Dr. Andreas Dräger

Completed research projects of the systems biology research group are listed at the bottom of this spearate page.

Projects funded by the European Union (FP7)

• AMBiCon: Automated multi-level modeling of biological systems considering physico-chemical constraints (2013 - 2015, funding reference 332020). This Marie Curie International Outgoing Fellowship (IOF) was conducted in collaboration with the University of California at San Diego (UCSD) within the Department for Bioengineering within the systems biology research group of Prof. Bernhard Ø. Palsson.

Project funded by the University of Tübingen

• Inference of biochemical reaction systems considering physico-chemical constraints (2011 - 2012, funding reference 18017002).

Student projects for open-source software

• Project under the umbrella of the National Resource for Network Biology Summer of Code 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 Inc. In our subproject the Java™ library JSBML was extended and new functions were implemented - Further information
• Google Summer of Code 2010

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

• 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 and multi-parallel computers (2006 - 2008, contract number 23-7532.24-4-18/1).

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)

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.

1. An integrated systems-biology approach reveals differences in formate metabolism in the genus Methanothermobacter
   Isabelle Casini, Tim McCubbin, Sofia Esquivel-Elizondo, Guillermo G. Luque, Daria Evseeva, Christian Fink, Sebastian Beblawy, Nicholas D. Youngblut, Ludmilla Aristilde, Daniel H. Huson, Andreas Dräger, Ruth E. Ley, Esteban Marcellin, Largus T. Angenent, Bastian Molitor
   iScience, September, 22^nd, 2023
   [ Details | Preprint | PDF | PubMed | BibTeX ]
2. Can Genome Sequencing Coupled to Flux Balance Analyses Offer Precision Guidance for Industrial Strain Development? The Lessons from Carbon Trafficking in Corynebacterium glutamicum ATCC 21573
   Eldin Kurpejović, Daniel Wibberg, Gülsüm Merve Bastem, Arthur Burgardt, Tobias Busche, Fatma Ece Altınışık Kaya, Andreas Dräger, Volker F. Wendisch und Berna Sarıyar Akbulut
   OMICS: A Journal of Integrative Biology, 27:9, September 14^th, 2023.
   [ Details | DOI | PDF | PubMed | BibTeX ]
3. Advancements in Computational Modelling of Biological Systems: seventh annual SysMod meeting
   Bhanwar Lal Puniya und Andreas Dräger
   Bioinformatics, September 14^th 2023.
   [ Details | DOI | PDF | PubMed | BibTeX ]
4. SBOannotator: a Python Tool for the Automated Assignment of Systems Biology Ontology Terms
   Nantia Leonidou, Elisabeth Fritze, Alina Renz, and Andreas Dräger
   Bioinformatics 2023, July, 14^th 2023.
   [ Details | DOI | Preprint | PDF | PubMed | BibTeX ]
5. New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells
   Nantia Leonidou, Alina Renz, Reihaneh Mostolizadeh, and Andreas Dräger
   PLOS Computational Biology, 19(3): e1010903. March 23^rd, 2023
   [ Details | DOI | Preprint | PDF | PubMed | BibTeX ]
6. Genome-scale model of Pseudomonas aeruginosa metabolism unveils virulence and drug potentiation
   Sanjeev Dahal, Alina Renz, Andreas Dräger, and Laurence Yang
   Communications Biology, 6, 165, February 10^th, 2023.
   [ Details | DOI | Preprint | PDF | PubMed | BibTeX ]
7. Hierarchical modelling of microbial communities
   Manuel Glöckler, Andreas Dräger, and Reihaneh Mostolizadeh
   Bioinformatics, January 17^th, 2023.
   [ Details | DOI | PDF | PubMed | BibTeX ]
8. Computational modelling in health and disease. Highlights of the 6^th annual SysMod meeting
   Anna Niarakis, Juilee Thakar, Matteo Barberis, María Rodríguez Martínez, Tomáš Helikar, Marc Birtwistle, Claudine Chaouiya, Laurence Calzone, and Andreas Dräger
   Bioinformatics, September 22^nd, 2022.
   [ Details | DOI | PDF | PubMed | BibTeX ]
9. Towards the human nasal microbiome: simulating D. pigrum and S. aureus
   Reihaneh Mostolizadeh, Manuel Glöckler, and Andreas Dräger
   Frontiers in Cellular and Infection Microbiology 2022, August 15^th, 2022
   [ Details | DOI | PDF | PubMed | BibTeX ]
10. FluxomicsExplorer: Differential visual analysis of flux sampling based on metabolomics
    Constantin Holzapfel, Miriam Hoene, Xinjie Zhao, Chunxiu Hu, Cora Weigert, Andreas Nieß, Guowang Xu, Rainer Lehmann, Andreas Dräger, and Michael Krone
