Andreas Dräger

Dr. Andreas Dräger

Background

  • Since 2013: Research Scholar at the University of California, San Diego (UCSD), United States, Bioengineering Dept., in the laboratory of Prof. Dr. Bernhard Ø. Palsson
  • Since 2011: Junior group leader at the Center for Bioinformatics (ZBIT), University of Tuebingen
  • 2010: Visiting research student at Keio University, Yokohama, Japan, in the group of Prof. Dr. Akira Funahashi
  • 2006 - 2011: 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
  • 2003: Laboratory training in the Leibniz Institute for Plant Biochemistry (IPB) in Halle (Saale) by the group of Dr. Stephan Clemens
  • 2001: Internship at the Max Planck Institute for Molecular Genetics, Berlin, at the group of Dr. Richard Reinhard
  • 2001 - 2002: Student representative of the Math and Computer Science Faculty of the Martin Luther University
  • 2000 - 2006: Studies of Bioinformatics at the Martin Luther University Halle-Wittenberg (MLU), Halle (Saale)

Awards and honors

  • Annually, 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.
  • Abitur (high-school diploma) with honors (1999), Gymnasium (high school) “Am Markt” Hettstedt, Germany

Editorial board memberships

Current projects

  • Marie-Curie International Outgoing Fellowship (IOF) as part of the 7th Framework Programme for Research and Technological Development funded by the European Union: This project with the title "automated multi-level modeling of biological systems considering physico-chemical constraints" (AMBiCon) is conducted in collaboration with the Center for Bioinformatics Tuebingen (ZBIT) that belongs to the University of Tuebingen, Germany.
  • National Institute of Health (NIH): "Continued Support of Essential SBML Software and Community Resources" in collaboration with Caltech, the University of Heidelberg, and the European Bioinformatics Institute (EBI). Our subproject focusses on the community library JSBML.

Completed projects

Publications

Journal Articles:

