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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.

Blog

Our group featured in the new btS ScieGuide!

We have been featured in the new btS ScieGuide 2018/19 (pdf). The btS Heidelberg is the Heidelberg branch of a German-wide initiative of students of the life sciences. In their new btS ScieGuide they present a number of local research groups with a brief description of what they do.

35th Chaos Communication Congress (35C3)

Jürgen Pahle gave a talk on Information Biology at the 35th Chaos Communication Congress in Leipzig, Germany (27.-30. December 2018). The video of the talk is embedded below. You can also watch it directly at media.ccc.de. Please find more information at https://fahrplan.events.ccc.de/congress/2018/Fahrplan/events/9734.html.

Research

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.

Projects

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

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

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.

Etc.

Members

Current Members

Dr. Jürgen Pahle Group Leader
Dr. Irina Surovtsova PostDoc
Sarah Kaspar PhD Student
Arne Schoch PhD Student
Martin Zauser PhD Student
Marisa God Research Assistant
Sirac Baz Master Student
Nicolas Huber Master Student
Michael Zengerling Master Student
Malte Hermes Bachelor Student
Mai Thu Nguyen Rotation Project Student

Alumni

Verena Clarmann von Clarenau Rotation Project Student
Jonas Förster Research Assistant
Clara Grundmann Research Assistant
Sonja Krausert Research Assistant
Anika Liu Research Assistant
Janos Löffler Master Student
Max Ross Research Assistant
Jens Schrodt Rotation Project Student
Philip Storck Rotation Project Student
Aarón Vázquez Jiménez Guest scientist

Opportunities

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.

Publications

  • N.J.​ ​Stanford,​ ​M.​ ​Scharm,​ ​J.​ ​Pahle,​ ​P.D.​ ​Dobson,​ ​M.​ ​Golebiewski, M. ​Hucka,​ ​V.​B.​ ​Kothamachu,​ ​S.​ ​Owen,​ ​D.​ ​Waltemath,​ ​J.​ ​Snoep,​ ​D. Nickerson and ​P.​ ​Mendes (2018)
    Book chapter: Standards, tools, databases and data management in Computational Systems Biology. Best Practices.
    To appear in the series Methods in Molecular Biology published by Springer.
  • 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