    Computers & Graphics, August 29^th, 2022.
    [ Details | DOI | PDF | PubMed | BibTeX ]
11. NCMW: A Python Package to Analyze Metabolic Interactions in the Nasal Microbiome
    Manuel Glöckler, Andreas Dräger, and Reihaneh Mostolizadeh
    Frontiers in Bioinformatics, February 25^th 2022.
    [ Details | DOI | PDF | PubMed | BibTeX ]
12. A Computational Model of Bacterial Population Dynamics in Gastrointestinal Yersinia enterocolitica Infections in Mice
    Janina K. Geißert, Erwin Bohn, Reihaneh Mostolizadeh, Andreas Dräger, Ingo B. Autenrieth, Sina Beier, Oliver Deusch, Alina Renz, Martin Eichner, and Monika S. Schütz.
    Biology, 11(2), 297; February 12^th 2022.
    [ Details | DOI | Preprint | PDF | PubMed | BibTeX ]
13. The Systems Biology Simulation Core Library
    Hemil Panchiwala, Shalin Shah, Hannes Planatscher, Mykola Zakharchuk, Matthias König, and Andreas Dräger
    Bioinformatics, Volume 38, Issue 3, Pages 864-865, February 1^st 2022.
    [ Details | DOI | Preprint | PubMed | PDF | BibTeX ]
14. High-Quality Genome-Scale Reconstruction of Corynebacterium glutamicum ATCC 13032
    Martina Feierabend, Alina Renz, Elisabeth Zelle, Katharina Nöh, Wolfgang Wiechert, and Andreas Dräger
    Frontiers in Microbiology, November 15^th 2021.
    [ Details | DOI | PDF | PubMed | BibTeX ]
15. COVID-19 Disease Map, a computational knowledge repository of SARS-CoV-2 virus-host interaction mechanisms
    Marek Ostaszewski, Anna Niarakis, Alexander Mazein, Inna Kuperstein, Robert Phair, Aurelio Orta-Resendiz, Vidisha Singh, Sara Sadat Aghamiri, Marcio Luis Acencio, Enrico Glaab, Andreas Ruepp, Gisela Fobo, Corinna Montrone, Barbara Brauner, Goar Frishman, Luis Cristóbal Monraz Gómez, Julia Somers, Matti Hoch, Shailendra Kumar Gupta, Julia Scheel, Hanna Borlinghaus, Tobias Czauderna, Falk Schreiber, Arnau Montagud, Miguel Ponce de Leon, Akira Funahashi, Yusuke Hiki, Noriko Hiroi, Takahiro G. Yamada, Andreas Dräger, Alina Renz, Muhammad Naveez, Zsolt Bocskei, Francesco Messina, Daniela Börnigen, Liam Fergusson, Marta Conti, Marius Rameil, Vanessa Nakonecnij, Jakob Vanhoefer, Leonard Schmiester, Muying Wang, Emily E. Ackerman, Jason E. Shoemaker, Jeremy Zucker, Kristie L. Oxford, Jeremy Teuton, Ebru Kocakaya, Gökçe Yağmur Summak, Kristina Hanspers, Martina Kutmon, Susan Coort, Lars Eijssen, Friederike Ehrhart, Rex D. A. B., Denise Slenter, Marvin Martens, Robin Haw, Bijay Jassal, Lisa Matthews, Marija Orlic-Milacic, Andrea Senff-Ribeiro, Karen Rothfels, Veronica Shamovsky, Ralf Stephan, Cristoffer Sevilla, Thawfeek Mohamed Varusai, Jean-Marie Ravel, Rupsha Fraser, Vera Ortseifen, Silvia Marchesi, Piotr Gawron, Ewa Smula, Laurent Heirendt, Venkata Satagopam, Guanming Wu, Anders Riutta, Martin Golebiewski, Stuart Owen, Carole Goble, Xiaoming Hu, Rupert Overall, Dieter Maier, Angela Bauch, John A. Bachman, Benjamin M Gyori, Carlos Vega, Valentin Grouès, Miguel Vazquez, Pablo Porras, Luana Licata, Marta Iannuccelli, Francesca Sacco, Denes Turei, Augustin Luna, Ozgun Babur, Sylvain Soliman, Alberto Valdeolivas, Marina Esteban-Medina, Maria Peña-Chilet, Tomáš Helikar, Bhanwar Lal Puniya, Anastasia Nesterova, Anton Yuryev, Anita de Waard, Dezso Modos, Agatha Treveil, Marton Laszlo Olbei, Bertrand De Meulder, Aurélien Naldi, Aurélien Dugourd, Vincent Noël, Laurence Calzone, Chris Sander, Emek Demir, Tamas Korcsmaros, Tom C. Freeman, Franck Augé, Jacques S. Beckmann, Jan Hasenauer, Olaf Wolkenhauer, Egon Willighagen, Alexander R. Pico, Chris Evelo, Marc Gillespie, Lincoln D. Stein, Henning Hermjakob, Peter DʼEustachio, Julio Saez-Rodriguez, Joaquin Dopazo, Alfonso Valencia, Hiroaki Kitano, Emmanuel Barillot, Charles Auffray, Rudi Balling, Reinhard Schneider, and the COVID-19 Disease Map Community
    Molecular Systems Biology 17: e10387, October 19^th 2021.
    [ Details | DOI | Preprint | PubMed | PDF | BibTeX ]
16. SBMLWebApp: Web-based Simulation, Steady-State Analysis, and Parameter Estimation of Systems Biology Models
    Takahiro G. Yamada, Kaito Ii, Matthias König, Martina Feierabend, Andreas Dräger, and Akira Funahashi
    Processes, 9(10), October 15^th 2021
    [ Details | DOI | Preprint | PubMed | PDF | BibTeX ]
17. An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism
    Dawson D. Payne, Alina Renz, Laura J. Dunphy, Taylor Lewis, Andreas Dräger, and Jason A. Papin