  • Alexander Dörr, Roland Keller, Andreas Zell, and Andreas Dräger. SBMLsimulator: a Java tool for model simulation and parameter estimation in systems biology. Computational Biology, December 2014 [ DOI | link ].
  • Andreas Dräger and Bernhard Ø. Palsson. Improving collaboration by standardization efforts in systems biology. Frontiers in Bioengineering, 2(61), December 2014. [ DOI | link ]
  • Claudine Chaouiya, Duncan Berenguier, Sarah M. Keating, Aurelien Naldi, Martijn P. van Iersel, Nicolas Rodriguez, Andreas Dräger, Finja Büchel, Thomas Cokelaer, Bryan Kowal, Benjamin Wicks, Emanuel Gonçalves, Julien Dorier, Michel Page, Pedro T. Monteiro, Axel von Kamp, Ioannis Xenarios, Hidde de Jong, Michael Hucka, Steffen Klamt, Dennis Thierffry, Nicolas Le Novère, Julio Saez-Rodriguez, and Tomáš Helikar. SBML Qualitative Models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. BMC Systems Biology, 7(1):135, December 2013. [ DOI | link | pdf ]
  • Johannes Eichner, Florian Topf, Andreas Dräger, Clemens Wrzodek, Dierk Wanke, and Andreas Zell. TFpredict and SABINE: Sequence-Based Prediction of Structural and Functional Characteristics of Transcription Factors. PLoS ONE, 8(12):e82238, December 2013. [ DOI | link | pdf ]
  • Finja Büchel, Nicolas Rodriguez, Neil Swainston, Clemens Wrzodek, Tobias Czauderna, Roland Keller, Florian Mittag, Michael Schubert, Mihai Glont, Martin Golebiewski, Martijn van Iersel, Sarah Keating, Matthias Rall, Michael Wybrow, Henning Hermjakob, Michael Hucka, Douglas B Kell, Wolfgang Müller, Pedro Mendes, Andreas Zell, Claudine Chaouiya, Julio Saez-Rodriguez, Falk Schreiber, Camille Laibe, Andreas Dräger, and Nicolas Le Novère. Path2Models: large-scale generation of computational models from biochemical pathway maps. BMC Systems Biology, 7(1):116, November 2013. [ DOI | link | PDF ]
  • Finja Büchel, Sandra Saliger, Andreas Dräger, Stephanie Hoffmann, Clemens Wrzodek, Andreas Zell, and Philipp J. Kahle. Parkinson's disease: dopaminergic nerve cell model is consistent with experimental finding of increased extracellular transport of α-synuclein. BMC Neuroscience, 14(136), November 2013. [ DOI | link | pdf ]
  • Roland Keller, Alexander Dörr, Akito Tabira, Akira Funahashi, Michael J. Ziller, Richard Adams, Nicolas Rodriguez, Nicolas Le Novère, Noriko Hiroi, Hannes Planatscher, Andreas Zell, and Andreas Dräger. The systems biology simulation core algorithm. BMC Systems Biology, 7:55, July 2013. [ DOI | link | pdf ]
  • Sebastian Vlaic, Bianca Hoffmann, Peter Kupfer, Michael Weber, and Andreas Dräger. GRN2SBML: Automated encoding and annotation of inferred gene regulatory networks complying with SBML. Bioinformatics, 29:2216-2217, June 2013. [ DOI | link | pdf ]
  • Clemens Wrzodek, Finja Büchel, Manuel Ruff, Andreas Dräger, and Andreas Zell. Precise generation of systems biology models from KEGG pathways. BMC Systems Biology, 7(1):15, January 2013. [ DOI | link | pdf ]
  • Finja Büchel, Clemens Wrzodek, Florian Mittag, Andreas Dräger, Johannes Eichner, Nicolas Rodriguez, Nicolas Le Novère, and Andreas Zell. Qualitative translation of relations from BioPAX to SBML qual. Bioinformatics, 28(20):2648-2653, August 2012. [ DOI | link | pdf ]
  • Matthias König, Andreas Dräger, and Hermann-Georg Holzhütter. CySBML: a Cytoscape plugin for SBML. Bioinformatics, 28(18):2402-2403, July 2012. [ DOI | link ]
  • 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 Villéger, 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 | link | pdf ]
  • 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 | link | pdf ]
  • 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 | link | pdf ]
  • 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 | link | pdf ]
  • 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 | link | pdf ]
  • 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 | link | pdf ]
  • Andreas Dräger, Hannes Planatscher, Dieudonné Motsou Wouamba, Adrian Schröder, Michael Hucka, Lukas Endler, Martin Golebiewski, Wolfgang Müller, and Andreas Zell. SBML2LATEX: Conversion of SBML files into human-readable reports. Bioinformatics, 25(11):1455-1456, April 2009. [ DOI | link | pdf ]
  • 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 | link | pdf ]
  • 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 | link | pdf ]
  • 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 | link | pdf ]

Book chapters:

  • Andreas Dräger and Hannes Planatscher. Encyclopedia of Systems Biology, chapter Metabolic Networks, pages 1249-1251. Springer-Verlag, New York, August 2013. [ DOI | link ]
  • Andreas Dräger and Hannes Planatscher. Encyclopedia of Systems Biology, chapter Parameter Estimation, Metabolic Network Modeling, pages 1627-1631. Springer-Verlag, New York, August 2013. [ DOI | link ]
  • 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 | link ]

Conference proceedings (peer-reviewed):

  • 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. IEEE. [ DOI | link | pdf ]
  • 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. [ pdf ]
  • 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. [ link ]
  • 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 | link ]
  • 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 | link ]
  • 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 | link ]

Technical reports:

  • 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 | link | pdf ]

Theses:

  • Andreas Dräger. Computational Modeling of Biochemical Networks. PhD thesis, University of Tuebingen, Tübingen, Germany, January 2011.
  • 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.
  • 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.

Contact Information

E-mail address: andraeger@eng.ucsd.edu

Phone: +1-858-534-9717

Mailing Address: 9500 Gilman Drive, Mail Code 0412, La Jolla, CA 92093-0412

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Location

Location

417 Powell-Focht Bioengineering Hall

9500 Gilman Drive La Jolla, CA 92093-0412

Contact Us

Contact Us

In Silico Lab:  858-822-1144

Wet Lab:  858-246-1625

FAX:   858-822-3120

Website Concerns: sbrgit@ucsd.edu

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