Jun.-Prof. Dr. Andreas Dräger

For up-to-date information, see http://draeger-lab.org.

Social Media

Twitter: https://twitter.com/dr_drae
orcid.org/0000-0002-1240-5553
YouTube: https://www.youtube.com/c/systemsbiology/

Background

Since 2018: Assistant Professor for Computational Systems Biology of Infection and Antimicrobial-Resistant Pathogens
2016 - 2018: Principal Investigator in the group of Prof. Oliver Kohlbacher at ZBIT, University of Tuebingen
2015 - 2016: Research Scholar at the Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen
2013 - 2015: Research Scholar at the University of California, San Diego (UCSD), United States, Bioengineering Dept., in the laboratory of Prof. Dr. Bernhard Ø. Palsson
2011 - 2013: 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)
1999 - 2000: Basic military service in the Special Pioneer Company PPL 300 in Höxter
1999 - 2004: Member of the local council in Welfesholz
1991 - 1999: Gymnasium (high school) “Am Markt” in Hettstedt

Research Interests

See Andreas Dräger's YouTube channel.

My special interest is the computational modeling of biochemical systems. I want to investigate and understand the complex mutual influences within living systems and am convinced 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 development of the open-source libraries JSBML, BioJava, and BioSQL
Software products: SBMLsimulator, KEGGtranslator, SBMLsqueezer, SBML2L^AT_EX, ProDGe, ModuleMaster, SABINE

Awards and honors

iGEM Bronce Award 2016 as mentor of team University of Tuebingen
Outstanding presentation award for the poster DOI issued by the F1000 Journal at Orlando, FL, USA
iGEM Gold Award 2014 as mentor of team UCSD in the category Software Development
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 (A-levels) with honors (1999), Gymnasium “Am Markt” (high school) Hettstedt, Germany

Press releases

August 31^st 2017: Modelling the essential genes of microbial life
August 11^th 2015: Minimalausstattung für den Mikroorganismus
August 10^th 2015: Bioengineers identify the key genes and functions for sustaining microbial life

Editorial board memberships

Since 2015 elected SBML editor
Since 2013 associate editor for BMC Systems Biology

Current Projects

Teach@Tübingen 2017 funded by the excellence initiative of the Federal Ministry of Education and Research
Recruitment of Excellent Junior Researchers funded by the University of Tuebingen
The following project is funded by the National Institute of Health (NIH, USA): “Continued Support of Essential SBML Software and Community Resources” in collaboration with Caltech, the University of Heidelberg, and the European Bioinformatics Institute (EBI).

Completed Projects

Projects funded by the European Union (FP7):

AMBiCon: Automated multi-level modeling of biological systems considering physico-chemical constraints (2013 - 2015, grant number 332020). This Marie Curie International Outgoing Fellowship (IOF) was conducted in conjunction with the University of California, San Diego (UCSD), Bioengineering Dept. in the Systems Biology Research Group of Prof. Bernhard Ø. Palsson.

Projects funded by the National Institutes of Health (NIH), USA:

“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.

Projects funded by the University of Tuebingen:

Inference of biochemical reaction systems considering physico-chemical constraints (2011 - 2012, project number 18017002)

Projects 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 (2010 - 2015, grant number 0315756)
German National Genome Research Network (Nationales Genomforschungsnetz, NGFN-Plus): medical genome research with focus on Parkinson's disease (2009 - 2013, grant number 01GS08134)
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 (2009 - 2012, grant number 0315384C).
HepatoSys: Systems biology of the human liver, especially detoxification processes in conjunction with statin treatment (2006 - 2010, grant number 0313080)
NGFN-II EP: Explorative Project about the reconstruction of gene-regulatory networks in the German National Genome Research Network (2005 - 2009, grant number 0313323)

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, 2006 - 2008, contract number 7532.22-26-18)
Tübinger Bioinformatik-Grid: development and application of new bioinformatics approaches and algorithms on high-performance, multiple-threading computers (2006 - 2008, contract number 23-7532.24-4-18/1).