    npj Systems Biology and Applications 7, 37, October 8^th 2021.
    [ Details | DOI | Preprint | PubMed | PDF | BibTeX ]
18. Curating and Comparing 114 Strain-Specific Genome-Scale Metabolic Models of Staphylococcus aureus
    Alina Renz and Andreas Dräger
    npj Systems Biology and Applications 7, 30, 29^th 2021
    [ Details | DOI | Preprint | PubMed | PDF | BibTeX ]
19. SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems
    Andreas Dräger Tomáš Helikar, Matteo Barberis, Marc Birtwistle, Laurence Calzone, Claudine Chaouiya, Jan Hasenauer, Jonathan R. Karr, Anna Niarakis, María Rodríguez Martínez, Julio Saez-Rodriguez, and Juilee Thakar.
    Bioinformatics, btab229, June 24^th 2021.
    [ Details | DOI | Preprint | PubMed | PDF | BibTeX ]
20. Genome-Scale Metabolic Model of Infection with SARS-CoV-2 Mutants Confirms Guanylate Kinase as Robust Potential Antiviral Target
    Alina Renz, Lina Widerspick, and Andreas Dräger
    Genes, 2021, 12, 796. May 24^th, 2021
    [ Details | DOI | Preprint | PubMed | PDF | BibTeX ]
21. First Genome-Scale Metabolic Model of Dolosigranulum pigrum Confirms Multiple Auxotrophies
    Alina Renz, Lina Widerspick, and Andreas Dräger
    Metabolites, 11(4), 232, April 9^th 2021
    [ Details | DOI | PubMed | PDF | BibTeX ]
22. FBA reveals guanylate kinase as a potential target for antiviral therapies against SARS-CoV-2
    Alina Renz, Lina Widerspick, and Andreas Dräger.
    Bioinformatics, , Volume 36, Issue Supplelment_2, Pages i813-i821, December 29^th 2020.
    [ Details | DOI | Zenodo | PubMed | YouTube | PDF | BibTeX ]
23. Computational Model Informs Effective Control Interventions against Y. enterocolitica Co-Infection
    Reihaneh Mostolizadeh and Andreas Dräger.
    Biology, 9(12), Special Issue Computational Biology, November 30^th 2020.
    [ Details | DOI | Preprint | PubMed | PDF | BibTeX ]
24. Longitudinal multi-omics analyses identify responses of megakaryocytes, erythroid cells and plasmablasts as hallmarks of severe COVID-19 trajectories
    Joana P. Bernardes, Neha Mishra, Florian Tran, Thomas Bahmer, Lena Best, Johanna I. Blase, Dora Bordoni, Jeanette Franzenburg, Ulf Geisen, Jonathan Josephs-Spaulding, Philipp Köhler, Axel Künstner, Elisa Rosati, Anna C. Aschenbrenner, Petra Bacher, Nathan Baran, Teide Boysen, Burkhard Brandt, Niklas Bruse, Jonathan Dörr, Andreas Dräger, Gunnar Elke, David Ellinghaus, Julia Fischer, Michael Forster, Andre Franke, Sören Franzenburg, Norbert Frey, Anette Friedrichs, Janina Fuß, Andreas Glück, Jacob Hamm, Finn Hinrichsen, Marc P. Höppner, Simon Imm, Ralf Juenker, Sina Kaiser, Ying H. Kan, Rainer Knoll, Christoph Lange, Georg Laue, Clemes Lier, Matthias Lindner, Georgios Marinos, Robert Markewitz, Jacob Nattermann, Rainer Noth, Peter Pickkers, Klaus F. Rabe, Alina Renz, Christoph Röcken, Jan Rupp, Annika Schaffarzyk, Alexander Scheffold, Jonas Schulte-Schrepping, Domagoj Schunck, Dirk Skowasch, Thomas Ulas, Klaus-Peter Wandinger, Michael Wittig, Johannes Zimmermann, Hauke Busch, Bimba F. Hoyer, Christoph Kaleta, Jan Heyckendorf, Matthijs Kox, Jan Rybniker, Stefan Schreiber, Joachim Schultze, and Philip Rosenstiel
    Immunity, November 26^th 2020.
    [ Details | DOI | MedRxiv | PubMed | PDF | BibTeX ]
25. Community standards to facilitate development and address challenges in metabolic modeling
    Maureen A. Carey, Andreas Dräger, Moritz E. Beber, Jason A. Papin, and James T. Yurkovich.
    Accepted in Molecular Systems Biology, July 9^th 2020.
    [ Details | DOI | BioRxiv | PubMed | PDF | BibTeX ]
26. SBML Level 3: an extensible format for the exchange and reuse of biological models
    Sarah M. Keating, Dagmar Waltemath, Matthias König, Fengkai Zhang, Andreas Dräger, Claudine Chaouiya, Frank T. Bergmann, Andrew Finney, Colin Gillespie, Tomáš Helikar, Stefan Hoops, Rahuman Malik-Sheriff, Stuart Moodie, Ion Moraru, Chris J. Myers, Aurélien Naldi, Brett Olivier, Sven Sahle, James Schaff, Lucian P. Smith, Maciej Swat, Denis Thieffry, Leandro Watanabe, Darren Wilkinson, Michael L. Blinov, Kimberly Begley, James Faeder, Harold Gómez, Thomas M. Hamm, Yuichiro Inagaki, Wolfram Liebermeister, Allyson Lister, Daniel Lucio, Eric Mjolsness, Carole Proctor, Karthik Raman, Nicolas Rodriguez, Clifford Shaffer, Bruce Shapiro, Joerg Stelling, Neil Swainston, Naoki