann, F. T., Bhalla, U. S., Britten, R., Chelliah, V., Cooling, M. T., Cooper, J., Crampin, E. J., et al. (2011) · PLoS Computational Biology

Scientific Computing and Data ManagementGene Regulatory Network Analysis

Cited by 168

A reappraisal of how to build modular, reusable models of biological systems.

Neal, M. L., Cooling, M. T., Smith, L. P., Thompson, C. T., Sauro, H. M., Carlson, B. E., Cook, D. L., & Gennari, J. H. (2014) · PLoS Computational Biology

Gene Regulatory Network AnalysisScientific Computing and Data Management

Cited by 49

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

Scientific Computing and Data ManagementGene Regulatory Network Analysis

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Improving reproducibility in computational biology research

Papin, J. A., Mac Gabhann, F., Sauro, H. M., Nickerson, D., & Rampadarath, A. (2020) · PLOS Computational Biology

Scientific Computing and Data ManagementResearch Data Management Practices

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Adapting modeling and simulation credibility standards to computational systems biology

Tatka, L. T., Smith, L. P., Hellerstein, J. L., & Sauro, H. M. (2023) · Journal of Translational Medicine

Philosophy of Biology and Scientific ExplanationScientific Computing and Data Management

Cited by 27

Adapting Modeling and Simulation Credibility Standards to Computational Systems Biology

Tatka, L. T., Smith, L. P., Hellerstein, J. L., & Sauro, H. M. (2023) · arXiv

Philosophy of Biology and Scientific ExplanationScientific Computing and Data Management

Cited by 24

Recent advances in biomedical simulations: a manifesto for model engineering

Hellerstein, J. L., Gu, S., Choi, K., & Sauro, H. M. (2019) · F1000Research

Scientific Computing and Data ManagementSimulation Techniques and Applications

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SBML and CellML translation in Antimony and JSim

Smith, L. P., Butterworth, E., Bassingthwaighte, J. B., & Sauro, H. M. (2014) · Bioinformatics

Gene Regulatory Network AnalysisModeling and Simulation Systems

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The simulation experiment description markup language (SED-ML): language specification for level 1 version 4

Smith, L. P., Bergmann, F. T., Garny, A., Helikar, T., Karr, J., Nickerson, D., Sauro, H., Waltemath, D., & König, M. (2021) · Journal of Integrative Bioinformatics

Scientific Computing and Data ManagementResearch Data Management Practices

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Standards, dissemination, and best practices in systems biology

Shin, J., Porubsky, V., Carothers, J., & Sauro, H. M. (2023) · Current Opinion in Biotechnology

Scientific Computing and Data ManagementGene Regulatory Network Analysis

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SBMate: A Framework for Evaluating Quality of Annotations in Systems Biology Models

Shin, W., Hellerstein, J. L., Munarko, Y., Neal, M. L., Nickerson, D. P., Rampadarath, A. K., Sauro, H. M., & Gennari, J. H. (2021) · bioRxiv (Cold Spring Harbor Laboratory)

Biomedical Text Mining and OntologiesGene Regulatory Network Analysis

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