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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

Talk at the Online BioQuant Internal Seminar by Kevin Siswandi

Kevin Siswandi, a Master student in our group, gave a talk in the BioQuant Internal Seminar series on 16. April 2020. Due to the Corona virus pandemic the seminar was exclusively held online. In his talk Kevin presented an AI project he has worked on last semester in our group with the title “Predicting the …

New book chapter on “Data Management in Computational Systems Biology” published

A new book chapter titled “Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices” with co-author Jürgen Pahle was published as part of the book “Yeast Systems Biology“, edited by Stephen G. Oliver and Juan I. Castrillo (pages 285-314). More details can be found here: doi:10.1007/978-1-4939-9736-7_17.

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 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.

Etc.

Members

Current Members

Dr. Jürgen PahleGroup Leader
Martin ZauserPhD Student
Marisa GodResearch Assistant
Tobias ElsässerMaster Student
Simon HemingMaster Student
Kevin SiswandiMaster Student
Sirac BazMaster Student
Jan KoßRotation Project Student

Alumni

Verena Clarmann von ClarenauRotation Project Student
Jonas FörsterResearch Assistant
Clara GrundmannResearch Assistant
Anton HankeResearch Project Student
Malte HermesBachelor Student
Nicolas HuberMaster Student
Dr. Sarah KasparPhD 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
Philip StorckRotation Project Student
Dr. Irina SurovtsovaPostDoc
Aarón Vázquez JiménezGuest scientist
Michael ZengerlingMaster Student

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

  • 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