Tanimura, John Wagner, Martin Meier-Schellersheim, Herbert Sauro, Bernhard Ø. Palsson, Hamid Bolouri, Hiroaki Kitano, Akira Funahashi, Henning Hermjakob, John C. Doyle, and Michael Hucka, and the SBML Level 3 Community members: Richard R. Adams, Nicholas A. Allen, Bastian R. Angermann, Marco Antoniotti, Gary D. Bader, Jan Červený, Mélanie Courtot, Chris D. Cox, Piero Dalle Pezze, Emek Demir, William S. Denney, Harish Dharuri, Julien Dorier, Dirk Drasdo, Ali Ebrahim, Johannes Eichner, Johan Elf, Lukas Endler, Chris T. Evelo, Christoph Flamm, Ronan M. T. Fleming, Martina Fröhlich, Mihai Glont, Emanuel Gonçalves, Martin Golebiewski, Hovakim Grabski, Alex Gutteridge, Damon Hachmeister, Leonard A. Harris, Benjamin D. Heavner, Ron Henkel, William S. Hlavacek, Bin Hu, Daniel R. Hyduke, Hidde Jong, Nick Juty, Peter D. Karp, Jonathan R. Karr, Douglas B. Kell, Roland Keller, Ilya Kiselev, Steffen Klamt, Edda Klipp, Christian Knüpfer, Fedor Kolpakov, Falko Krause, Martina Kutmon, Camille Laibe, Conor Lawless, Lu Li, Leslie M. Loew, Rainer Machne, Yukiko Matsuoka, Pedro Mendes, Huaiyu Mi, Florian Mittag, Pedro T. Monteiro, Kedar Nath Natarajan, Poul M. F. Nielsen, Tramy Nguyen, Alida Palmisano, Jean‐Baptiste Pettit, Thomas Pfau, Robert D. Phair, Tomas Radivoyevitch, Johann M. Rohwer, Oliver A. Ruebenacker, Julio Saez‐Rodriguez, Martin Scharm, Henning Schmidt, Falk Schreiber, Michael Schubert, Roman Schulte, Stuart C. Sealfon, Kieran Smallbone, Sylvain Soliman, Melanie I. Stefan, Devin P. Sullivan, Koichi Takahashi, Bas Teusink, David Tolnay, Ibrahim Vazirabad, Axel Kamp, Ulrike Wittig, Clemens Wrzodek, Finja Wrzodek, Ioannis Xenarios, Anna Zhukova, and Jeremy Zucker.
    Molecular Systems Biology, August 26^th 2020.
    [ Details | DOI | PDF | PubMed | BibTeX ]
27. Systems biology markup language (SBML) level 3 package: multistate, multicomponent and multicompartment species, version 1, release 2
    Fengkai Zhang, Lucian P. Smith, Michael L. Blinov, James Faeder, William S. Hlavacek, José-Juan Tapia, Sarah M. Keating, Nicolas Rodriguez, Andreas Dräger, Leonard A. Harris, Andrew Finney, Bin Hu, Michael Hucka, and Martin Meier-Schellersheim
    Journal of Integrative Bioinformatics, July 6^th 2020.
    [ Details | DOI | PubMed | PDF | BibTeX ]
28. Systems biology graphical notation markup language (SBGNML) version 0.3
    Frank T. Bergmann, Tobias Czauderna, Ugur Dorusoz, Adrien Rougny, Andreas Dräger, Vasundra Touré, Alexander Mazein, Michael L. Blinov, and Augustin Luna.
    Journal of Integrative Bioinformatics, June 22^nd 2020.
    [ Details | DOI | Link | PubMed | PDF | BibTeX ]
29. COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms
    Marek Ostaszewski, Alexander Mazein, Marc E. Gillespie, Inna Kuperstein, Anna Niarakis, Henning Hermjakob, Alexander R. Pico, Egon L. Willighagen, Chris T. Evelo, Jan Hasenauer, Falk Schreiber, Andreas Dräger, Emek Demir, Olaf Wolkenhauer, Laura I. Furlong, Emmanuel Barillot, Joaquin Dopazo, Aurelio Orta-Resendiz, Francesco Messina, Alfonso Valencia, Akira Funahashi, Hiroaki Kitano, Charles Auffray, Rudi Balling, and Reinhard Schneider.
    Scientific Data 7, 136. May 5^th 2020.
    [ Details | DOI | PubMed | PDF | BibTeX ]
30. Visualizing metabolic network dynamics through time-series metabolomic 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 Dräger.
    BMC Bioinformatics 21, 130. April 3^rd 2020.
    [ Details | DOI | PubMed | BioRxiv | PDF | BibTeX ]
31. MEMOTE for standardized genome-scale metabolic model testing
    Christian Lieven, Moritz E. Beber, Brett G. Olivier, Frank T. Bergmann, Meric Ataman, Parizad Babaei, Jennifer A. Bartell, Lars M. Blank, Siddharth Chauhan, Kevin Correia, Christian Diener, Andreas Dräger, Brigitta E. Ebert, Janaka N. Edirisinghe, José P. Faria, Adam M. Feist, Georgios Fengos, Ronan M. T. Fleming, Beatriz García-Jiménez, Vassily Hatzimanikatis, Wout van Helvoirt, Christopher S. Henry, Henning Hermjakob, Markus J. Herrgård, Ali Kaafarani, Hyun Uk Kim, Zachary A. King, Steffen Klamt, Edda Klipp, Jasper J. Koehorst, Matthias König, Meiyappan Lakshmanan, Dong-Yup Lee, Sang Yup Lee, Sunjae Lee, Nathan E. Lewis, Filipe Liu, Hongwu Ma, Daniel Machado, Radhakrishnan Mahadevan, Paulo Maia, Adil Mardinoglu, Gregory L. Medlock, Jonathan M. Monk, Jens Nielsen, Lars Keld Nielsen, Juan Nogales, Intawat Nookaew, Bernhard O. Palsson, Jason A. Papin, Kiran R. Patil, Nathan D. Price, Osbaldo Resendis-Antonio, Anne Richelle, Isabel Rocha, Benjamín J. Sánchez, Peter J. Schaap, Rahuman S. Malik Sheriff, Saeed Shoaie, Nikolaus Sonnenschein, Bas Teusink, Paulo Vilaça, Jon Olav Vik, Judith A. H. Wodke, Joana C. Xavier, Qianqian Yuan, Maksim Zakhartsev, and Cheng Zhang.
