Prof. Dr. Jens Timmer
Faculty of Mathematics and Physics Freiburg, Germany
Freiburg Institute for Advanced Studies
School of Life Sciences - LifeNet
79104 Freiburg im Breisgau
Jens Timmer has studied Physics at the Universities of Oldenburg and Freiburg. He received his Ph.D. in 1994 from the University of Freiburg. Since this time, he is leading the research group “Data Analysis and Modelling of Dynamic Processes in the Life Sciences''. During his postdoc research, he was visiting scientist at Boulder University, ETH Lausanne, New York University, Humboldt University, Max-Planck Institute for Physics of Complex Systems in Dresden, and the Universities of Potsdam and Heidelberg. Since 2005, he is Professor of Theoretical Physics at the University of Freiburg. He is speaker of the German Systems Biology Competence Network HepatoSys and member of the Board of Directors of the Centre for Data Analysis and Modelling as well as the Centre for Systems Biology at the University of Freiburg. He is vice-speaker of the Freiburg Initiative for Systems Biology.
Jens Timmer's research focuses on the development and interdisciplinary application of mathematical methods to analyse and model dynamical processes in biology and medicine. Dynamic processes are ubiquitous in the life sciences. They can be found from the regulation in cells up to oscillations in tremor. Malfunction of these dynamical processes can be a cause or a sign of diseases. In interdisciplinary projects, his group develops and applies mathematical methods to analyse and model these processes based on measured data. The final aim is to help to turn the life sciences from a qualitative descriptive into a quantitative predictive science.
Jens Timmer's projects in FRIAS concentrate on mathematical modelling and systems' analysis of cell biological systems with application to signalling, gene regulatory networks and pattern formation. In cooperation with the collaboration partners from the Department of Biology, mathematical models will be set up. Parameters in the models will be estimated from time-resolved experimental data. Based on experimentally validated models, the systems' properties of the biological processes will be inferred.
- L. Sommerlade, M. Thiel, B. Platt, A. Plano, G. Riedel, C. Grebogi, J. Timmer, B. Schelter: Inference of Granger causal time-dependent influences in noisy multivariate time series. J Neurosci Methods, 2012; 203 (1): 173-185. http://dx.doi.org/10.1016/j.jneumeth.2011.08.042
- C. Kreutz, J.S. Gehring, D. Lang, R. Reski, J. Timmer, S.A. Rensing: TSSi - An R package for transcription start site identification from 5’ mRNA tag data, Bioinformatics, 2012. doi: 10.1093/bioinformatics/bts189.
- C. Kreutz, A. Raue, J. Timmer: Likelihood based observability analysis and confidence intervals for predictions of dynamic models. Bmc Syst Biol, 2012; 6(1): 120. http://dx.doi.org/10.1186/1752-0509-6-120
- J. Rausenberger, A. Tscheuschler, W. Nordmeier, F. Wuest, J. Timmer, E. Schaefer, C. Fleck, A. Hiltbrunner: Photoconversion and Nuclear Trafficking Cycles Determine Phytochrome A’s Response Profile to Far-Red Light, Cell, 2011; 146 (5): 813-825. doi:10.1016/j.cell.2011.07.023
- J. Bachmann, A. Raue, M. Schilling, H. Busch, J. Timmer, U. Klingmüller: Division of Labor by Dual Feedback Regulators Controls JAK2/STAT5 Signaling over Broad Ligand Range Mol Syst Biol, 2011; 7:516
- D. Onichtchouk, F. Geier, B. Polok, D.M. Messerschmidt, R. Mossner, V. Taylor, J. Timmer, W. Driever: Oct4/Pou5f1 controls differentiation timing in early zebrafish embryo Developmental Biology, 2010; 344 (1): 415-415
- A.C. Pfeifer, D. Kaschek, J. Bachmann, U. Klingmuller, J. Timmer: Model-based extension of high-throughput to high-content data. BMC Syst Biol, 2010; 4: 106
- V. Becker, M. Schilling, J. Bachmann, U. Baumann, A. Raue, T. Maiwald, J. Timmer, U. Klingmüller. Covering a broad dynamic range: Information processing at the erythropoietin receptor. Science, 2010; 328 (5984): 1404-1408
- D. Onichtchouk, F. Geier, B. Polok, D. Messerschmidt, R. Mössner, B. Wendik, S. Song, V. Taylor, J. Timmer, W. Driever. Zebrafish Pou5f1-dependent transcriptional networks in temporal control of early development. Molecular Systems Biology 6, 2010, 354
- C. Kreutz, J. Timmer: Systems biology: experimental design Febs Journal, 2009; 276 (4): 923-942
- K. Wester, S. Digiuni, F. Geier, J. Timmer, C. Fleck, M. Huelskamp: Functional diversity of R3 single-repeat genes in trichome development Development, 2009; 136: 1487-1496
- M. Schilling, T. Maiwald, S. Hengl, D. Winter, C. Kreutz, W. Kolch, W.D. Lehmann, J. Timmer, U. Klingmüller. Theoretical and experimental analysis links isoform-specific ERK signalling to cell fate decisions. Molecular Systems Biology 5, 2009, 334
- N. Borisov, E. Aksamitiene, A. Kiyatkin, S. Legewie, J. Berkhout, T. Maiwald, N.P. Kaimachnikov, J. Timmer, J.B. Hoek, B.N. Kholodenko. Systems-level interactions between insulin-EGF networks amplify mitogenic signaling. Mol. Sys. Bio. 5, 2009, 256
S. Digiuni, S. Schellmann, F. Geier, B. Greese, M. Pesch. K. Wester, B. Dartan, V. Mach, B. P. Srinivas, J. Timmer, C. Fleck, M. Hülskamp. A competitive complex formation mechanism underlies trichome patterning on Arabidopsis leaves. Mol. Sys. Bio. 4, 2008, 217.
D. Bouyer, F. Geier, F. Kragler, A. Schnittger, M. Pesch, K. Wester, R. Balkunde, J. Timmer, C. Fleck, M. Hülskamp. Two-dimensional patterning by a trapping/depletion mechanism: The role of TTG1 and GL3 in Arabidopsis trichome formation. PloS Biology 6, 2008, e141.
E. Anastasiou, S. Kenz, M. Gerstung, D. MacLean, J. Timmer, C. Fleck, M. Lenhard. Control of plant organ size by KLUH/CYP78A5-dependent intracellular signalling. Developmental Cell 13, 2007, 843-856.
D. Pfeifer, M. Pantic, I. Skatulla, J. Rawluk, C. Kreutz, U. Martens, P. Fisch, J. Timmer, H. Veelken. Genome-wide analysis of DNA copy number changes in CLL using high-density SNP arrays. Blood 109, 2007, 1202-1210.
S. Sick, S. Reinker, J. Timmer, T. Schlake. WNT and DKK determine hair follicle spacing through a reaction-diffusion mechanism. Science 314, 2006, 1447-1450.
M. Kollmann, K. Bartholome, L. Lovdok, J. Timmer, V. Sourjik. Design principles of a bacterial signalling network. Nature 438, 2005, 504-507.
I. Swameye, T.G. Müller, J. Timmer, O. Sandra, U. Klingmüller. Identification of nucleocytoplasmic cycling as a remote sensor in cellular signaling by data-based modeling. Proc. Natl. Acad. Sci. 100, 2003, 1028-1033.
B. Hellwig, S. Häußler, B. Schelter, M. Lauk, B. Guschlbauer, J. Timmer, C.H. Lücking. Tremor-correlated cortical activity in essential tremor. The Lancet 357, 2001, 519-523