University of Tübingen: Dr. Andreas Dräger

Dr. Andreas Dräger

Background

Since 2011: Junior group leader at the Center for Bioinformatics (ZBIT), University of Tuebingen
March through June 2010: Visiting research student at Keio University, Yokohama, Japan, at the group of Prof. Dr. Akira Funahashi
2006 - 2010: Research assistant and PhD student at the Center for Bioinformatics (ZBIT), University of Tuebingen
2004: Internship at the University of Illinois at Chicago, United States, Microbiology and Immunology at the group of Prof. Dr. Simon Silver
2001: Internship at the Max Planck Institute for Molecular Genetics, Berlin, at the group
of Dr. Richard Reinhard
2000 - 2006: Studies of Bioinformatics at the Martin Luther University Halle-Wittenberg (MLU)
1991 - 1999: Gymnasium (high school) “Am Markt” in Hettstedt

Research Interests

My special interest is the computational modeling of biochemical systems. I want to investigate and understand the complex mutual influences within living systems and believe that methods from engineering such as modeling and simulation can help to reach this goal. My main focus comprises:

Systems biology, in particular metabolic, signaling, and gene-regulatory networks
Model building, simulation, and calibration using evolutionary algorithms
Application and developement of the open-source libraries JSBML, BioJava, and BioSQL
Software products: SBMLsimulator, KEGGtranslator, SBMLsqueezer, SBML2L^AT_EX, ProDGe, ModuleMaster, SABINE

Current Projects

Projects funded by the University of Tuebingen:

Inference of biochemical reaction systems considering physico-chemical constraints

The following projects are all funded by the Federal Ministry of Education and Research (Bundesministerium für Bildung und Forschung, BMBF, Germany):

The Virtual Liver: A project with the aim to build a comprehensive model of the human liver
German National Genome Research Network (Nationales Genomforschungsnetz, NGFN-Plus): medical genome research with focus on Parkinson's disease
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.

Completed Projects

Projects funded by the Federal Ministry of Education and Research (Bundesministerium für Bildung und Forschung, BMBF, Germany):

HepatoSys: Systems biology of the human liver, especially detoxification processes in conjunction with statin treatment
NGFN-II EP: Explorative Project about the reconstruction of gene-regulatory networks in the German National Genome Research Network)

Projects funded by the German federal state of Baden-Württemberg:

Identifikation und Analyse metabolischer Netze aus experimentellen Daten (Identification and analysis of metabolic networks given experimental data)
Tübinger Bioinformatik-Grid: development and application of new bioinformatics approaches and algorithms on high-performance, multiple-threading computers.

Projects funded by companies:

Mentorship in the Google Summer of Code 2010

Teaching

Office hours

Tuesdays 2 p.m. through 4 p.m.

Theses

[1]	Andreas Dräger. Computational Modeling of Biochemical Networks. PhD thesis, University of Tuebingen, Tübingen, Germany, January 2011. [ details \| link ]
[2]	Andreas Dräger. Automatische und vergleichende Analyse bakterieller Genome mit Schwerpunkt auf Ralstonia/Cupriavidus-Arten sowie verwandten Proteobakerien. Diplomarbeit, Martin-Luther-Universität Halle-Wittenberg, von-Seckendorff-Platz 1, 06120 Halle (Saale), December 2005. [ details \| pdf ]
[3]	Andreas Dräger. Suche häufiger Proteinfragmente unter Berücksichtigung von Mutationen und Lücken. Projektarbeit, Martin-Luther-Universität Halle-Wittenberg, von-Seckendorff-Platz 1, 06120 Halle (Saale), August 2003. [ details ]

Awards and honors

A-levels with honors
Annualy, the University of Tuebingen bestows the dissertation award on the most outstanding doctoral theses of each faculty. In 2011, the Math and Science faculty awarded Dr. Andreas Dräger for his PhD thesis.