    Nature Biotechnology, March 2^nd 2020.
    [ Details | DOI | BioRxiv | PDF | PubMed | BibTeX ]
32. BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree
    C. J. Norsigian, N. Pusarla, J. L. McConn, J. T. Yurkovich, A. Dräger, B. O. Palsson, and Z. A. King
    Nucleic Acids Research, gkz1054, November 7^th 2019
    [ Details | DOI | PDF | PubMed | BibTeX ]
33. 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 20^th 2019.
    [ Details | DOI | Link | PubMed | BibTeX ]
34. 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, and Augustin Luna.
    Journal of Integrative Bioinformatics, June 13^th 2019.
    [ Details | DOI | Link | PubMed | BibTeX ]
35. 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 18^th 2019.
    [ Details | DOI | PDF | PubMed | BibTeX ]
36. 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.
    [ Details | DOI | PDF | BioRxiv | PubMed | BibTeX ]
37. 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, and Bernhard O Palsson.
    Nucleic Acids Research, August 23^th 2018.
    [ DOI | link | PDF | PubMed | BibTeX ]
38. 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 26^th 2018.
    [ DOI | link | PDF ]
39. 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 9^th 2018.
    [ DOI | link | PDF ]
40. 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 19^th 2018.
    [ DOI | link | PDF ]
41. 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 ]
42. 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 ]
43. 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 ]
44. 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 ]
45. 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 ]
46. BiGG Models: A platform for integrating, standardizing and 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 ]
47. 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 ]
48. 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 ]
49. 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 ]
50. 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. Li, 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 ]
51. 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 ]
52. 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 Dräger.
    Bioinformatics, June 2015.
    [ DOI | arXiv | link | PDF ]
53. SBMLsimulator: a Java tool for model simulation and parameter estimation in systems biology
    Alexander Dörr, Roland Keller, Andreas Zell, and Andreas Dräger.
    Computation, 2(4):246-257, December 2014.
    [ DOI | link | PDF ]
54. Improving collaboration by standardization efforts in systems biology
    Andreas Dräger and Bernhard Ø. Palsson.
    Frontiers in Bioengineering, 2(61), December 2014.
    [ DOI | link | PDF ]
55. 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 ]
56. 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 ]
57. 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 ]
58. 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 ]
59. 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 Dräger.
    BMC Systems Biology, 7:55, July 2013.
    [ DOI | link | PDF ]
60. 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 ]
61. 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 ]
62. 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 ]
63. CySBML: a Cytoscape plugin for SBML
    Matthias König, Andreas Dräger, and Hermann-Georg Holzhütter.
    Bioinformatics, 28(18):2402-2403, July 2012.
    [ DOI | link ]
64. 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 ]
65. 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 ]
66. 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 ]
67. 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 ]
68. 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 ]
69. 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 ]
70. 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 ]
71. 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 ]
72. 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 ]
73. 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 ]

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 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, Januar 2007. Imperial College Press. [ DOI | link | PDF ]

1. Genome-Scale Metabolic Modeling of Escherichia coli and Its Chassis Design for Synthetic Biology Applications.
   Bashir Sajo Mienda and Andreas Dräger
   Computational Methods in Synthetic Biology, Mario Andrea Marchisio (editor), part of the series Methods in Molecular Biology (MIMB, volume 2189), pp. 217-229, November 13^th 2020.
   [ Details | DOI | PubMed | PDF | BibTeX ]
2. Overview: Standards for Modeling in Systems Medicine.
   Andreas Dräger and Dagmar Waltemath
   Systems Medicine. Integrative, Qualitative and Computational Approaches. Olaf Wolkenhauer (Editor), Volume 3, 2021, Pages 245–353, August 28^th 2020.
   [ Details | DOI | PubMed | PDF | BibTeX ]
3. Clinical Applications of Metabolic Models in SBML Format.
   Alina Renz, Reihaneh Mostolizadeh, and Andreas Dräger
   Reference Module in Biomedical Sciences, Elsevier, January 30^th 2020
   [ Details | DOI | PDF | PubMed | BibTeX ]
4. The Systems Biology Graphical Notation: Current Status and Applications in Systems Medicine.
   Vasundra Touré, Andreas Dräger, Augustin Luna, Ugur Dogrusoz, and Adrien Rougny
   Reference Module in Biomedical Sciences, Elsevier, January 25^th 2020
   [ Details | DOI | PDF | PubMed | BibTeX ]
5. 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.
   [ Details | DOI | link | PubMed | BibTex ]
6. 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 ]
7. 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 ]
8. Automating mathematical modeling of biochemical reaction networks.
   Andreas Dräger, Adrian Schröder, and Andreas Zell. Systems Biology for Signaling Networks, volume 1 of Systems Biology, chapter, pages 159-205. Springer-Verlag, July 2010.
   [ DOI | link ]

1. Genome-scale metabolic models consistently predict in vitro characteristics of Corynebacterium striatum
   Famke Bäuerle, Gwendolyn O. Gusak, L. Camus, S. Heilbronner, and Andreas Dräger
   BioRxiv, April, 29^th 2023.
   [ Details | DOI | PDF | PubMed | BibTeX ]
2. Standard-GEM: Standardization of open-source genome-scale metabolic models
   Mihail Anton,  Eivind Almaas, Rui Benfeitas, Sara Benito-Vaquerizo, Lars M. Blank, Andreas Dräger, John M. Hancock, Cheewin Kittikunapong, Matthias König, Feiran Li, Ulf W. Liebal, Hongzhong Lu, Hongwu Ma, Radhakrishnan Mahadevan, Adil Mardinoglu, Jens Nielsen, Juan Nogales, Marco Pagni, Jason A. Papin, Kiran Raosaheb Patil, Nathan D. Price, Jonathan L. Robinson, Benjamín J. Sánchez, Maria Suarez Diez, Snorre Sulheim, L. Thomas Svensson, Bas Teusnik, Wanwipa Vongsangnak, Hao Wang, Ahmad A. Zeidan, and Eduard J. Kerkhoven.
   BioRxiv, March 23^rd, 2023
   [ Details | DOI | PDF | BibTeX ]
3. Metabolic Modeling Elucidates Phenformin and Atpenin A5 as Broad-Spectrum Antiviral Drugs
   Alina Renz, Mirjam Hohner, Maximilian Breitenbach, Jonathan Josephs-Spaulding, Johanna Dürrwald, Lena Best, Raphaël Jami, Georgios Marinos, Filipe Cabreiro, Andreas Dräger, Michael Schindler, and Christoph Kaleta
   Preprints 2022, 2022100223, October 17^th, 2022.
   [ Details | DOI | PDF | PubMed | BibTeX ]
4. ProDGe: investigating protein-protein interactions at the domain level
   Finja Büchel, Clemens Wrzodek, Florian Mittag, Andreas Dräger, Adrian Schröder, and Andreas Zell.
   Nature Precedings, August 2011.
   [ DOI | link | PDF ]