Projects funded by companies and non-profit organizations:

Co-PI of the iGEM team at University of Tuebingen (annual synthetic biology competition)
National Resource for Network Biology Summer of Code project for the development of CySBML as a new Cytoscape App for SBML support.
Google Summer of Code 2014: an open source project for international students funded by Google. In our subproject, the Java™ library JSBML has been extended and further features were implemented. For details, see sbml.org/GSoC2014.
Mentorship in the Google Summer of Code 2010

Teaching

Practical Course: Software Engineering (2 SWS, summer 2017)
Systems Biolgy I: Properties of Reconstructed Networks (2 + 2 SWS, summer 2017)
Systems Biology: Simulation of Dynamic Network States (2 + 2 SWS, winter 2016)
Practical Course: Software Engineering (2 SWS, summer 2016)
Bioengineering 123 (2 + 2 SWS, winter quart at UCSD 2014)
Übungen Künstliche Intelligenz (2 SWS, winter, 2012)
Proseminar: Artificial Life (2 SWS, summer, 2012)
Praktikum Software Engineering (2 SWS, summer, 2012)
Seminar: Systembiologie (2 SWS, winter, 2011)
Proseminar: Moderne evolutionäre Optimierungsverfahren (2 SWS, winter, 2011)
Übungen Evolutionäre Algorithmen (2 SWS, summer, 2011)
Praktikum Software Engineering (2 SWS, summer, 2011)
Seminar: Regulatorische und metabolische Netze in der Systembiologie (2 SWS, summer, 2009)
Proseminar: Einführung in die Systembiologie (2 SWS, winter, 2008)
Seminar: Regulatorische und metabolische Netze (2 SWS, summer, 2008)
Practical Course: Software Engineering (2 SWS, summer, 2007)
Seminar: Inference of Regulatory and Metabolic Networks in Systems Biology (2 SWS, summer, 2007)
Seminar: Inferenz regulatorischer und metabolischer Netze in der Systembiolgie (2 SWS, winter, 2006)
Proseminar: Mashine Learning (2 SWS, summer, 2006)

Supervised theses

Submitted	Kind	Title (translated)	Announcement
2017	Bachelor thesis	Dynamic visualization of metabolic networks
2017	Bachelor thesis	Visualization of time-series data with Escher
2012	Bachelor thesis	Extension of SBMLsimulator with a module for flux balance analysis	[ pdf ]
2012	Bachelor thesis	Visual simulation of biochemical networks	[ pdf ]
2012	Bachelor thesis	Automatic biomodel documentation	[ pdf ]
2011	Bachelor thesis	Implementation of a flux balance analysis method in Java	[ pdf ]
2009	Bachelor thesis	Dynamics of reconstructed gene-regulatory networks	[ pdf ]
2009	Bachelor thesis	Implementation of a stability analysis for biochemical networks	[ pdf ]
2009	Diploma thesis	Automated mathematical modeling of biochemical reaction networks	[ pdf ]
2008	Diploma thesis	Comparative analysis of the models in BioModels Database	[ pdf ]
2008	Diploma thesis	Simulation of gene-regulatory networks with JCell	[ pdf ]
2008	Diploma thesis	Integration, visualization, and analysis of SNP data	[ pdf ]
2008	Student research project	Comparison of JavaEvA and BioJava with respect to metabolic networks	[ pdf ]
2007	Student research project	Metabolic control analysis
2007	Diploma thesis	Automatic generation of kinetic equations based on stoichiometries	[ pdf ]

Office hours

Mondays 11 to 12 a.m. or with individual appointment.

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 ]

Publications

Also see Andreas Dräger's bibliography at NCBI and his Google Scholar profile.

