computational
modeling in
biology

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Selected publications by topic

Data analysis and machine learning

[1] F. Blöchl and F.J. Theis. Estimating hidden influences in metabolic and gene regulatory networks. In Proc. ICA 2009, volume 5441 of LNCS, pages 387-394, Paraty, Brazil, 2009. Springer. [ .pdf ]
[2] F.J. Theis, P. Gruber, I.R. Keck, and E.W. Lang. A robust model for spatiotemporal dependencies. Neurocomputing, 71(10-12):2209-2216, 2008. [ DOI | .pdf ]
[3] F.J. Theis. Towards a general independent subspace analysis. In Proc. NIPS 2006, 2007. [ .pdf ]
[4] F.J. Theis, P. Georgiev, and A. Cichocki. Robust sparse component analysis based on a generalized hough transform. EURASIP Journal on Applied Signal Processing, 2007. [ DOI | .pdf ]
[5] F.J. Theis, C.G. Puntonet, and E.W. Lang. Median-based clustering for underdetermined blind signal processing. IEEE Signal Processing Letters, 13(2):96-99, 2006. [ DOI | .pdf ]
[6] F.J. Theis. A new concept for separability problems in blind source separation. Neural Computation, 16:1827-1850, 2004. [ DOI | .pdf ]

Modeling

[1] D.M. Wittmann, J. Krumsiek, J. Saez-Rodriguez, D.A. Lauffenburger, S. Klamt, and F.J. Theis. Transforming boolean models to continuous models: Methodology and application to t-cell receptor signaling. BMC Systems Biology, 3(98), 2009. [ DOI | .pdf ]
[2] D.M. Wittmann, F. Blöchl, N. Prakash, D. Trümbach, W. Wurst, and F.J. Theis. Spatial analysis of expression patterns predicts genetic interactions at the mid-hindbrain boundary. PLoS Computational Biology, 5(11):e1000569, 2009. [ DOI ]
[3] B. Adamcio, D. Sargin, A. Stradomska, L. Medrihan, C. Gertler, F.J. Theis, M. Zhang, M. Müller, I. Hassouna, K. Hannke, S. Sperling, K. Radyushkin, A. El-Kordi, L. Schulze, A. Ronnenberg, F. Wolf, N. Brose, J. Rhee, W. Zhang, and H. Ehrenreich. Erythropoietin enhances hippocampal long-term potentiation and memory. BMC Biology, 6(37), 2008. [ DOI | .pdf ]
[4] M. Begemann, D. Sargin, M.J. Rossner, C. Bartels, F.J. Theis, S.P. Wichert, N. Stender, B. Fischer, S. Sperling, S. Stawicki, A. Wiedl, P. Falkai, K.A. Nave, and H. Ehrenreich. Episode-specific differential gene expression of peripheral blood mononuclear cells in rapid cycling supports novel treatment approaches. Mol Med, 14(9-10):546-552, 2008. [ DOI | .PDF ]
[5] A. Meyer-Bäse and F.J. Theis. Gene regulatory networks simplified by nonlinear balanced truncation. In SPIE Proceedings, volume 6979, 2008. [ .pdf ]
[6] D. Lutter, P. Ugocsai, M. Grandl, E. Orso, F.J. Theis, E.W. Lang, and G. Schmitz. Analyzing m-csf dependent monocyte/macrophage differentiation: expression modes and meta-modes derived from an independent component analysis. BMC Bioinformatics, 9(100), 2008. [ DOI | .pdf ]
[7] F.J. Theis and G.A. García. On the use of sparse signal decomposition in the analysis of multi-channel surface electromyograms. Signal Processing, 86(3):603-623, 2006. [ DOI | .pdf ]

Networks

[1] S. Klamt, U. Haus, and F.J. Theis. Hypergraphs and cellular networks. PLoS Computational Biology, 5(5), 2009. [ DOI | .pdf ]
[2] D.M. Wittmann, D. Schmidl, F. Blöchl, and F.J. Theis. Reconstruction of graphs based on random walks. Journal of Theoretical Computer Science, 410:3826-3838, 2009. [ DOI | .pdf ]
[3] P Wong, S Althammer, A Hildebrand, A Kirschner, P Pagel, B Geissler, P Smialowski, F Bloechl, M Oesterheld, T Schmidt, N Strack, FJ Theis, A Ruepp, and D Frishman. An evolutionary and structural characterization of mammalian protein complex organization. BMC Genomics, 9(1):629, Dec 2008. [ DOI | .pdf ]
[4] D. Brockmann and F.J. Theis. Money circulation, trackable items, and the emergence of universal human mobility patterns. IEEE Pervasive Computing, 7(4):28-35, 2008. [ DOI | .pdf ]

Tools

[1] A. Ruepp, A. Kowarsch, D. Schmidl, F. Buggenthin, B. Brauner, I. Dunger, G. Fobo, G. Frishman, C. Montrone, and F.J. Theis. Phenomir: a knowledgebase for microrna expression in diseases and biological processes. Genome Biology, 11(1):R6, Jan 2010. [ DOI ]
[2] K.J. Webb, W.H.J. Norton, D. Trümbach, A.H. Meijer, J. Ninkovic, S. Topp, D. Heck, C. Marr, W. Wurst, F.J. Theis, H.P. Spaink, and L. Bally-Cuif. Zebrafish reward mutants reveal novel transcripts mediating the behavioral effects of amphetamine. Genome Biology, 10(7):R81, 2009. [ DOI | .pdf ]
[3] R.A. Neher, M. Mitkovski, F. Kirchhoff, E. Neher, F.J. Theis, and A. Zeug. Blind source separation techniques for the decomposition of multiply labeled fluorescence images. Biophysical Journal, 96(9):3791-3800, 2009. [ DOI | .pdf ]
[4] F.J. Theis, Z. Kohl, C. Guggenberger, H.G. Kuhn, C.G. Puntonet, and E.W. Lang. ZANE - an algorithm for counting labelled cells in section images. In Proc. MEDSIP 2004, Malta, 2004.