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