Welcome to the Biological Information Processing Group

Variability, fluctuations and information transfer or processing are important characteristics of biological systems. We use different computational methods, such as data analysis, stochastic modelling and simulation, information theoretic measures, etc., to investigate biological systems, ranging from calcium signalling, to MAP kinase signalling, protein translation, and others.


New Master’s thesis: Lena Lenkeit on “Design, development, and experimental verification of a framework for fully-differentiable, gradient-based optimal control of biological systems”

Lena Lenkeit defended her Master’s thesis titled “Design, development, and experimental verification of a framework for fully-differentiable, gradient-based optimal control of biological systems” on 23. October 2023. This work was done in collaboration with Dr. Dr. Stefan Kallenberger who is also based at the BioQuant.

New Master and Bachelor theses: Emma Kray finished her Bachelor’s thesis and Pascal Lukas defended his Master’s thesis

Emma Kray finished her Bachelor’s thesis titled “A model-based investigation of immune system composition upon vaccinations against influenza” in August. Pascal Lukas defended his Master’s thesis on “Analyzing and modeling the spatio-temporal dynamics of the interferon response to Dengue virus infection” on 29. September 2023. Both projects were done in collaboration with the group of …

30th International Dynamics & Evolution of Human Viruses conference

The 30th International Dynamics & Evolution of Human Viruses conference is taking place from April 19 to 22, 2023 at the German Cancer Research Center (DKFZ) and the Marriott in Heidelberg. This meeting series was designed to promote discussion between specialists in quantitative and computational approaches in two areas in the field of virology where these …


The main aim of our research is to analyse how living systems take up, process, store and transfer information. To achieve this aim we are active in different areas.

First, we are building kinetic models of biochemical systems, for instance, models that describe how oscillations in the ubiquitous second messenger calcium arise, how they are modulated, and how these dynamics lead to specific regulation of different downstream calcium-dependent proteins. We particularly focus on how variable or reliable these systems are. Therefore, we explicitly consider intrinsic fluctuations in particle numbers by utilising stochastic simulations methods.

Second, we apply ideas from information theory to biological systems. For instance, we are using information-theoretic measures, such as mutual information or transfer entropy, to investigate how different properties of these systems contribute to or subtract from their information processing capacity and what consequences this has for the functioning of real biological systems.

Third, we are also working on method development. This includes extending the widely-used software COPASI (www.copasi.org) for the modeling and simulation of biochemical systems as part of the COPASI developer team. It further includes the development of packages for the R programming environment that allows users to set up workflows ranging from the stochastic simulation of biochemical models to different analysis methods, for instance, the quantification of the variability in these systems or the estimation of information-theoretic measures.


Copasi logo

COPASI (Complex Pathway Simulator, www.copasi.org)

CoRC logo

CoRC (Copasi R Connector, jpahle.github.com/CoRC)

OscillatorGenerator, for the generation of artificial calcium concentration time series (R-package on CRAN).

FRONTIER Innovation Fund Project “Cell-to-cell communication and decision making in plants: an integrated experimental and information-theoretic approach” (ZVK49125.2.154).

Multiplexing and promoter architecture in B. subtilis quorum sensing.

Information decomposition of multi-dimensional AR processes and its dependence on coupling parameters.

Information flow and complex decoding capabilities in calcium signalling pathways with different topologies.



Current Members

Dr. Jürgen PahleGroup Leader
Dr. Martin ZauserPostDoc
Antonia NetzlResearch Assistant
Johanna DaasMaster Student
Tim IngenbrandMaster Student
Ege BayraktarBachelor Student
Jonas JürgensenRotation Project Student
Pablo NaranjoRotation Project Student
Mario WisbarRotation Project Student


Sirac BazMaster Student
Verena Clarmann von ClarenauRotation Project Student
Tobias ElsässerMaster Student
Jonas FörsterResearch Assistant
Marisa GodResearch Assistant
Clara GrundmannResearch Assistant
Anton HankeResearch Project Student
Simon HemingMaster Student
Malte HermesBachelor Student
Nicolas HuberMaster Student
Dr. Sarah KasparPhD Student
Jan KoßRotation Project Student
Sonja KrausertResearch Assistant
Anika LiuResearch Assistant
Janos LöfflerMaster Student
Mai Thu NguyenRotation Project Student
Max RossResearch Assistant
Dr. Arne SchochPhD Student
Jens SchrodtRotation Project Student
Kevin SiswandiMaster Student
Philip StorckRotation Project Student
Dr. Irina SurovtsovaPostDoc
Aarón Vázquez JiménezGuest scientist
Michael ZengerlingMaster Student


We are always interested to hear from good students who would like to work at the interface between systems biology (calcium and other signalling systems etc.) and computer science (information theory, stochastic modelling and simulation, scientific programming).

