by phynix

Dr. Jürgen Pahle

Center for Quantitative Analysis of Molecular and Cellular Biosystems (BioQuant)
Heidelberg University, Germany

github: github.com/jpahle ORCID: 0000-0002-7637-7547 Linkedin: www.linkedin.com/in/juergen-pahle

Interests

Projects

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

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

Biological memory: a computational investigation of the capacity and dynamics of biological memory - from bacteria to the human immune system (funded by the Klaus Tschira Foundation).

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

Encoding, decoding and crosstalk: Information-theoretic investigation of intra- and intercellular communication (funded by the Center for Modelling and Simulation in the Biosciences (BIOMS))

Calcium Models Library - a library of calcium-dependent protein models.

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.

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

Other projects ➚

Publications 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
• 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 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 261:215-220, 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