Journal publications

[1]	Bin Du, Daniel Zielinski, Andreas Dräger, Justin Tan, Zhen Zhang, Kayla Ruggiero, Garry Arzumanyan, and Bernhard O. Palsson. Evaluation of rate law approximations in bottom-up kinetic models of metabolism. BMC Systems Biology, 10(1):1--15, June 2016. [ DOI \| details \| link \| pdf ]
[2]	Melissa A. Scranton, Joseph T. Ostrand, D. Ryan Georgianna, Shane M. Lofgren, Daphne Li, Rosalie C. Ellis, David N. Carruthers, Andreas Dräger, David L. Masica, and Stephen P. Mayfield. Synthetic promoters capable of driving robust nuclear gene expression in the green alga Chlamydomonas reinhardtii. Algal Research, 15:135--142, February 2016. [ DOI \| details \| link \| pdf ]
[3]	Michael Römer, Johannes Eichner, Andreas Dräger, Clemens Wrzodek, Finja Wrzodek, and Andreas Zell. ZBIT Bioinformatics Toolbox: a Web-Platform for Systems Biology and Expression Data Analysis. PLoS ONE, 11(2):e0149263, February 2016. [ DOI \| details \| link ]
[4]	Roland Keller, Marcus Klein, Maria Thomas, Andreas Dräger, Ute Metzger, Markus F. Templin, Thomas O. Joos, Wolfgang E. Thasler, Andreas Zell, and Ulrich M. Zanger. Coordinating role of RXRα in downregulating hepatic detoxification during inflammation revealed by fuzzy-logic modeling. PLoS Computational Biology, 12(1):e1004431, January 2016. [ DOI \| details \| link ]
[5]	Zachary A. King, Justin S. Lu, Andreas Dräger, Philip C. Miller, Stephen Federowicz, Joshua A Lerman, Ali Ebrahim, Bernhard O. Palsson, and Nathan E. Lewis. BiGG Models: A platform for integrating, standardizing, and sharing genome-scale models. Nucleic Acids Research, October 2015. [ DOI \| details \| link \| pdf ]
[6]	Ali Ebrahim, Eivind Almaas, Eugen Bauer, Aarash Bordbar, Anthony P. Burgard, Roger L. Chang, Andreas Dräger, Iman Famili, Adam M. Feist, Ronan M. T. Fleming, Stephen S. Fong, Vassily Hatzimanikatis, Markus J. Herrgard, Allen Holder, Michael Hucka, Daniel Hyduke, Neema Jamshidi, Sang Yup Lee, Nicolas Le Novère, Joshua A. Lerman, Nathan E. Lewis, Ding Ma, Radhakrishnan Mahadevan, Costas Maranas, Harish Nagarajan, Ali Navid, Jens Nielsen, Lars K. Nielsen, Juan Nogales, Alberto Noronha, Csaba Pal, Bernhard O. Palsson, Jason A. Papin, Kiran R. Patil, Nathan D. Price, Jennifer L. Reed, Michael Saunders, Ryan S. Senger, Nikolaus Sonnenschein, Yuekai Sun, and Ines Thiele. Do Genome-scale Models Need Exact Solvers or Clearer Standards? Molecular Systems Biology, 11(10):831, October 2015. [ DOI \| details \| link \| pdf ]
[7]	Andreas Dräger, Daniel C. Zielinski, Roland Keller, Matthias Rall, Johannes Eichner, Bernhard O. Palsson, and Andreas Zell. SBMLsqueezer 2: Context-sensitive creation of kinetic equations in biochemical networks. BMC Systems Biology, 9(1):1--17, September 2015. [ DOI \| details \| link \| pdf ]
[8]	Michael Hucka, Frank T. Bergmann, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Lucian P. Smith, Dagmar Waltemath, and Darren J. Wilkinson. Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions. Journal of Integrative Bioinformatics, 12(2):271, September 2015. [ DOI \| details \| link \| pdf ]
[9]	Laurence Yang, Justin Tan, Edward J. O'Brien, Jonathan Monk, Donghyuk Kim, Howard J. Lia, Pep Charusantia, Ali Ebrahim, Colton J. Lloyd, James T. Yurkovich, Bin Du, Andreas Dräger, Alex Thomas, Yuekai Sun, Michael A. Saunders, and Bernhard O. Palsson. Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data. Proceedings of the National Academy of Sciences, August 2015. [ DOI \| details \| link \| pdf ]
