Dr. Andreas Dräger

Assistant Professor for Computational Systems Biology of Infections and Antimikrobial-Resistant Pathogens

Office

Department for Computer Science
Center for Bioinformatics Tübingen (ZBIT)
Sand 14 ・ 2nd floor ・ Office C320
 +49 7071 29-70459
draegerspam prevention@informatik.uni-tuebingen.de

Bibliography

Google-Scholar-Profil
NCBI-Pubmed-Profil

Social Media

Twitter-Channel
YouTube-Channel
ORCID Profile
GitHub Profile
Publons Profile

Office Hours

Mondays
10:00 to 12:00 a.m.
or by appointment


Research

Main Focus

The working group develops and uses computer models to investigate two major topics:

  1. Optimization of biotechnological processes
  2. Origin and course of diseases at the molecular level

By simulating these models, a better understanding of the complex interactions that take place inside living organisms and their microbial ecosystems can be gained. The work is divided into:

  • Systems biology modeling, in particular, the dynamics of biological networks, including metabolic, signal transduction and gene regulatory networks using a variety of technologies including machine learning
  • Development of efficient algorithms for model creation, simulation, and calibration
  • Application and development of open source software, libraries, and standards for the representation and efficient processing of models
  • Mapping of biological data on models for visualization and interpretation of results

Current research projects

Computational Systems Biology of Infections and Antimicrobial-Resistant Pathogens

Completed Research Projects

Completed Research Projects

Student Projects
Projects funded by the University of Tübingen from the Excellence Initiative of the Federal Ministry of Education and Research (BMBF)
  • Teach@Tübingen 2017 on the internationalization and diversification of the university's educational offer
  • Recruitment of excellent junior researchers funded by the University of Tübingen

Previous Research Projects

Projects funded by the European Union (FP7)
Project funded by the University of Tübingen
Student projects for open-source software
Projects funded by the Federal Ministry of Research and Education (BMBF)
  • The Virtual Liver: A project with the goal of creating a comprehensive model of the human liver (2010 - 2015, funding reference 0315756).
  • National Genome Research Network (NGFN-Plus): medical genome research with focus on the Parkinson's disease (2009 - 2013, funding reference 01GS08134).
  • Spher4Sys: a systems biology-based approach for the preclinical development of lead structures using an in vivo-like spheroid test system. This project contributes to the network of medical systems biology (MedSys, 2009 - 2012, funding reference 0315384C).
  • HepatoSys: Systems biology of the human liver, in particular the detoxification processes in connection with statin treatment (2006 - 2010, funding reference 0313080).
  • NGFN-II EP: Explorative Project for the Reconstruction of Gene Regulatory Networks in the National Genome Research Network (2005 - 2009, funding reference 0313323).
Projects funded by the state of Baden-Württemberg

Curriculum Vitae

Since 2018
Assistant Professor

at the University of Tübingen with focus on computational systems biology of infections and antimicrobiall-resistant pathogens

2017
Awarded the Baden-Württemberg certificate for university didactics

Qualification as a university teacher by the University Didactics Center of the Universities of Baden-Wuerttemberg.

2016-2018
Principal investigator and lecturer

in the Chair of Applied Bioinformatics at the Centre for Bioinformatics (ZBIT) at the University of Tübingen, headed by Prof. Dr.-Ing. Oliver Kohlbacher

2015-2016
Postdoctoral fellow

in the research group for cognitive systems led by Prof. Dr. Andreas Zell at the Institute of Computer Science at the University of Tübingen

2013-2015
Research scholar in San Diego

at the University of California, San Diego (UCSD), in Prof. Dr. Bernhard Ø. Palsson's Systems Biology Research Group within the Department of Bioengineering

2011-2013
Junior research group leader

at the Center for Bioinformatics (ZBIT) at the University of Tübingen

2011
Doctorate with distinction

Dissertation Award of the Year of the Faculty of Mathematics and Natural Sciences of the University of Tübingen

2010
Visiting Ph.D. student in Yokohama

in the working group of Prof. Dr. Akira Funahashi at the Institute of Biosciences and Computer Science at Keio University in Yokohama, Japan

2006-2011
Research Assistant and Doctoral Candidate

in the Department of Computer Architecture at the Institute of Computer Science of the University of Tübingen

2006
Diploma in Bioinformatics

at the Martin-Luther-University Halle-Wittenberg in Halle (Saale)

2004
Research Internship in Chicago

in Prof. Dr. Simon Silvers' research group at the Institute of Microbiology and Immunology at the University of Illinois, Chicago