Please contact the group leader for possible PhD projects, Master/Bachelor theses, lab rotation projects, research assistantships (HiWi), etc.


  • J.C.J. Daas, J.D. Förster and J. Pahle (2022)
    Dynamic Publication Media with the COPASI R Connector (CoRC).
    Mathematical Biosciences, 348:108822, doi:10.1016/j.mbs.2022.108822
  • J. Förster, F.T. Bergmann and J. Pahle (2021)
    CoRC – the COPASI R Connector.
    Bioinformatics, 37(17):2778-2779, doi:10.1093/bioinformatics/btab033
  • M. Zauser (2021)
    Communication in Plants: Analysis and Modeling of Calcium Signatures in Arabidopsis thaliana
    Dissertation, Heidelberg University, doi:10.11588/heidok.00030325
  • E. Stalidzans, M. Zanin, P. Tieri, F. Castiglione, A. Polster, S. Scheiner, J. Pahle, B. Stres, M. List, J. Baumbach, M. Lautizi, K. Van Steen and H.H.H.W. Schmidt (2020)
    Mechanistic modeling and multiscale applications for precision medicine: theory and practice.
    Network and Systems Medicine 3(1):36-56, doi:10.1089/nsm.2020.0002
  • N.J. Stanford, M. Scharm, P.D. Dobson, M.Golebiewski, M. Hucka, V.B. Kothamachu, D. Nickerson, S. Owen, J. Pahle, U. Wittig, D. Waltemath, C. Goble, P. Mendes and J. Snoep (2019)
    Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices.
    Book chapter in Yeast Systems Biology pp. 285-314, doi:10.1007/978-1-4939-9736-7_17
  • A. Schoch (2019)
    Quantitative Analysis of Information Transfer in Signal Transduction.
    Dissertation, Heidelberg University, doi.org/10.11588/heidok.00026833
  • S. Kaspar (2019)
    The role of promoter architecture in transduction, integration and multiplexing of environmental signals in bacteria.
    Dissertation, Heidelberg University, doi.org/10.11588/heidok.00026814
  • A. Schoch and J. Pahle (2019)
    Requirements for band-pass activation of Ca2+-sensitive proteins such as NFAT.
    Biophysical Chemistry 245:41-52, doi:10.1016/j.bpc.2018.10.005
  • F.T. Bergmann, S. Hoops, B. Klahn, U. Kummer, P. Mendes, J. Pahle and S. Sahle (2017)
    COPASI and its Applications in Biotechnology.
    Journal of Biotechnology 261:215, doi:10.1016/j.jbiotec.2017.06.1200
  • F. Graw, F. Matthäus and J. Pahle (eds.) (2017)
    Modeling Cellular Systems,
    Springer International Publishing, Cham, Switzerland, ISBN 978-3-319-45831-1, springer.com, amazon.de, doi:10.1007/978-3-319-45833-5
  • P.H.G.M. Willems, J. Pahle, X.L. Stalpers, D. Mugahid, A. Nikolaew, W.J.H. Koopman and U. Kummer (2015)
    PKC-mediated inhibitory feedback of the cholecystokinin 1 receptor controls the shape of oscillatory Ca2+ signals.
    FEBS Journal 282(11):2187-2201, doi:10.1111/febs.13267
  • C. Zimmer, S. Sahle and J. Pahle (2015)
    Exploiting intrinsic fluctuations to identify model parameters.
    IET Systems Biology 9(2):64-73, doi:10.1049/iet-syb.2014.0010
  • H. Summersgill, H. England, G. López-Castejón, C.B. Lawrence, N.M. Luheshi, J. Pahle, P. Mendes and D. Brough (2014)
    Zinc depletion regulates the processing and secretion of IL-1β.
    Cell Death and Disease 5:e1040, doi:10.1038/cddis.2013.547
  • H. Firczuk, S. Kannambath, J. Pahle, A. Claydon, R. Beynon, J. Duncan, H. Westerhoff, P. Mendes and J.E.G. McCarthy (2013)
    An in vivo control map for the eukaryotic mRNA translation machinery.
    Molecular Systems Biology 9:635, doi:10.1038/msb.2012.73
  • J.D. Challenger, A.J. McKane and J. Pahle (2012)
    Multi-compartment linear noise approximation.
    J. Stat. Mech. 2012(11):P11010, doi:10.1088/1742-5468/2012/11/P11010
  • J. Pahle, J.D. Challenger, P. Mendes and A.J. McKane (2012)
    Biochemical fluctuations, optimisation and the linear noise approximation.
    BMC Systems Biology 6:86, doi:10.1186/1752-0509-6-86
  • Lecture “Computational Systems Biology” (2012)
    Saarland University, Saarbrücken, Germany (April 2012 – September 2012), website/material
