Clemens Wrzodek

Background

  • Since 03/2009 Research assistant at the Centre for Bioinformatics (ZBIT), University of Tübingen
  • Since 1998 Software development as freelancer. References include Smart Software Development Ltd. London, Deutsche Managementgesellschaft für Gesundheit (DMGG), da Vinci Diabetes Care GmbH, Professor Dr. Baum GmbH
  • 2009 Diploma in Computer Science (Bioinformatics). Thesis: Modelling of transcriptional networks by integrating expression data and promoter analysis
  • 2008 Internship as patent attorney at Stolmár Scheele & Partner, Munich
  • 10/2007-02/2009 Continued studies of Bioinformatics at the University of Tübingen.
  • 07/2006-07/2007 Studies of Computer Sciences and Biology at the San Diego State University, CA, USA
  • 10/2003-07/2006 Studies of Bioinformatics at the University of Tübingen
  • Until 10/2003 Gymnasium (high school) Waldschule Degerloch in Stuttgart

 

Research Interests

My main research focuses on developing novel methods and software that helps understanding the various mutual influences within living systems across multiple layers. In particular:
  • Systems biology, especially analysis, visualization and modeling of regulatory, metabolic and signaling networks
    (see JSBML, KEGGtranslator)
  • Microarray data analysis, in particular cross-platform microarray data integration, analysis and visualization
    (see InCroMAP)
  • Computational epigenetics (see CpG island feature generator)
  • Analysis and detection of gene-regulatory relationships (see ModuleMaster, SABINE)
  • Application and software development in general (see Software products)

 

Current Projects

International projects, funded by the european union:
  • EU IMI MARCAR: towards novel biomarkers for cancer risk assessment.

The following projects are all funded by the Federal Ministry of Education and Research (Bundesministerium für Bildung und Forschung, BMBF, Germany):
  • Spher4Sys: a systems-biology-based approach for preclinical lead compound development using an in-vivo like spheroid test system. This project is contributes to the medical systems biology network MedSys.
  • German National Genome Research Network (Nationales Genomforschungsnetz, NGFN-Plus): medical genome research with focus on Parkinson's disease.

 

Software products

Main projects:
  • InCroMAP: Integrated analysis of Cross-platform MicroArray and Pathway data.
  • KEGGtranslator: Visualizing and translating the KEGG PATHWAY database
  • CpG island feature generator: Generating features to distinct between methylated and unmethylated CpG islands
  • ModuleMaster: A new tool to decipher transcriptional regulatory networks

 

Contributions:
  • JSBML: A flexible Java library for working with SBML.
  • SBMLsimulator: An efficient Java™ solver implementation for SBML.
  • ProDGe: Investigating protein-protein interactions at the domain level.
  • SBML2LaTeX: Conversion of SBML files into human-readable reports.
  • SABINE: Prediction of the binding specificity of transcription factors using support vector regression.
  • ZBIT Bioinformatics Toolbox: A web-based Galaxy framework for bioinformatics tools.

Teaching

Awards and honors

  • 2001/2002: Reaching the finals in the 20th german federal competition for informatics (20. BWINF).
  • 2008: Diploma thesis has been avarded the EVE Award for Evolutionary Biology ("EvE-Förderpreis für Evolutionsbiologie") of the Volkswagen Foundation.

Publications

[1] Clemens Wrzodek, Finja Büchel, Georg Hinselmann, Johannes Eichner, Florian Mittag, and Andreas Zell. Linking the epigenome to the genome: Correlation of different features to DNA methylation of CpG islands. PLoS ONE, 7(4):e35327, 04 2012. [ DOI | details | link | pdf ]
[2] Finja Büchel, Clemens Wrzodek, Florian Mittag, Andreas Dräger, Adrian Schröder, and Andreas Zell. ProDGe: investigating protein-protein interactions at the domain level. Technical report, Nature Precedings, August 2011. [ DOI | details | link | pdf ]
[3] Adrian Schröder, Johannes Wollnik, Clemens Wrzodek, Andreas Dräger, Michael Bonin, Oliver Burk, Maria Thomas, Wolfgang E. Thasler, Ulrich M. Zanger, and Andreas Zell. Inferring statin-induced gene regulatory relationships in primary human hepatocytes. Bioinformatics, 27(18):2473-2477, July 2011. [ DOI | arXiv | details | link | pdf ]
[4] Andreas Dräger, Nicolas Rodriguez, Marine Dumousseau, Alexander Dörr, Clemens Wrzodek, Nicolas Le Novère, Andreas Zell, and Michael Hucka. JSBML: a flexible Java library for working with SBML. Bioinformatics, 27(15):2167-2168, June 2011. [ DOI | arXiv | details | link | pdf ]
[5] Adrian Schröder, Clemens Wrzodek, Johannes Wollnik, Andreas Dräger, Dierk Wanke, Kenneth W. Berendzen, and Andreas Zell. Inferring transcriptional regulators for sets of co-expressed genes by multi-objective evolutionary optimization. In IEEE Congress on Evolutionary Computation (CEC 2011), New Orleans, USA, June 2011. [ DOI | details | link | pdf ]
[6] Clemens Wrzodek, Andreas Dräger, and Andreas Zell. KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats. Bioinformatics, 27(16):2314-2315, June 2011. [ DOI | arXiv | details | link | pdf ]
[7] Clemens Wrzodek, Adrian Schröder, Andreas Dräger, Dierk Wanke, Kenneth W. Berendzen, Marcel Kronfeld, Klaus Harter, and Andreas Zell. ModuleMaster: A new tool to decipher transcriptional regulatory networks. Biosystems, 99(1):79-81, January 2010. [ DOI | details | link ]
[8] Simon Rieche, Klaus Wehrle, Leo Petrak, and Clemens Wrzodek. Cerco: Supporting range queries with a hierarchically structured peer-to-peer system. In Proceedings of 31st IEEE Conference on Local Computer Networks (LCN 2006), Tampa, Florida, USA, November 2006. [ details | link | pdf ]

Export all publications as BibTeX / Endnote / rich text format (RTF)

 

Theses

[1] Clemens Wrzodek. Modelling of transcriptional networks by integrating expression data and promoter analysis. Diplomarbeit, University of Tuebingen, November 2008. [ details | pdf ]
[2] Clemens Wrzodek. Range queries in hierarchically structured peer-to-peer systems. Studienarbeit, University of Tuebingen, 2006.

 

Address, Phone, Fax, Email

Eberhard-Karls-Universität Tübingen
Wilhelm-Schickard-Institut für Informatik
Lehrstuhl Kognitive Systeme
Sand 1
D - 72076 Tübingen
Germany

Tel: (+49/0) 7071 / 29 70436
Fax: (+49/0) 7071 / 29 5091
Email: