Thomas M. Hamm

Diplom Biologe (t.o.)


Department for Computer Science
Center for Bioinformatics Tübingen (ZBIT)
Sand 14 ・ 2nd floor ・ Office C321

 +49 7071 29-70460

Research interests

  • Biology: human biology; microbiology

  • Systems biology: quantitative dynamic modeling of biological processes; constraint-based modeling of metabolic networks

  • Software development: developing software to answer questions in systems biology (e.g. JSBML)

Completed Research Projects

Conceptual Design of a German infection-related OMICS Data Exchange (GirOD) Platform
Development of essential software and resources for the scientific community for systems biology modelling via Java™

Supported by the US National Institutes of Health (NIH), grant № 2R01GM070923-13 from July 2013 to September 2016 and subsequently from October 2016 till May 2020.

Google Summer of Code 2019


  1. Sarah M. Keating, Dagmar Waltemath, Matthias König, Fengkai Zhang, Andreas Dräger, Claudine Chaouiya, Frank T. Bergmann, Andrew Finney, Colin Gillespie, Tomáš Helikar, Stefan Hoops, Rahuman Malik-Sheriff, Stuart Moodie, Ion Moraru, Chris J. Myers, Aurélien Naldi, Brett Olivier, Sven Sahle, James Schaff, Lucian P. Smith, Maciej Swat, Denis Thieffry, Leandro Watanabe, Darren Wilkinson, Michael L. Blinov, Kimberly Begley, James Faeder, Harold Gómez, Thomas M. Hamm, Yuichiro Inagaki, Wolfram Liebermeister, Allyson Lister, Daniel Lucio, Eric Mjolsness, Carole Proctor, Karthik Raman, Nicolas Rodriguez, Clifford Shaffer, Bruce Shapiro, Joerg Stelling, Neil Swainston, Naoki Tanimura, John Wagner, Martin Meier-Schellersheim, Herbert Sauro, Bernhard Ø. Palsson, Hamid Bolouri, Hiroaki Kitano, Akira Funahashi, Henning Hermjakob, John C. Doyle, Michael Hucka, and the SBML Level 3 community. SBML Level 3: an extensible format for the exchange and reuse of biological models. Molecular Systems Biology, August 26 2020.
  2. Thomaseth, Caterina, Patrick Weber, Thomas Hamm, Kenji Kashima, and Nicole Radde. 2013. “Modeling Sphingomyelin Synthase 1 Driven Reaction at the Golgi Apparatus Can Explain Data by Inclusion of a Positive Feedback Mechanism.” Journal of Theoretical Biology 337 (November): 174–80.
  3. Knoll, Michael, Thomas M. Hamm, Florian Wagner, Virginia Martinez, and Jürgen Pleiss. 2009. “The PHA Depolymerase Engineering Database: A Systematic Analysis Tool for the Diverse Family of Polyhydroxyalkanoate (PHA) Depolymerases.” BMC Bioinformatics 10 (1): 89.