[10]	Zachary A. King, Andreas Dräger, Ali Ebrahim, Nikolaus Sonnenschein, Nathan E. Lewis, and Bernhard O. Palsson. Escher: A web application for building, sharing, and embedding data-rich visualizations of biological pathways. PLoS Computational Biology, 11(8):e1004321, August 2015. [ DOI \| details \| link ]
[11]	Nicolas Rodriguez, Alex Thomas, Leandro Watanabe, Ibrahim Y. Vazirabad, Victor Kofia, Harold F. Gómez, Florian Mittag, Jakob Matthes, Jan D. Rudolph, Finja Wrzodek, Eugen Netz, Alexander Diamantikos, Johannes Eichner, Roland Keller, Clemens Wrzodek, Sebastian Fröhlich, Nathan E. Lewis, Chris J. Myers, Nicolas Le Novère, Bernhard Ø. Palsson, Michael Hucka, and Andreas Dräger. JSBML 1.0: providing a smorgasbord of options to encode systems biology models. Bioinformatics, June 2015. [ DOI \| arXiv \| details \| link \| pdf ]
[12]	Alexander Dörr, Roland Keller, Andreas Zell, and Andreas Dräger. SBMLsimulator: a Java tool for model simulation and parameter estimation in systems biology. Computation, 2(4):246--257, December 2014. [ DOI \| details \| link \| link ]
[13]	Andreas Dräger and Bernhard Ø. Palsson. Improving collaboration by standardization efforts in systems biology. Frontiers in Bioengineering, 2(61), December 2014. [ DOI \| details \| link \| link ]
[14]	Claudine Chaouiya, Duncan Bérenguier, Sarah M. Keating, Aurélien 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 \| arXiv \| details \| link \| pdf ]
[15]	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 \| details \| link \| link ]
[16]	Finja Büchel, Nicolas Rodriguez, Neil Swainston, Clemens Wrzodek, Tobias Czauderna, Roland Keller, Florian Mittag, Michael Schubert, Mihai Glont, Martin Golebiewski, Martijn van Iersel, Sarah M. 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 \| details \| link \| pdf ]
[17]	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 \| details \| link \| pdf ]
[18]	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 \| details \| link \| pdf ]
[19]	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 \| details \| link \| pdf ]
[20]	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 \| details \| link \| pdf ]
[21]	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 \| details \| link \| pdf ]
[22]	Matthias König, Andreas Dräger, and Hermann-Georg Holzhütter. CySBML: a Cytoscape plugin for SBML. Bioinformatics, 28(18):2402--2403, July 2012. [ DOI \| details \| link ]
[23]	Mélanie Courtot, Nick Juty, Christian Knüpfer, Dagmar Waltemath, Anna Zhukova, Andreas Dräger, Michel Dumontier, Andrew Finney, Martin Golebiewski, Janna Hastings, Stefan Hoops, Sarah M. 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 \| details \| link \| pdf ]
[24]	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 \| details \| link \| pdf ]
[25]	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 \| details \| link \| pdf ]
[26]	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 \| details \| link \| pdf ]
[27]	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 \| pdf ]
[28]	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 ]
[29]	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 \| details \| link \| pdf ]
[30]	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 ]
[31]	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 ]
[32]	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 ]

