Bergmann, Frank T.

MEMOTE for standardized genome-scale metabolic model testing

Lieven, C., Beber, M. E., Olivier, B. G., Bergmann, F. T., Ataman, M., Babaei, P., Bartell, J. A., Blank, L. M., Chauhan, S., Correia, K., et al. (2020) · Nature Biotechnology

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 509

The Systems Biology Markup Language (SBML): language specification for level 3 version 2 core release 2

Hucka, M., Bergmann, F. T., Chaouiya, C., Dräger, A., Hoops, S., Keating, S. M., König, M., Novère, N. L., Myers, C. J., Olivier, B. G., et al. (2019) · Journal of Integrative Bioinformatics

Gene Regulatory Network AnalysisScientific Computing and Data Management

Cited by 258

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

Cited by 173

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

The Impact of Neural Invasion Severity in Gastrointestinal Malignancies: A Clinicopathological Study

Liebl, F., Demir, I. E., Mayer, K., Schuster, T., D'Haese, J. G., Becker, K., Langer, R., Bergmann, F., Wang, K., Rosenberg, R., et al. (2014) · Annals of Surgery

Gastric Cancer Management and OutcomesPancreatic and Hepatic Oncology Research

Cited by 131

PEtab—Interoperable specification of parameter estimation problems in systems biology

Schmiester, L., Schälte, Y., Bergmann, F. T., Camba, T., Dudkin, E., Egert, J., Fröhlich, F., Fuhrmann, L., Hauber, A. L., Kemmer, S., et al. (2021) · PLOS Computational Biology

Gene Regulatory Network AnalysisScientific Computing and Data Management

Cited by 96

SBML Level 3 Package: Flux Balance Constraints version 2

Olivier, B. G., & Bergmann, F. T. (2018) · Journal of Integrative Bioinformatics

Microbial Metabolic Engineering and BioproductionGene Regulatory Network Analysis

Cited by 94

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3)

Bergmann, F. T., Cooper, J., König, M., Moraru, I., Nickerson, D., Le Novère, N., Olivier, B. G., Sahle, S., Smith, L., & Waltemath, D. (2018) · Journal of Integrative Bioinformatics

Scientific Computing and Data ManagementGene Regulatory Network Analysis

Cited by 37

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

Cited by 17

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions

Hucka, M., Bergmann, F. T., Dräger, A., Hoops, S., Keating, S. M., Le Novère, N., Myers, C. J., Olivier, B. G., Sahle, S., Schaff, J. C., et al. (2015) · Journal of Integrative Bioinformatics

Gene Regulatory Network AnalysisScientific Computing and Data Management

Cited by 16