Jochen Supper

Background

  • since 04/2005 research assistant at the Centre for Bioinformatics (ZBIT), University of Tübingen
  • 07/2003-03/2005 cont. University of Tübingen, diploma in Computer Science (Bioinformatics).
  • 02/2004-04/2004 Internship at the Biofrontera AG, Leverkusen,
  • 11/2002-06/2003 Graduate student at the University of Washington
  • 10/1999-10/2002 Computer science student at the University of Tübingen

Research Interests

  • Decipher regulatory signals controlling gene expression
  • Analyze the robustness of Signaling pathways
  • Cluster multi-conditioned microarray datasets
  • Immunoinformatics

Current Projects

  • Robustness analysis of signal transduction models in collaboration with Christian Lorenz Müller, Computational Biophysics Lab ETH Zurich
  • Identifying Gene Expression Modules in Arabidopsis thaliana in collaboration with Prof. Dr. Harter, ZMBP Tübingen
  • BMBF-Project: NGFN 2 (National Genome Research Network): Explorative Project - Inferring Genetic Networks from Gene Expression Data

Publications

[1] Adrian Schröder, Johannes Eichner, Jochen Supper, Jonas Eichner, Dierk Wanke, Carsten Henneges, and Andreas Zell. Predicting DNA-Binding Specificities of Eukaryotic Transcription Factors. PLoS ONE, 5(11):e13876, November 2010. [ DOI | details | link | pdf ]
[2] Hannes Planatscher, Jochen Supper, Oliver Poetz, Dieter Stoll, Thomas Joos, Markus Templin, and Andreas Zell. Optimal selection of epitopes for txp-immunoaffinity mass spectrometry. Algorithms for Molecular Biology, 5(1):28, June 2010. [ DOI | details | link ]
[3] Jochen Supper, Lucía Spangenberg, Hannes Planatscher, Andreas Dräger, Adrian Schröder, and Andreas Zell. BowTieBuilder: modeling signal transduction pathways. BMC Systems Biology, 3(1):67, June 2009. [ DOI | details | link | pdf ]
[4] Andreas Dräger, Marcel Kronfeld, Michael J. Ziller, Jochen Supper, Hannes Planatscher, Jørgen B. Magnus, Marco Oldiges, Oliver Kohlbacher, and Andreas Zell. Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies. BMC Systems Biology, 3(5):5, January 2009. [ DOI | details | link | pdf ]
[5] Andreas Dräger, Nadine Hassis, Jochen Supper, Adrian Schröder, and Andreas Zell. SBMLsqueezer: a CellDesigner plug-in to generate kinetic rate equations for biochemical networks. BMC Systems Biology, 2(1):39, April 2008. [ DOI | details | link | pdf ]
[6] Andreas Dräger, Jochen Supper, Hannes Planatscher, Jørgen B. Magnus, Marco Oldiges, and Andreas Zell. Comparing Various Evolutionary Algorithms on the Parameter Optimization of the Valine and Leucine Biosynthesis in Corynebacterium glutamicum. In Dipti Srinivasan and Lipo Wang, editors, IEEE Congress on Evolutionary Computation (CEC 2007), pages 620-627, Singapore, September 2007. IEEE Computational Intelligence Society, IEEE Press. [ DOI | details | link | pdf ]
[7] Andreas Dräger, Marcel Kronfeld, Jochen Supper, Hannes Planatscher, Jørgen B. Magnus, Marco Oldiges, and Andreas Zell. Benchmarking Evolutionary Algorithms on Convenience Kinetics Models of the Valine and Leucine Biosynthesis in C. glutamicum. In Dipti Srinivasan and Lipo Wang, editors, IEEE Congress on Evolutionary Computation (CEC 2007), pages 896-903, Singapore, 2007. IEEE Computational Intelligence Society, IEEE Press. [ DOI | details | link | pdf ]