  • Seminar “Information processing in living systems” (2012)
    Saarland University, Saarbrücken, Germany (June 2012), website/material
  • B.G. Small, B.W. McColl, R. Allmendinger, J. Pahle, G. López-Castejón, N.J. Rothwell, J. Knowles, P. Mendes, D. Brough and D.B. Kell (2011)
    Efficient discovery of anti-inflammatory small-molecule combinations using evolutionary computing.
    Nature Chemical Biology 7:902-908, doi:10.1038/nchembio.689
  • J. Pahle (2009)
    Biochemical simulations: stochastic, approximate stochastic and hybrid approaches.
    Briefings in Bioinformatics 10(1):53-64, doi:10.1093/bib/bbn050
  • J. Pahle, A.K. Green, C.J. Dixon and U. Kummer (2008)
    Information transfer in signaling pathways: a study using coupled simulated and experimental data.
    BMC Bioinformatics 9:139, doi:10.1186/1471-2105-9-139
  • R. Gauges, U. Kummer, J. Pahle and P. Willy (eds.) (2008)
    Proceedings of the 5th Workshop on Computation of Biochemical Pathways and Genetic Networks, Bioquant, Heidelberg, September 22-23, 2008,
    Logos-Verlag, Berlin, ISBN 978-3-8325-1993-3, Logos-Verlag, amazon.de
  • J. Pahle (2008)
    Stochastic simulation and analysis of biochemical networks.
    Dissertation, Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät I, urn:nbn:de:kobv:11-10090448
  • Presentation “Information transfer in calcium signal transduction” (2007)
    European Conference on Complex Systems (ECCS) 2007, Dresden, Germany, October 1, 2007, videolectures.net
  • K. Fortney, J. Pahle, J. Delgado, G. Obernosterer, V. Shah, M. Wojnowicz and N. Qaisar (2007)
    Effects of simulated brain damage on small-world neural networks.
    Proceedings of the Complex Systems Summer School 2007, Santa Fe, NM, USA, June 3-29, 2007, pdf
  • O. Bochmann, J.T. Lizier, J. Mahoney, G. Obernosterer and J. Pahle (2007)
    Computational mechanics and information measures in food webs.
    Proceedings of the Complex Systems Summer School 2007, Santa Fe, NM, USA, June 3-29, 2007, pdf
  • S. Hoops, S. Sahle, R. Gauges, C. Lee, J. Pahle, N. Simus, M. Singhal, L. Xu, P. Mendes and U. Kummer (2006)
    COPASI – a COmplex PAthway SImulator.
    Bioinformatics 22(24):3067, doi:10.1093/bioinformatics/btl485
  • I. Surovtsova, S. Sahle, J. Pahle and U. Kummer (2006)
    Approaches to complexity reduction in a systems biology research environment (Sycamore).
    Proceedings of the 2006 Winter Simulation Conference, Monterey, CA, USA, December 3-6, 2006, p. 1683, doi:10.1109/WSC.2006.322943
  • S. Sahle, R. Gauges, J. Pahle, N. Simus, U. Kummer, S. Hoops, C. Lee, M. Singhal, L. Xu and P. Mendes (2006)
    Simulation of biochemical networks using Copasi – a complex pathway simulator.
    Proceedings of the 2006 Winter Simulation Conference, Monterey, CA, USA, December 3-6, 2006, p. 1698, doi:10.1109/WSC.2006.322945
  • U. Kummer, B. Krajnc, J. Pahle, A.K. Green, C.J. Dixon and M. Marhl (2005)
    Transition from stochastic to deterministic behavior in calcium oscillations.
    Biophysical Journal 89(3):1603, doi:10.1529/biophysj.104.057216
  • U. Kummer, J. Pahle, I. Surovtsova and J. Zobeley (eds.) (2005)
    Proceedings of the 4th Workshop on Computation of Biochemical Pathways and Genetic Networks, Villa-Bosch, Heidelberg, September 12-13, 2005,
    Logos-Verlag, Berlin, ISBN 978-3-8325-1018-3, Logos-Verlag, amazon.de
  • R. Gauges, U. Kummer, J. Pahle and U. Rost (eds.) (2003)
    Proceedings of the 3rd Workshop on Computation of Biochemical Pathways and Genetic Networks, Villa-Bosch, Heidelberg, October 6-7, 2003,
    Logos-Verlag, Berlin, ISBN 978-3-8325-0375-8, Logos-Verlag, amazon.de
  • J. Pahle, I. Valova, G. Georgiev, N. Georgieva (2000)
    Oscillatory simulation of mitral and granule cell behavior in the olfactory bulb.
    Proceedings of the IC-AI 2000, Las Vegas, NV, USA, June 26-29, 2000, p. 483, pdf