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Modelling of Biological Processes

Dr. Frank T. Bergmann

Dr. Frank T. Bergmann
Dr. Frank T. Bergmann
INF 267
69120 Heidelberg
Fon +49 6221 54-51277
frank.bergmann AET bioquant.uni-heidelberg.de

Current Research:

  • Spatial Simulations of biochemichemical networks with COPASI
  • Development of Model Exchange Standards & Infrastructure

Research Projects:

Teaching:

Selected Publications:

Bergmann, F. T., J. Cooper, M. König, I. Moraru, D. P. Nickerson, N. Le Novère, B. G. Olivier, S. Sahle, L. P. Smith, and D. Waltemath, Simulation experiment description markup language (SED-ML) level 1 version 3 (L1V3), Journal of integrative bioinformatics, 15 (1), 2018

Bergmann, F. T., S. Hoops, B. Klahn, U. Kummer, P. Mendes, J. Pahle, S. Sahle, COPASI and its applications in biotechnology, Journal of biotechnology, 2017,

Bergmann, F. T., D. P. Nickerson, D. Waltemath, and M. Scharm, SED-ML web tools: generate, modify and export standard-compliant simulation studies, Bioinformatics, 33(8), 2017

Großeholz, R., C. Koh, N. Veith, T. Fiedler, M. Strauss, B. G. Olivier, B. C. Collins, O. T. Schubert, F. T. Bergmann, B. Kreikemeyer, R. Aebersold, and U. Kummer, Integrating highly quantitative proteomics and genome-scale metabolic modeling to study pH adaptation in the human pathogen Enterococcus faecalis, NPJ systems biology and applications, 2, 2016

Waltemath, D., J. R. Karr, F. T. Bergmann, V. Chelliah, M. Hucka, M. Krantz, W. Liebermeister, P. Mendes, C. J. Myers, P. Pir, B. Alaybeyoglu, N. K. Aranganathan, K. Baghalian, A. T. Bittig, P. E. P. Burke, M. Cantarelli, Y. H. Chew, R. S. Costa, J. Cursons, T. Czauderna, A. P. Goldberg, H. F. Gómez, J. Hahn, T. Hameri, D. F. H. Gardiol, D. Kazakiewicz, I. Kiselev, V. Knight-Schrijver, C. Knüpfer, M. König, D. Lee, A. Lloret-Villas, N. Mandrik, J K. Medley, B. Moreau, H. Naderi-Meshkin, S. K. Palaniappan, D. Priego-Espinosa, M. Scharm, M. Sharma, K. Smallbone, N. J. Stanford, J. Song, T. Theile, M. Tokic, N. Tomar, V. Toure, J. Uhlendorf, T. M. Varusai, L. H. Watanabe, F. Wendland, M. Wolfien, J. T. Yurkovich, Y. Zhu, A. Zardilis, A. Zhukova, and F. Schreiber, Toward community standards and software for whole-cell modeling, IEEE Transactions on Biomedical Engineering, 63 (10), 2016

Lubitz, T., J. Hahn, F. T. Bergmann, E. Noor, E. Klipp, and W. Liebermeister, SBtab: a flexible table format for data exchange in systems biology, Bioinformatics, 32(16), 2016

Bergmann, F. T., S. Sahle, and C. Zimmer, Piecewise parameter estimation for stochastic models in COPASI, Bioinformatics, 32(10), 2016

Olivier, B. G., and F. T. Bergmann, The systems biology markup language (SBML) level 3 package: Flux balance constraints, Journal of integrative bioinformatics, 12(2), 2015

Gauges, R, U. Rost, S. Sahle, K. Wengler, and F. T. Bergmann, The systems biology markup language (SBML) level 3 package: layout, version 1, Journal of integrative bioinformatics, 12(2), 2015

Hucka, M., D. P. Nickerson, G. D. Bader, F. T. Bergmann, J. Cooper, E. Demir, A. Garny, M. Golebiewski, C. J., and F. Schreiber, Promoting coordinated development of community-based information standards for modeling in biology: the COMBINE initiative, Frontiers in bioengineering and biotechnology, 3, 19, 2015

Bergmann, F. T., J. Jonathan, N. Le Novere, D. P. Nickerson, and D. Waltemath, Simulation experiment description markup language (SED-ML) Level 1 Version 2, Journal of integrative bioinformatics, 12(2), 119-212, 2015