2003
Pre-diploma in Bioinformatics

at the Martin-Luther-University Halle-Wittenberg in Halle (Saale)

2001-2002
Elected student representative

Member of the Student Council of the Institute for Mathematics and Computer Science of the Martin Luther University Halle-Wittenberg

2001
Working student in Berlin (Dahlem)

in the research group of Dr. Richard Reinhard at the Max Planck Institute for Molecular Genetics

2000-2006
Study of Bioinformatics

at the Martin-Luther-University Halle-Wittenberg in Halle (Saale)

1999
High school graduation with distinction

High School "Wilhelm and Alexander von Humboldt" in Hettstedt


Awards and Honors

  1. iGEM bronze medal 2016 as mentor of the team of the University of Tübingen
  2. Award for an excellent presentation of the F1000 journal in Orlando, Florida, USA, for the poster about Escher and the BiGG models data base [ DOI ]
  3. iGEM gold medal 2014 for software development in the team of the University of California, San Diego (UCSD)
  4. Dissertation prize 2011 of the Faculty of Science of the University of Tübingen
  5. High school graduation with distinction by the high school "Alexander and Wilhelm von Humboldt" in Hettstedt

Publications and Talks

Monographs (theses)

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

Journal Articles

  1. Community standards to facilitate development and address challenges in metabolic modeling
    Maureen A. Carey, Andreas Dräger, Jason A. Papin, and James T. Yurkovich.
    bioRxiv, July 15th 2019.​​​​​​​
    DOI​​​​​​​ | PDF ]​​​​​​​
  2. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2
    Michael Hucka, Frank T. Bergmann, Claudine Chaouiya, Andreas Dräger, Stefan Hoops, Sarah M. Keating, Matthias König, Nicolas Le Novère, Chris J. Myers, Brett G. Olivier, Sven Sahle, James C. Schaff, Rahuman Sheriff, Lucian P. Smith, Dagmar Waltemath, Darren J. Wilkinson, and Fengkai Zhang.
    Journal of Integrative Bioinformatics, June 20th 2019.
    [ Details | DOI | Link | PubMed | BibTeX ]
  3. Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0
    Adrien Rougny, Vasundra Touré, Stuart Moody, Irina Balaur, Tobias Czauderna, Hanna Borlinghaus, Ugur Dogrusoz, Alexander Mazein, Andreas Dräger, Michael L. Blinov, Alice C. Villéger, Robin Haw, Emek Demir, Huaiyu Mi, Anatoly Sorokin, Falk Schreiber und Augustin Luna.
    Journal of Integrative Bioinformatics, June 13th 2019.
    [ Details | DOI | Link | PubMed | BibTeX ]
  4. The 2017 Network Tools and Applications in Biology (NETTAB) Workshop: aims, topics, and outcomes
    Paolo Romano, Arnaud Céol, Andreas Dräger, Antonino Fiannaca, Rosalba Giugno, Massimo La Rosa, Luciano Milanesi, Ulrich Pfeffer, Riccardo Rizzo, Soo-Yong Shin, Junfeng Xia, and Alfonso Urso
    BMC Bioinformatics, April 18th 2019.
    [ Details | DOI | PDF | PubMed | BibTeX ]
  5. Harmonizing semantic annotations for computational models in biology
    Maxwell L Neal,  Matthias König, David Nickerson, Göksel Mısırlı, Reza Kalbasi, Andreas Dräger, Koray Atalag, Vijayalakshmi Chelliah, Michael Cooling, Daniel L Cook, Sharon Crook, Miguel de Alba, Samuel H Friedman, Alan Garny, John H Gennari,  Padraig Gleeson, Martin Golebiewski, Michael Hucka, Nick Juty, Chris Myers, Brett G Olivier, Herbert M Sauro, Martin Scharm, Jacky L Snoep, Vasundra Touré, Anil Wipat, Olaf Wolkenhauer, and Dagmar Waltemath. Briefings in Bioinformatics, November 2018.
    [ DetailsDOI | PDF | BioRxiv | PubMed | BibTeX ]
  6. Visualizing metabolic network dynamics through time-series metabolomics data
    Lea F. Buchweitz, James T. Yurkovich, Christoph Blessing, Veronika Kohler, Fabian Schwarzkopf, Zachary A. King, Laurence Yang, Freyr Jóhannsson, Ólafur Sigurjónsson, Óttar Rolfsson, Julian Heinrich, and Andreas DrägerbioRxiv, 26. September 2018.
    [ DOI | PDF ]
  7. Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655
    Ye Gao, James T. Yurkovich, Sang Woo Seo, Ilyas Kabimoldayev, Andreas Dräger, Ke Chen, Anand V. Sastry, Xin Fang, Nathan Mih, Laurence Yang, Johannes Eichner, Byung-Kwan Cho, Donghyuk Kim und Bernhard O Palsson. Nucleic Acids Research, August 23th 2018.
    DOI | link | PDF | PubMed | BibTeX ]
  8. Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite
    Christian Lieven, Moritz Emanuel Beber, Brett G. Olivier, Frank T. Bergmann, Parizad Babaei, Jennifer A. Bartell, Lars M. Blank, Siddharth Chauhan, Kevin Correia, Christian Diener, Andreas Dräger, Birgitta Elisabeth Ebert, Janaka N. Edirisinghe, Ronan M. T. Fleming, Beatriz Garcia-Jimenez, Wout van Helvoirt, Christopher Henry, Henning Hermjakob, Markus J. Herrgård, Hyun Uk Kim, Zachary A. King, Jasper Jan Koehorst, Steffen Klamt, Edda Klipp, Meiyappan Lakshmanan, Nicolas Le Novère, Dong-Yup Lee, Sang Yup Lee, Sunjae Lee, Nathan E. Lewis, Hongwu Ma, Daniel Machado, Radhakrishnan Mahadevan, Paulo Maia, Adil Mardinoglu, Greg L. Medlock, Jonathan Monk, Jens Nielsen, Lars K. Nielsen, Juan Nogales, Intawat Nookaew, Osbaldo Resendis, Bernhard O. Palsson, Jason A. Papin, Kiran Raosaheb Patil, Nathan D. Price, Anne Richelle, Isabel Rocha, Peter Schaap, Rahuman S. Malik Sheriff, Saeed Shoaie, Nikolaus Sonnenschein, Bas Teusink, Paulo Vilaca, Jon Olav Vik, Judith A. Wodke, Joana C. Xavier, Qianqian Yuan, Maksim Zakhartsev, and Cheng Zhang. BioRxiv, June 21st 2018.
    [ DOI | PDF ]
  9. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core
    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. Journal of Integrative Bioinformatics, April 26th 2018.
    DOI | link | PDF ]
  10. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core
    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. Journal of Integrative Bioinformatics, March 9th 2018.
    DOI | link | PDF ]
  11. Recon3D enables a three-dimensional view of gene variation in human metabolism
    Elizabeth Brunk, Swagatika Sahoo, Daniel C Zielinski, Ali Altunkaya, Andreas Dräger, Nathan Mih, Francesco Gatto, Avlant Nilsson, German Andres Preciat Gonzalez, Maike Kathrin Aurich, Andreas Prlić, Anand Sastry, Anna D Danielsdottir, Almut Heinken, Alberto Noronha, Peter W Rose, Stephen K Burley, Ronan M T Fleming, Jens Nielsen, Ines Thiele, and Bernhard O Palsson. Nature Biotechnology, February 19th 2018.
    DOI | link | PDF ]
  12. A Padawan Programmer's Guide to Developing Academic Software Libraries
    James T. Yurkowich, Benjamin J. Jurkowich, Andreas Dräger, Bernhard O. Palsson, and Zachary A. King. Cell Systems, October 2017.
    DOI | link | PDF ]
  13. Evaluation of rate law approximations in bottom-up kinetic models of metabolism
    Bin Du, Daniel Zielinski, Andreas Dräger, Justin Tan, Zhen Zhang, Kayla Ruggiero, Garry Arzumanyan, and Bernhard O. Palsson. BMC Systems Biology, 10(1):1-15, June 2016.
    DOI | link | PDF ]
  14. Synthetic promoters capable of driving robust nuclear gene expression in the green alga Chlamydomonas reinhardtii
    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. Algal Research, 15:135-142, February 2016.
    DOI | link | PDF ]
  15. ZBIT Bioinformatics Toolbox: a Web-Platform for Systems Biology and Expression Data Analysis
    Michael Römer, Johannes Eichner, Andreas Dräger, Clemens Wrzodek, Finja Wrzodek, and Andreas Zell. PLoS ONE, 11(2):e0149263, February 2016.
    DOI | link ]
  16. Coordinating role of RXRα in downregulating hepatic detoxification during inflammation revealed by fuzzy-logic modeling
    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. PLoS Computational Biology, 12(1):e1004431, January 2016.
    DOI | link ]
  17. BiGG Models: A platform for integrating, standardizing und sharing genome-scale models
    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. Nucleic Acids Research, October 2015.
    DOI | link | PDF ]
  18. Do Genome-scale Models Need Exact Solvers or Clearer Standards?
    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. Molecular Systems Biology, 11(10):831, October 2015.
    DOI | link | PDF ]
  19. SBMLsqueezer 2: Context-sensitive creation of kinetic equations in biochemical networks
    Andreas Dräger, Daniel C. Zielinski, Roland Keller, Matthias Rall, Johannes Eichner, Bernhard O. Palsson, and Andreas Zell. BMC Systems Biology, 9(1):1-17, September 2015.
    DOI | link | PDF ]
  20. Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions
    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. Journal of Integrative Bioinformatics, 12(2):271, September 2015.
    DOI | link | PDF ]
  21. Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data
    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. Proceedings of the National Academy of Sciences, August 2015.
    DOI | link | PDF ]
  22. Escher: A web application for building, sharing, and embedding data-rich visualizations of biological pathways
    Zachary A. King, Andreas Dräger, Ali Ebrahim, Nikolaus Sonnenschein, Nathan E. Lewis, and Bernhard O. Palsson. PLoS Computational Biology, 11(8):e1004321, August 2015.
    DOI | link ]
  23. JSBML 1.0: providing a smorgasbord of options to encode systems biology models
    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 DrägerBioinformatics, June 2015.
    DOI | arXiv | link | PDF ]
  24. SBMLsimulator: a Java tool for model simulation and parameter estimation in systems biology
    Alexander Dörr, Roland Keller, Andreas Zell und Andreas DrägerComputation, 2(4):246-257, December 2014.
    DOI | link | PDF ]
  25. Improving collaboration by standardization efforts in systems biology
    Andreas Dräger and Bernhard Ø. Palsson. Frontiers in Bioengineering, 2(61), December 2014.
    DOI | link | PDF ]
  26. SBML Qualitative Models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools
    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. BMC Systems Biology, 7(1):135, December 2013.
    DOI | arXiv | link | PDF ]
  27. TFpredict and SABINE: Sequence-Based Prediction of Structural and Functional Characteristics of Transcription Factors
    Johannes Eichner, Florian Topf, Andreas Dräger, Clemens Wrzodek, Dierk Wanke, and Andreas Zell. PLoS ONE, 8(12):e82238, December 2013.
    DOI | link | PDF ]
  28. Path2Models: large-scale generation of computational models from biochemical pathway maps
    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. BMC Systems Biology, 7(1):116, November 2013.
    DOI | link | PDF ]
  29. Parkinson's disease: dopaminergic nerve cell model is consistent with experimental finding of increased extracellular transport of α-synuclein
    Finja Büchel, Sandra Saliger, Andreas Dräger, Stephanie Hoffmann, Clemens Wrzodek, Andreas Zell, and Philipp J. Kahle. BMC Neuroscience, 14(136), November 2013.
    DOI | link | PDF ]
  30. The systems biology simulation core algorithm
    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 DrägerBMC Systems Biology, 7:55, July 2013.
    DOI | link | PDF ]
  31. GRN2SBML: Automated encoding and annotation of inferred gene regulatory networks complying with SBML
    Sebastian Vlaic, Bianca Hoffmann, Peter Kupfer, Michael Weber, and Andreas Dräger. Bioinformatics, 29:2216-2217, June 2013.
    DOI | link | PDF ]
  32. Precise generation of systems biology models from KEGG pathways
    Clemens Wrzodek, Finja Büchel, Manuel Ruff, Andreas Dräger, and Andreas Zell. BMC Systems Biology, 7(1):15, January 2013.
    DOI | link | PDF ]
  33. Qualitative translation of relations from BioPAX to SBML qual
    Finja Büchel, Clemens Wrzodek, Florian Mittag, Andreas Dräger, Johannes Eichner, Nicolas Rodriguez, Nicolas Le Novère, and Andreas Zell. Bioinformatics, 28(20):2648-2653, August 2012.
    DOI | link | PDF ]
  34. CySBML: a Cytoscape plugin for SBML
    Matthias König, Andreas Dräger, and Hermann-Georg Holzhütter. Bioinformatics, 28(18):2402-2403, July 2012.
    DOI | link ]
  35. Controlled vocabularies and semantics in systems biology
    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. Molecular Systems Biology, 7(1):543, September 2011.
    DOI | link | PDF ]
  36. Inferring statin-induced gene regulatory relationships in primary human hepatocytes
    Adrian Schröder, Johannes Wollnik, Clemens Wrzodek, Andreas Dräger, Michael Bonin, Oliver Burk, Maria Thomas, Wolfgang E. Thasler, Ulrich M. Zanger, and Andreas Zell. Bioinformatics, 27(18):2473-2477, July 2011.
    DOI | link | PDF ]
  37. JSBML: a flexible Java library for working with SBML
    Andreas Dräger, Nicolas Rodriguez, Marine Dumousseau, Alexander Dörr, Clemens Wrzodek, Nicolas Le Novère, Andreas Zell, and Michael Hucka. Bioinformatics, 27(15):2167-2168, June 2011.
    DOI | link | PDF ]
  38. KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats
    Clemens Wrzodek, Andreas Dräger, and Andreas Zell. Bioinformatics, 27(16):2314-2315, June 2011.
    DOI | link | PDF ]
  39. ModuleMaster: A new tool to decipher transcriptional regulatory networks
    Clemens Wrzodek, Adrian Schröder, Andreas Dräger, Dierk Wanke, Kenneth W. Berendzen, Marcel Kronfeld, Klaus Harter, and Andreas Zell. Biosystems, 99(1):79-81, January 2010.
    DOI | link | PDF ]
  40. BowTieBuilder: modeling signal transduction pathways
    Jochen Supper, Lucía Spangenberg, Hannes Planatscher, Andreas Dräger, Adrian Schröder, and Andreas Zell. BMC Systems Biology, 3(1):67, June 2009.
    DOI | link | PDF ]
  41. SBML2LaTeX: Conversion of SBML files into human-readable reports
    Andreas Dräger, Hannes Planatscher, Dieudonné Motsou Wouamba, Adrian Schröder, Michael Hucka, Lukas Endler, Martin Golebiewski, Wolfgang Müller, and Andreas Zell. Bioinformatics, 25(11):1455-1456, April 2009.
    DOI | link | PDF ]
  42. Modeling metabolic networks in C. glutamicum: a comparison of rate laws in combination with various parameter optimization strategies
    Andreas Dräger, Marcel Kronfeld, Michael J. Ziller, Jochen Supper, Hannes Planatscher, Jørgen B. Magnus, Marco Oldiges, Oliver Kohlbacher, and Andreas Zell. BMC Systems Biology, 3(5):5, January 2009.
    DOI | link | PDF ]
  43. BioJava: an open-source framework for bioinformatics
    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. Bioinformatics, 24(18):2096-2097, August 2008.
    DOI | link | PDF ]
  44. SBMLsqueezer: a CellDesigner plug-in to generate kinetic rate equations for biochemical networks
    Andreas Dräger, Nadine Hassis, Jochen Supper, Adrian Schröder, and Andreas Zell. BMC Systems Biology, 2(1):39, April 2008.
    DOI | link | PDF ]

