University of Heidelberg
BIOQUANT

News

BIOMS workshop modeling cellular systems

Publications

  • 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 accepted for publication, 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. 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
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