Hucka, M, F. T. Bergmann, S. Hoops, S. M. Keating, S. Sahle, J. Schaff, L. P. Smith, and D. J. Wilkinson, The Systems Biology Markup Language (SBML): language specification for level 3 version 1 core, Journal of integrative bioinformatics, 12 (2), 3820549, 2015

Bergmann, F. T., R. Adams, S. Moodie, J. Cooper, M. Glont, M. Golebiewski, M. Hucka, C. Laibe, A. K. Miller, and D. P. Nickerson, COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project, BMC bioinformatics, 15(1), 369, 2014

Van Iersel, M. P., A. C. Villéger, T. Czauderna, S. E. Boyd, F. T. Bergmann, A. Luna, E. Demir, A. Sorokin, U. Dogrusoz and Y. Matsuoka, Software support for SBGN maps: SBGN-ML and LibSBGN, Bioinformatics, 28 (15), 2016-2021, 2012

Waltemath, D., R. Adams, F. T. Bergmann, M. Hucka, F. Kolpakov, A. K. Miller, I. Moraru, D. Nickerson, S. Sahle, and J. L. Snoep, Reproducible computational biology experiments with SED-ML-the simulation experiment description markup language, BMC systems biology, 5 (1), 198, 2011/12

Hucka, M, F. T. Bergmann, S. M. Keating, and L. P. Smith, A profile of today's SBML-compatible software, 2011 IEEE Seventh International Conference on e-Science Workshops, 143-150, 2011

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., Garny, A., Hoops, S., Hucka, M., Hunter, P., Klipp, E., Laibe, C.,Miller, A.K., Moraru, I., Nickerson, D., Nielsen, P., Nikolski, M., Sahle, S., Sauro, H.M.,Schmidt, H., Snoep, J.L., Tolle, D., Wolkenhauer, O. & Le Novère, N (2011). Minimum information about a simulation experiment (MIASE). PLoS computational biology, 7(4), e1001122.

Hucka, M., Bergmann, F. T., Keating, S. M., Schaff, J. C., & Smith, L. P. (2010). The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version.

Chandran, Deepak, Frank T. Bergmann, and Herbert M. Sauro. "TinkerCell: modular CAD tool for synthetic biology." J Biol Eng 3.1 (2009): 19.

Smith, L. P., Bergmann, F. T., Chandran, D., & Sauro, H. M. (2009). Antimony: a modular model definition language. Bioinformatics, 25(18), 2452-2454.

Le Novère, N, Hucka, M, Mi, H, Moodie, S, Schreiber, F, Sorokin, A, Demir, E, Wegner, K, Aladjem, MI, Wimalaratne, SM, Bergmann, F.T., Gauges, R, Ghazal, P, Kawaji, H, Li, L, Matsuoka, Y, Villéger, A, Boyd, SE, Calzone, L, Courtot M, Dogrusoz, U, Freeman, TC, Funahashi, A, Ghosh, S, Jouraku, A, Kim, S, Kolpakov, F, Luna, A, Sahle, S, Schmidt, E, Watterson, S, Wu, G, Goryanin, I, Kell, DB, Sander, C, Sauro, H, Snoep, JL, Kohn, K & Kitano, H. (2009). The systems biology graphical notation. Nature biotechnology, 27(8), 735-741.

Bergmann, F. T., & Sauro, H. M. (2008). Comparing simulation results of SBML capable simulators. Bioinformatics, 24(17), 1963-1965.

Bergmann,F.T.,  Vallabhajosyula, R.R. & H.M. SauroComputational Tools for Modeling Protein Networks. Current Proteomics Pp. 181-197 Volume 3(3),(2006)

Bergmann, F.T., Sauro, H.M. Computational systems biology: modularity and composition: SBW - a modular framework for systems biology. Proceedings of the 37th conference on Winter simulation WSC ‘06 Publisher: Winter Simulation Conference Pages: 1637 – 1645

Deckard A, Bergmann FT, Sauro HMSupporting the SBML layout extension. Bioinformatics. 2006 Oct 11;

Chickarmane V, Paladugu SR, Bergmann FT, Sauro HM. Bifurcation discovery tool. Bioinformatics. 2005 Sep 15;21(18):3688-90.

Contact

Dr. Frank T. Bergmann
INF 267
69120 Heidelberg
Fon +49 6221 54-51277
frank.bergmann AET bioquant.uni-heidelberg.de


/var/www/cos/ / https://www.cos.uni-heidelberg.de/ Dr. Frank T. Bergmann _e