Conference Proceedings

  1. Inferring transcriptional regulators for sets of co-expressed genes by multi-objective evolutionary optimization.
    Adrian Schröder, Clemens Wrzodek, Johannes Wollnik, Andreas Dräger, Dierk Wanke, Kenneth W. Berendzen, and Andreas Zell. In IEEE Congress on Evolutionary Computation (CEC 2011), New Orleans, USA, June 2011. IEEE. [ DOI | link | PDF ]
  2. Network inference by considering multiple objectives: Insights from in vivo transcriptomic data generated by a synthetic network.
    Sandro Lambeck, Andreas Dräger, and Reinhard Guthke. 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 ]
  3. On the Benefits of Multimodal Optimization for Metabolic Network Modeling.
    Marcel Kronfeld, Andreas Dräger, Moritz Aschoff, and Andreas Zell. In Ivo Grosse, Steffen Neumann, Stefan Posch, Falk Schreiber, and Peter Stadler (editors) German Conference on Bioinformatics (GCB 2009), volume P-157 of the Lecture Notes in Informatics, pages 191-200, Halle (Saale), Germany, September 2009. German Society for Computer Science. [ link | PDF ]
  4. 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 B. Magnus, Marco Oldiges, and Andreas Zell. In Dipti Srinivasan und Lipo Wang (editors), IEEE Congress on Evolutionary Computation (CEC 2007), pages 896-903, Singapore, September 2007. IEEE Computational Intelligence Society, IEEE Press. [ DOI | link | PDF ]
  5. Comparing Various Evolutionary Algorithms on the Parameter Optimization of the Valine and Leucine Biosynthesis in Corynebacterium glutamicum.
    Andreas Dräger, Jochen Supper, Hannes Planatscher, Jørgen B. Magnus, Marco Oldiges, and Andreas Zell. In Dipti Srinivasan and Lipo Wang, Editoren, IEEE Congress on Evolutionary Computation (CEC 2007), pages 620-627, Singapore, September 2007. IEEE Computational Intelligence Society, IEEE Press. [ DOI | link | PDF ]
  6. Inferring gene regulatory networks by machine learning methods.
    Jochen Supper, Holger Fröhlich, Christian Spieth, Andreas Dräger, and Andreas Zell. 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, Januar 2007. Imperial College Press. [ DOI | link | PDF ]

Book Chapters

  1. Insights into Dynamic Network States Using Metabolomics Data.
    Reihaneh Mostolizadeh​​​​​Andreas Dräger and Neema Jamshidi. In: Angelo D’Alessandro (eds) High-Throughput Metabolomics. Methods in Molecular Biology, volume 1978, Chapter, pages 243-258. Humana, New York, NY, May 2019. [ DetailsDOI | link | PubMed | BibTex ]
  2. Metabolic Networks.
    Andreas Dräger and Hannes Planatscher. Encyclopedia of Systems Biology, Chapter, pages 1249-1251. Springer-Verlag, Springer New York Heidelberg Dorodrecht London, August 2013. [ DOI | link ]
  3. Parameter Estimation, Metabolic Network Modeling.
    Andreas Dräger and Hannes Planatscher. Encyclopedia of Systems Biology, Chapter, pages 1627-1631. Springer-Verlag, Springer New York Heidelberg Dorodrecht London, August 2013. [ DOI | link ]
  4. Automating mathematical modeling of biochemical reaction networks.
    Andreas Dräger, Adrian Schröder und Andreas Zell. Systems Biology for Signaling Networks, volume 1 of Systems Biology, chapter, pages 159-205. Springer-Verlag, July 2010. [ DOI | link ]

Technical Reports

  1. ProDGe: investigating protein-protein interactions at the domain level.
    Finja Büchel, Clemens Wrzodek, Florian Mittag, Andreas Dräger, Adrian Schröder, and Andreas Zell. Technical Report, Nature Precedings, August 2011. [ DOI | link | PDF ]

Selected Talks

  1. InSilico: an Eclipse-based framework for plugin-development and standards interoperability
    Andreas Dräger, Roman Schulte, and Matthias König, HARMONY 2019​​​​​​​, Pasadena, CA, USA (25. März 2019)
  2. Visualizing Metabolic Network Dynamics through Time-Series Metabolomics Data
    Lea F. Buchweitz, James T. Yurkovich, Christoph M. Blessing, Veronika Kohler, Fabian Schwarzkopf, Zachary A. King, Laurence Yang, Freyr Jóhannsson, Ólafur Sigurjónsson, Óttar Rolfsson, Julian Heinrich, and Andreas Dräger, COMBINE 2018, Boston, MA, USA (October 10th 2018)
  3. Representation of ME-Models in SBML
    Marc Alexander Voigt, Colton J. Lloyd, Laurence Yang, Zachary A. King, Oliver Kohlbacher, Kay Nieselt, and Andreas Dräger, COMBINE 2018, Boston, MA, USA (October 11th 2018)
  4. Model-Based Prediction of Yersinia enterocolitica Infection Outcome
    Janina Geißert, Martin Eichner, Erwin Bohn, Reihaneh MostolizadehAndreas Dräger, Ingo B. Autenrieth, Sina Beier, and Monika Schütz, COMBINE 2018, Boston, MA, USA (October 11th 2018)
  5. Modeling of Potentially Virulence-Associated Metabolic Pathways in Pseudomonas aeruginosa PA14 Including Experimental Verification
    Alina Renz, Erwin Bohn, Monika Schütz, and Andreas Dräger, COMBINE 2018, Boston, MA, USA (October 12th 2018)
  6. Visualization and Creation of Biochemical Networks with Escher
    Andreas Dräger, Zachary A. King, James T. Yurkovich, Christoph Blessing, Devesh Khandelwal, Ali Ebrahim, Nikolaus Sonnenschein, Nathan E. Lewis, and Bernhard O. Palsson  COMBINE 2017, Mailand, Italien (October 11th 2017).
  7. The JSBML project: a fully featured Java API for working with systems biological models
    Nicolas Rodriguez, Thomas M. Hamm, Roman Schulte, Leandro Watanabe, Ibrahim Y. Vazirabad, Victor Kofia, Chris J. Myers, Akira Funahashi, Nicolas Le Novère, Michael Hucka und Andreas DrägerCOMBINE 2017, Milan, Italy (October 10th 2017).
  8. Visualization and Creation of Biochemical Networks with Escher
    Andreas Dräger, Zachary A. King, James T. Yurkovich, Christoph Blessing, Devesh Khandelwal, Ali Ebrahim, Nikolaus Sonnenschein, Nathan E. Lewis, Bernhard O. Palsson. BioVis Special Interest Group meeting during ISMB 2017 in Prag, Czech Republic (July 24th 2017).
  9. The ZBIT Systems Biology Software and Web-Service Collection
    Andreas Dräger, eingeladener Vortrag, Helmholtz-Zentrum München, Germany (November 15th 2016).
  10. The ZBIT Systems Biology Software and Web-Service Collection
    Andreas Dräger​​​​​​​, COMBINE 2016, Newcastle, UK (Setember 21st 2016). [ Folien ]
  11. The ZBIT Systems Biology Software and Web-Service Collection
    Andreas Dräger​​​​​​​​​​​​​​, eingeladener Vortrag, Universität Luxemburg, Esch Belval, Luxemburg (September 1st 2016).
  12. Biochemical Pathways and Large-Scale Metabolic Networks
    Andreas Dräger​​​​​​​​​​​​​​ und Nathan E. Lewis - Lecture day on reconstruction and modeling of metabolic systems at genome-scale Summer School, eingeladener Vortrag, SIB Siwss Institut für Bioinformatik, Lausanne, Schweitz (August 30th 2016).
  13. The ZBIT systems biology software and web service collection
    Andreas Dräger​​​​​​​​​​​​​​. First SysMod Special Interest Group meeting during ISMB 2016, Orlando, FL, USA (July 9th 2016). [ DOI | Slides ]
  14. New Standard Resources for Systems Biology: BiGG 2 Database and Visual Pathway Editing with Escher
    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. COMBINE 2015, Salt Lake City, UT, USA (October 13th 2015). [ Slides ]
  15. SED-ML in the simulation core library
    Andreas Dräger​​​​​​​​​​​​​​. COMBINE 2013, Paris, Frankreich.
  16. From KEGG to dynamic pathway models: a collection of tools to facilitate the modeling of biochemical networks
    Andreas Dräger​​​​​​​​​​​​​​. COMBINE 2011, Heidelberg, Deutschland.
  17. JSBML—The SBML Java™ library
    Andreas Dräger​​​​​​​​​​​​​​ and Nicolas Rodriguez. HARMONY Workshop 2011, invited talk, New York, USA (April 18th 2011).
  18. Context-based generation of kinetic equations with SBMLsqueezer 1.3
    Andreas Dräger​​​​​​​​​​​​​​, Sandra Nitschmann, Alexander Dörr, Johannes Eichner, Michael J. Ziller, and Andreas Zell. COMBINE 2010, Edinburgh (October 9th 2010). [ Slides ]
  19. Inferring Genetic Networks from Gene Expression Data
    Andreas Dräger​​​​​​​​​​​​​​, Nora Speer, Christian Spieth, Jochen Supper, and Andreas Zell. Biotechnica 2009International Trade Fair for Biotechnology, invited talk, Hannover, Germany (October 8th 2009).
  20. Metabolic modeling of Corynebacterium glutamicum: a comparison of rate laws in combination with various parameter optimization strategies
    Andreas Dräger​​​​​​​​​​​​​​, Marcel Kronfeld, Michael J Ziller, Jochen Supper, Hannes Planatscher, Jørgen B Magnus, Marco Oldiges, Oliver Kohlbacher, and Andreas Zell. ACHEMA 200929. international exhibition congress for chemical technique, environmental protection and biotechnology, invited talk, Frankfurt (Main), Deutschland (May 13th 2009).

Selected Posters

  1. Representation of ME-Models in SBML
    Marc Alexander Voigt, Colton J. Lloyd, Laurence Yang, Zachary A. King, Oliver Kohlbacher, Kay Nieselt, and Andreas Dräger
    COBRA 2018, Seattle, WA, USA
  2. Metabolic Network Reconstruction of Treponema pallidum ssp. pallidum
    Silvia Morini, Isabella Casini, Reihaneh Mostolizadeh, Thomas M. Hamm, Kay Nieselt, and Andreas Dräger
    COBRA 2018, Seattle, WA, USA
  3. Modeling of Potentially Virulence-Associated Metabolic Pathways in Pseudomonas aeruginosa PA14 Including Experimental Verification
    Alina Renz, Erwin Bohn, Monika Schütz, and Andreas Dräger
    COBRA 2018, Seattle, WA, USA
  4. Model-based Prediction of Yersinia enterocolitica Infection Outcome
    Janina Geißert, Martin Eichner, Erwin Bohn, Reihaneh Mostolizadeh, Andreas Dräger, Ingo B. Autenrieth, Sina Beier, and Monika Schütz
    SysMod Special Interest Group Meeting during ISMB 2018 in Chicago, Il, USA.
  5. Visualization and creation of biochemical networks with Escher
    Andreas Dräger, Zachary A. King, James T. Yurkovich, Christoph Blessing, Devesh Khandelwal, Ali Ebrahim, Nikolaus Sonnenschein, Nathan E. Lewis, and Bernhard O. Palsson. [version 1; not peer reviewed]. F1000Research 2017, 6(ISCB Comm J):1570 [ DOI ]
  6. New standard resources for systems biology: BiGG Models database and the visual pathway editor Escher
    Andreas Dräger, Zachary A. King, Justin S. Lu et al. [v1; not peer reviewed]. Presented at the BioVis Special Interest Group meeting at ISMB 2016 in Orlando, FL, USA, 6th Conference on Systems Biology of Mammalian Cells (SBMC) 2016 in Munich, Germany, the 6th Conference on Modeling Biological Networks (COMBINE) 2015 in Salt Lake City, UT, USA F1000Research 2016, 5:1928 [ DOI | PDF ]
  7. Using Time Course Metabolomics to Elucidate Genome-Scale Pathway Utilization for CHO-S Cell Lines in Batch Culture
    Alex Thomas, Andreas Dräger, and Nathan Lewis. Hackathon on Resources for Modeling in Biology (HARMONY 2015), Wittenberg, Germany (22.-25. April 2015). [PDF ]
  8. Support for Flux Balance Constraints Models in JSBML
    Nicolas Rodriguez, Alex Thomas, Michael Hucka, Nicolas Le Novère, Bernhard Ø Palsson, and Andreas Dräger. 3rd Conference on Constraint-Based Reconstruction and Analysis, Charlottesville, VA, USA (20.-23. Mai 2014). 
  9. Modelling IL-6 mediated regulation of ADME genes
    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. 20th International Symposium on Microsomes and Drug Oxidations, 2014. [ link ]
  10. Modeling and simulating the effects of atorvastatin on the central carbon metabolism of rat hepatocytes using SBMLsimulator
    Andreas Dräger​​​​​​​, Ute Hofmann, Roland Keller, Stephanie Tscherneck, Benjamin Kandel, Maria Thomas, Marcus Klein, Klaus Maier, Klaus Mauch, Ulrich M. Zanger, and Andreas Zell. 4th Conference on Systems Biology of Mammalian Cells (SBMC), 2012. [ PDF ]
  11. JSBML: a flexible and entirely Java-based library for working with SBML
    Nicolas Rodriguez, Marine Dumousseau, Andreas Dräger​​​​​​​​​​​​​​, Clemens Wrzodek, Alexander Dörr, Sarah M. Keating, Akiya Jouraku, Nicolas Le Novère, Andreas Zell, and Michael Hucka. COMBINE 2010, Edinburg, UK. [ PDF ]
  12. A Tool for Interactive Comparative Sequence Analysis
    Andreas Dräger​​​​​​​​​​​​​​, Dietrich H. Nies, and Stefan Posch. German Conference on Bioinformatics (GCB) 2006, Tübingen, Germany. [ PDF ]

Functions / Memberships

  • Since Januar 2019 member of the Gender Equality Governance Board of the Tübinger cluster of excellence CMFI - "Controlling Microbes to Fight Infections"
  • Since January 2019 member of the German Society for Computer Science within the professional group for bioinformatics
  • Since April 2018 member of the Society for Biological Engineering
  • Since January 2018 elected SBGN editor
  • Since 2015: member of the Organizing Comitee of the Systems Modeling Interest Group (SysMod), which meets annually in the framework of the ISMB Conference (Intelligent Systems for Molecular Biology).
  • Since 2015: member of the Marie-Curie Alumni Organization
  • January 2015 to December 2017: elected SBML-Editor
  • Since 2013: member of the DAAD alumni
  • 2013-2015 Organizer of the local GAIN (German Academic International Network) and GSO (German Scholar Organization) groups in San Diego, California, USA
  • Since 2013: associated editor for the journal BMC Systems Biology
  • Since 2009: member of the international society for computational biology