Conference proceedings (peer-reviewed)

[1]	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 \| details \| link \| pdf ]
[2]	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 ]
[3]	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 ]
[4]	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, September 2007. IEEE Computational Intelligence Society, IEEE Press. [ DOI \| details \| link \| pdf ]
[5]	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 ]
[6]	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 5^th 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 ]

Book chapters

[1]	Andreas Dräger and Hannes Planatscher. Encyclopedia of Systems Biology, chapter Metabolic Networks, pages 1249--1251. Springer-Verlag, Springer New York Heidelberg Dorodrecht London, August 2013. [ DOI \| details \| link ]
[2]	Andreas Dräger and Hannes Planatscher. Encyclopedia of Systems Biology, chapter Parameter Estimation, Metabolic Network Modeling, pages 1627--1631. Springer-Verlag, Springer New York Heidelberg Dorodrecht London, August 2013. [ DOI \| details \| link ]
[3]	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 ]

Technical reports

[1]	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 ]

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

Selected Presentations

[1]	Andreas Dräger. The ZBIT systems biology software and web service collection. 1^st SysMod Special Interest Group meeting at ISMB 2016, Orlando, FL, USA (9 July 2016). [ link ]
[2]	Andreas Dräger, Zachary A. King, Justin S. Lu, Ali Ebrahim, Nikolaus Sonnenschein, Philip C. Miller, Joshua A. Lerman, Bernhard O. Palsson, and Nathan E. Lewis. New Standard Resources for Systems Biology: BiGG 2 Database and Visual Pathway Editing with Escher. COMBINE Workshop 2015, Salt Lake City, UT, USA (13 October 2015). [ slides ]
[3]	Andreas Dräger. SED-ML in the simulation core library, COMBINE 2013, Paris, France.
[4]	Andreas Dräger. From KEGG to dynamic pathway models: a collection of tools to facilitate the modeling of biochemical networks. COMBINE 2011, Heidelberg, Germany
[5]	Andreas Dräger and Nicolas Rodriguez. JSBML—The SBML Java™ library. HARMONY Workshop 2011, New York, USA (18 April 2011).
[6]	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.
[7]	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).
[8]	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, Zachary A. King, James T. Yurkovich, Christoph Blessing, Devesh Khandelwal, Ali Ebrahim, Nikolaus Sonnenschein, Nathan E. Lewis, Bernhard O. Palsson. Visualization and creation of biochemical networks with Escher [version 1; not peer reviewed]. F1000Research 2017, 6(ISCB Comm J):1570 [ DOI ]
[2]	Andreas Dräger, Zachary A. King, Justin S. Lu et al. New standard resources for systems biology: BiGG Models database and the visual pathway editor Escher [v1; not peer reviewed]. Presented at the BioVis Special Interest Group meeting at ISMB 2016 in Orlando, FL, USA, 6^th Conference on Systems Biology of Mammalian Cells (SBMC) 2016 in Munich, Germany, the 6^th Conference on Modeling Biological Networks (COMBINE) 2015 in Salt Lake City, UT, USA F1000Research 2016, 5:1928 [ DOI \| PDF ]
[3]	Alex Thomas, Andreas Dräger, and Nathan Lewis. Using Time Course Metabolomics to Elucidate Genome-Scale Pathway Utilization for CHO-S Cell Lines in Batch Culture Hackathon on Resources for Modeling in Biology (HARMONY 2015), Wittenberg, Germany (22-25 April 2015). [details \| PDF ]
[4]	Nicolas Rodriguez, Alex Thomas, Michael Hucka, Nicolas Le Novère, Bernhard Ø Palsson, and Andreas Dräger Support for Flux Balance Constraints Models in JSBML. 3^rd Conference on Constraint-Based Reconstruction and Analysis, Charlottesville, VA, USA (20-23 May 2014).
[5]	Roland Keller, Marcus Klein, Maria Thomas, Ute Metzger, Markus F. Templin, Thomas O. Joos, Stephanie Hoffmann, Benjamin Kandel, Andreas Dräger, Ulrich M. Zanger, and Andreas Zell. Modelling IL-6 mediated regulation of ADME genes. 20^th International Symposium on Microsomes and Drug Oxidations, 2014. [ link ]
[6]	Andreas Dräger, Ute Hofmann, Roland Keller, Stephanie Tscherneck, Benjamin Kandel, Maria Thomas, Marcus Klein, Klaus Maier, Klaus Mauch, Ulrich M. Zanger and Andreas Zell. Modeling and simulating the effects of atorvastatin on the central carbon metabolism of rat hepatocytes using SBMLsimulator. 4^th Conference on Systems Biology of Mammalian Cells (SBMC), 2012. [ pdf ]
[7]	Nicolas Rodriguez, Marine Dumousseau, Andreas Dräger, Clemens Wrzodek, Alexander Dörr, Sarah M. Keating, Akiya Jouraku, Nicolas Le Novère, Andreas Zell, and Michael Hucka. JSBML: a flexible and entirely Java-based library for working with SBML. COMBINE 2010, Edinburgh, UK. [ details \| pdf ]
[8]	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

Eberhard-Karls-Universität Tübingen

Wilhelm-Schickard-Institut für Informatik

Abteilung Kognitive Systeme

Sand 14 #C320

72076 Tübingen

Germany

Phone:	+49-7071-29-70459
Fax:	+49-7071-29-5152
E-Mail:	draeger@informatik.uni-tuebingen.de