[8] Martin Strauch, Jochen Supper, Christian Spieth, Dierk Wanke, Joachim Kilian, Klaus Harter, and Andreas Zell. A two-step clustering for 3-d gene expression data reveals the main features of the arabidopsis stress response. Journal of Integrative Bioinformatics, 4(1), 2007. [ DOI | details | pdf ]
[9] Jochen Supper, Holger Fröhlich, Christian Spieth, Andreas Dräger, and Andreas Zell. Inferring gene regulatory networks by machine learning methods. In David Sankoff, Lusheng Wang, and Francis Chin, editors, Proceedings of the 5th Asia-Pacific Bioinformatics Conference (APBC 2007), volume 5 of Series on Advances in Bioinformatics and Computational Biology, pages 247-256, 57 Shelton Street, Govent Garden, London WC2H 9HE, UK, January 2007. Imperial College Press. [ DOI | details | link | pdf ]
[10] Jochen Supper, Holger Fröhlich, and Andreas Zell. Gene regulatory network inference via regression based topological refinement. In David Sankoff, Lusheng Wang, and Francis Chin, editors, Asia-Pacific Bioinformatics Conference (APBC 2007), volume 5 of Advances in Bioinformatics and Computational Biology, pages 267-276, Hong Kong, China, January 2007. Imperial College Press. [ details | pdf ]
[11] Jochen Supper, Christian Spieth, and Andreas Zell. Reconstructing linear gene regulatory networks. In Elena Marchiori, Jason H. Moore, and Jagath C. Rajapakse, editors, Proceedings of the 5th European Conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics (EvoBIO 2007), volume 4447 of Lecture Notes in Computer Science, pages 270-279, Valencia, Spain, 2007. Springer. [ details ]
[12] Jochen Supper, Martin Strauch, Dierk Wanke, Klaus Harter, and Andreas Zell. EDISA: extracting biclusters from multiple time-series of gene expression profiles. BMC Bioinformatics, 8(1):334, 2007. [ DOI | details | link ]
[13] Christian Spieth, Nadine Hassis, Felix Streichert, Jochen Supper, Nora Speer, Klaus Beyreuther, and Andreas Zell. Comparing mathematical models on the problem of network inference. In Genetic and Evolutionary Computation Conference (GECCO 2006), Lecture Notes in Computer Science, pages 305-306, Seattle, USA, 2006. Springer. [ details | pdf ]
[14] Christian Spieth, Jochen Supper, Felix Streichert, Nora Speer, and Andreas Zell. JCell - a java-based framework for inferring regulatory networks from time series data. Bioinformatics, 22(16):2051-2052, 2006. [ details | link ]
[15] Christian Spieth, Felix Streichert, Jochen Supper, Nora Speer, and Andreas Zell. Feedback memetic algorithms for modelling gene regulatory networks. In IEEE Symposium on Computational Intelligence and Computational Biology, pages 61-67, San Diego, USA, November 2005. IEEE Press. [ details | pdf ]
[16] Jochen Supper, Christian Spieth, and Andreas Zell. Reverse engineering non-linear gene regulatory networks based on the bacteriophage lambda ci circuit. In Proceedings of the 2005 IEEE Symposium on Computational Intelligence and Computational Biology (CIBCB '05), pages 325-332, San Diego, USA, November 2005. IEEE. [ DOI | details | pdf ]

Theses

Predicting MHC class I binding peptides based on amino acid properties using decision trees and support vector machines
Studienarbeit, University of Tübingen, 2005
Reconstruction of pseudo-linear under-determined networks
Master thesis, University of Tübingen, 2004

Address, phone and fax number, email

Eberhard-Karls-Universität Tübingen
Wilhelm-Schickard-Institut für Informatik
Lehrstuhl Rechnerarchitektur
Sand 14
D - 72076 Tübingen
 
Germany

Phone: (+49/0) 7071 / 29 70436 
Fax: (+49/0) 7071 / 29 5091
Email: Jochen.Supper at uni-tuebingen.de