Publications

[1]	Mélanie Courtot, Nick Juty, Christian Knüpfer, Dagmar Waltemath, Anna Zhukova, Andreas Dräger, Michel Dumontier, Andrew Finney, Martin Golebiewski, Janna Hastings, Stefan Hoops, Sarah Keating, Douglas B. Kell, Samuel Kerrien, James Lawson, Allyson Lister, James Lu, Rainer Machne, Pedro Mendes, Matthew Pocock, Nicolas Rodriguez, Alice Villeger, Darren J. Wilkinson, Sarala Wimalaratne, Camille Laibe, Michael Hucka, and Nicolas Le Novère. Controlled vocabularies and semantics in systems biology. Molecular Systems Biology, 7(1):543, September 2011. [ 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]	Andreas Dräger, Adrian Schröder, and Andreas Zell. Systems Biology for Signaling Networks, volume 1 of Systems Biology, chapter Automating mathematical modeling of biochemical reaction networks, pages 159-205. Springer-Verlag, July 2010. [ DOI \| details \| link ]
[8]	Sandro Lambeck, Andreas Dräger, and Reinhard Guthke. Network inference by considering multiple objectives: Insights from in vivo transcriptomic data generated by a synthetic network. In Hamid R. Arabnia, Quoc-Nam Tran, Rui Chang, Matthew He, Andy Marsh, Ashu M. G. Solo, and Jack Y. Yang, editors, International Conference on Bioinformatics and Computational Biology, BIOCOMP 2010, volume 2, pages 734-742. CSREA Press, July 2010. [ details \| pdf ]
[9]	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 ]
[10]	Marcel Kronfeld, Andreas Dräger, Moritz Aschoff, and Andreas Zell. On the Benefits of Multimodal Optimization for Metabolic Network Modeling. In Ivo Grosse, Steffen Neumann, Stefan Posch, Falk Schreiber, and Peter Stadler, editors, German Conference on Bioinformatics (GCB 2009), volume P-157 of Lecture Notes in Informatics, pages 191-200, Halle (Saale), Germany, September 2009. German Informatics society. [ details \| link \| pdf ]
[11]	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 ]
[12]	Andreas Dräger, Hannes Planatscher, Dieudonné Motsou Wouamba, Adrian Schröder, Michael Hucka, Lukas Endler, Martin Golebiewski, Wolfgang Müller, and Andreas Zell. SBML2L^AT_EX: Conversion of SBML files into human-readable reports. Bioinformatics, 25(11):1455-1456, April 2009. [ DOI \| arXiv \| details \| link \| pdf ]
[13]	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 ]
[14]	Richard C. G. Holland, Thomas Down, Matthew Pocock, Andreas Prlić, David Huen, Keith James, Sylvain Foisy, Andreas Dräger, Andy Yates, Michael Heuer, and Mark J. Schreiber. BioJava: an Open-Source Framework for Bioinformatics. Bioinformatics, 24(18):2096-2097, August 2008. [ DOI \| details \| link \| pdf ]
[15]	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 ]
[16]	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 ]
[17]	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 ]
[18]	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 ]

Export list of publications as BibTeX / Endnote / Rich Text Format (RTF)

Selected Presentations

[1]	Andreas Dräger and Nicolas Rodriguez. JSBML—The SBML Java. library. HARMONY Workshop 2011, New York, USA (18 April 2011).
[2]	Andreas Dräger, Sandra Nitschmann, Alexander Dörr, Johannes Eichner, Michael J Ziller, and Andreas Zell. Context-based generation of kinetic equations with SBMLsqueezer 1.3. COMBINE Workshop 2010, Edinburgh (9 October 2010). Slides available at Nature Precedings.
[3]	Andreas Dräger, Nora Speer, Christian Spieth, Jochen Supper, and Andreas Zell. Inferring Genetic Networks from Gene Expression Data. Biotechnica 2009, Internationale Messe für Biotechnologie, Hannover, Germany, (8 October 2009).
[4]	Andreas Dräger, Marcel Kronfeld, Michael J Ziller, Jochen Supper, Hannes Planatscher, Jørgen B Magnus, Marco Oldiges, Oliver Kohlbacher, and Andreas Zell. Metabolic modeling of Corynebacterium glutamicum: a comparison of rate laws in combination with various parameter optimization strategies. ACHEMA 2009, 29. internationaler Ausstellungskongress für chemische Technik, Umweltschutz und Biotechnologie, Frankfurt am Main, Germany, (13 May 2009).

Selected Posters

[1]	Andreas Dräger, Dietrich H. Nies, and Stefan Posch. A Tool for Interactive Comparative Sequence Analysis. German Conference on Bioinformatics (GCB) 2006, Tübingen, Germany. [ pdf ]

Address, Phone, Fax, E-Mail

University of Tuebingen
Center for Bioinformatics Tuebingen (ZBIT)
Department Cognitive Systems
Room A313
Sand 1
72076 Tübingen
Germany

Phone:	+49 70 71 29-7 89 82
Fax:	+49 70 71 29-50 91
E-Mail:	andreas.draeger@uni-tuebingen.de