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

BowTieBuilder: modeling signal transduction pathways
Jochen Supper, Lucía Spangenberg, Hannes Planatscher, Andreas Dräger, Adrian Schröder, and Andreas Zell
BMC Systems Biology 2009, (30 June 2009).
[BibTeX], [pdf]
Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies
Andreas Dräger, Marcel Kronfeld, Michael Johannes Ziller, Jochen Supper, Hannes Planatscher, Jørgen Barsett Magnus, Marco Oldiges, Oliver Kohlbacher, and Andreas Zell
BMC Systems Biology 2009, 3:5 (14 January 2009).
[BibTeX], [pdf]
Modeling gene regulation and spatial organization of sequence based motifs
Jochen Supper, Claas aufm Kampe, Dierk Wanke, Kenneth W. Berendzen, Klaus Harter, Richard Bonneau, and Andreas Zell
8th IEEE international conference on BioInformatics and BioEngineering (BIBE 2008)
[online]
SBMLsqueezer: a CellDesigner plug-in to generate kinetic rate equations for biochemical networks
Andreas Dräger, Nadine Hassis, Jochen Supper, Adrian Schröder, Andreas Zell
BMC Systems Biology 2008, 2:39.
[BibTeX], [pdf]
The analysis of gene expression and cis-regulatory elements in large microarray expression datasets
Dierk Wanke, Joachim Kilian, Jochen Supper, Kenneth W. Berendzen, Andreas Zell and Klaus Harter
Quantum Bio-Informatics, edited by Luigi Accardi, Wolfgang Freudenberg and Masanori Ohya, pp. 294-314, 2008
EDISA: extracting biclusters from multiple time-series of gene expression profiles
Jochen Supper, Martin Strauch, Dierk Wanke, Klaus Harter, and Andreas Zell
BMC Bioinformatics, 2007, 12;8 (1):334.
[pdf]
A Two-Step Clustering for 3-D Gene Expression Data Reveals the Main Features of the Arabidopsis Stress Response
Martin Strauch, Jochen Supper, Christian Spieth, Dierk Wanke, Joachim Kilian, Klaus Harter, Andreas Zell
Journal of Integrative Bioinformatics, 4(1):54, 2007. Online Journal: http://journal.imbio.de/index.php?paper_id=54
Benchmarking Evolutionary Algorithms on Convenience Kinetics Models of the Valine and Leucine Biosynthesis in C. glutamicum
Andreas Dräger, Marcel Kronfeld, Jochen Supper, Hannes Planatscher, Jørgen Magnus, Marco Oldiges and Andreas Zell
IEEE Congress on Evolutionary Computation 2007, Singapore, pp. 896-903, 2007.
[BibTeX], [pdf]
Comparing Various Evolutionary Algorithms on the Parameter Optimization of the Valine and Leucine Biosynthesis in Corynebacterium glutamicum
Andreas Dräger, Jochen Supper, Hannes Planatscher, Jørgen Magnus, Marco Oldiges and Andreas Zell
IEEE Congress on Evolutionary Computation 2007, Singapore, pp. 620-627, 2007
[BibTeX], [pdf]
Reconstructing Linear Gene Regulatory Networks
Jochen Supper, Christian Spieth and Andreas Zell
Fifth European Conference on Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics (EvoBIO 2007), pp. 270-279, 2007
Gene Regulatory Network Inference via Regression Based Topological Refinement
Jochen Supper, Holger Fröhlich and Andreas Zell
Series on Advances in Bioinformatics and Computational Biology, vol 5, pp. 267-276, Asia-Pacific Bioinformatics Conference (APBC 2007)
Infering Gene Regulatory Networks by Machine Learning Methods
Jochen Supper, Holger Fröhlich, Christian Spieth, Andreas Dräger and Andreas Zell
Series on Advances in Bioinformatics and Computational Biology, vol 5, pp. 247-256, Asia-Pacific Bioinformatics Conference (APBC 2007)
JCell - a Java based framework for inferring regulatory networks from time series data
C. Spieth, J. Supper, F. Streichert, N. Speer, and A. Zell
Bioinformatics 2006, vol. 22(16), pp. 2051-2052.
[pdf]
Comparing Mathematical Models on the Problem of Network Inference
C. Spieth, N. Hassis, F. Streichert, J. Supper, N. Speer, K. Beyreuther, and A. Zell
Genetic and Evolutionary Computation Conference (GECCO 2006), Seattle, USA
Comparing Evolutionary Algorithms on the Problem of Network Inference
C. Spieth, R. Worzischek, F. Streichert, J. Supper, N. Speer, and A. Zell
Genetic and Evolutionary Computation Conference (GECCO 2006), Seattle, USA
Reverse Engineering Non-Linear Gene Regulatory Networks Based on the Bacteriophage λ cI Circuit
Jochen Supper, Christian Spieth and Andreas Zell
IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2005), San Diego, USA
Proceedings, pp. 325-332, IEEE press
Feedback Memetic Algorithms for Modeling Gene Regulatory Networks
C. Spieth, F. Streichert, J. Supper, N. Speer, and A. Zell
IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB 2005), San Diego, USA
Proceedings, pp. 61-67, IEEE press
Analysis of MHC-Peptide Binding Using Amino Acid Property-Based Decision Rules
Jochen Supper, Pierre Dönnes and Oliver Kohlbacher
Springer Lecture Notes in Computer Science (LNCS) 2005, 3686:446-453.
[pdf]

Posters

Modeling Differential Co-Stimulation of the T Cell Signal Transduction Pathway Based on the CD3 and CD28 receptors
Jochen Supper, Adrian Schröder, Karsten Köhler, Christian Spieth, Roland Brock and Andreas Zell
Conference on Systems Biology of Mammalian Cells (SBMC) 2006, Heidelberg, Germany
[pdf]
Analysis of MHC-Peptide Binding Using Amino Acid Property-Based Decision Rules
Jochen Supper, Pierre Dönnes and Oliver Kohlbacher
International Conference on Advances in Pattern Recognition (ICAPR) 2005, Bath, England
[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