Welcome!
Welcome to the research group 'Computational Modeling in Biology' at the Institute of Bioinformatics and Systems Biology at the Helmholtz Zentrum München - German Research Center for Environmental Health. We are interested in applying methods from biostatistics and statistical machine learning to the analysis of biological problems, ranging from regulatory networks to neural recordings.
Currently, we put most focus on the analysis of microRNA-influenced gene regulation. For this we build qualitative interaction models, if possible transform them into quantitative models and try to fit them to realistic data. Key applications are stem cell differentiation and neural development.
Thank you for your visit. For further details, please use the menu on the left hand side.
News
Social transfer of pathogenic fungus promotes active immunisation in ant colonies! Read the original article by Konrad et al. in PLoS Biology, where we contributed an epidemiological model to explore the adaptive value and colony-level long-term effects of social immunisation, and have a look on the media coverage (Süddeutsche Zeitung, Spiegel Online, Interview with Sylvia Cremer in rbb).
We have several new master and HiWi projects! Please have a look at our open positions!
Spring School 2012 on Systems Biology
We continue the series of Systems Biology symposia and workshops in the Helmholtz Association and are pleased to announce the 5th Spring School on Systems Biology at Kloster Seeon. It will take place from March 28th through March 30th 2012, already traditionally in the beautiful setting near the largest Bavarian lake, the Chiemsee.
12th Bioinformatics Spring School Altes Kloster Hainburg 2012
The 12th edition of the Spring School of Bioinformatics for Molecular Biologists will be held from 17th through 21th of March 2012.
Recently, we received an ERC-starting-grant for modeling latent causes in molecular networks. Please check our open positions if you are interested.
We welcome our newest group members Jan Hasenauer, Nikola Müller and Justin Feigelman.
We are happy to announce the release of Applications of MATLAB in Science and Engineering
The chapter From Discrete to Continuous Gene Regulation Models – A Tutorial Using the Odefy Toolbox has been written by Jan Krumsiek, Dominik M. Wittmann and Fabian J. Theis
We are always looking for interested diploma and PhD students! Email or visit us to get more details!
Selected recent publications
| [1] | M. Konrad, M. Vyleta, F. Theis, M. Stock, S. Tragust, M. Klatt, V. Drescher, C. Marr, L. Ugelvig and S. Cremer. Social Transfer of Pathogenic Fungus Promotes Active Immunisation in Ant Colonies. PLoS Biology, 10(4):e1001300, 2012. 10.1371/journal.pbio.1001300. [ DOI ] |
| [2] | S. Krug, G. Kastenmüller, F. Stückler, M. Rist, T. Skurk, M. Sailer, J. Raffler, W. Römisch-Margl, J. Adamski, C. Prehn, T. Frank, K. Engel, T. Hofmann, B. Luy, R. Zimmermann, F. Moritz, P. Schmitt-Kopplin, J. Krumsiek, W. Kremer, F. Huber, U. Oeh, F. Theis, W. Szymczak, H. Hauner, K. Suhre and H. Daniel. The dynamic range of the human metabolome revealed by challenges. FASEB J., pages fj.11-198093, 2012. 10.1096/fj.11-198093. [ DOI | PubMed ] |
| [3] | A. Raue, C. Kreutz, F. Theis and J. Timmer. Joining Forces of Bayesian and Frequentist Methodology: A Study for Inference in the Presence of Non-Identifiability. Phil. Trans. Roy. Soc. A, accepted, 2012. |
| [4] | M. Strasser, F. Theis and C. Marr. Stability and multi-attractor dynamics of a gene switch based on a two-stage model of gene expression. Biophysical Journal, 102:19-29, 2012. 10.1016/j.bpj.2011.11.4000. [ DOI ] |
| [5] | I. Laaser, F. Theis, M. H. de Angelis, H. Kolb and J. Adamski. Huge Splicing Frequency in Human Y Chromosomal UTY Gene. OMICS A journal of Integrative Biology, 15(3):141-154, 2011. 10.1089/omi.2010.0107. [ DOI | PubMed | .pdf ] |
| [6] | A. Kowarsch, M. Preusse, C. Marr and F. Theis. miTALOS: analyzing the tissue-specific regulation of signaling pathways by human and mouse microRNAs. RNA, 17(809-819), 2011. 10.1261/rna.2474511. [ DOI | PubMed ] |
| [7] | F. Theis, N. Latif, P. Wong and D. Frishman. Complex principal component and correlation structure of 16 yeast genomic variables. Molecular Biology and Evolution, 28(9):2501-2512, 2011. 10.1093/molbev/msr077. [ DOI | PubMed | .pdf ] |
| [8] | J. Krumsiek, K. Suhre, T. Illig, J. Adamski and F. Theis. Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data. BMC Systems Biology, 5(21), 2011. 10.1186/1752-0509-5-21. [ DOI | PubMed | .pdf ] |
| [9] | F. Theis, S. Bohl and U. Klingmüller. Theoretical analysis of time-to-peak responses in biological reaction networks. Bulletin of Mathematical Biology, 73(5):978-1003, 2011. 10.1007/s11538-010-9548-x. [ DOI | PubMed | .pdf ] |
| [10] | A. Kowarsch, C. Marr, D. Schmidl, A. Ruepp and F. Theis. Tissue-specific target analysis of disease-associated microRNAs in human signaling pathways. PLoS ONE, 5(6):e11154, 2010. 10.1371/journal.pone.0011154. [ DOI | PubMed | .pdf ] |