1. Systematische Modellierung des Mikrobioms im Menschlichen Atmungstrakt
   Andreas Dräger
   JUNITE – Netzwerk Junge Infektionsmedizin e.V., March 4^th, 2023 in Halberstadt, Germany
   https://www.netzwerk-infektionsmedizin.de
2. Model Representation and Exchange in Systems Biology
   Andreas Dräger
   SmartAge ITN Winter School 2023 of the University Hospital Kiel, January 31^st, 2023, in Kiel, Germany (via Zoom)
3. Computationally Modeling the Human Microbiome of the Respiratory Tract
   Andreas Dräger
   1st International Conference on Antimicrobial Computational Pharmacology, December 14^th, 2022 in Melbourne, Australia (via Zoom)
4. Computationally Modeling the Human Microbiome of the Respiratory Tract
   Andreas Dräger
   Part of the Lecture Series ”Modeling Discussion at DTU Biosustain”, December 12^th, 2022 at the Danish Technical University at Kopenhagen, Denmark (via Zoom)
5. Computationally Modeling the Human Microbiome of the Respiratory Tract
   Andreas Dräger
   International Conference on Systems Biology (ICSB) 2022, October 9^th 2022 in Berlin, Germany
6. Introduction to SysMod 2022
   Andreas Dräger
   SysMod Meeting as part of the ISMB 2022 in Madison, Wisconsin, USA at July 11^th, 2022
7. SBMLWebApp: Web-based Simulation, Steady-State Analysis, and Parameter Estimation of Systems Biology Models
   Andreas Dräger, Takahiro G. Yamada, Kaito Ii, Matthias König, Martina Feierabend, and Akira Funahashi
   Rocky Mountain Bioinformatics Annual Conference 2021, December 2^nd 2021
8. Day 2 closing remarks
   Andreas Dräger
   Virtual SysMod Meeting as part of the ISMB 2020 at July 14^th 2020
9. How Animated Time-Series Data bring Metabolic Network Models to Life e.g. of COVID-19
   Andreas Dräger
   Predictive Analytics World Healthcare, session "Corona Community Special" at May 11^th 2020
10. Modeling the Human Nasal Microbiome
    Alina Renz, Reihaneh Mostolizadeh, Niklas Henle, Pia Rautenstrauch, and Andreas Dräger
    Annual Congress of the German Center for Infection Research, Bad Nauheim (November 22^nd 2019)
11. Introduction to SysMod 2019
    Andreas Dräger
    ISMB/ECCB 2019, Basel, CH (July 22^nd 2019)
12. InSilico: an Eclipse-based framework for plugin-development and standards interoperability
    Andreas Dräger, Roman Schulte, and Matthias König
    HARMONY 2019​​​​​​​, Pasadena, CA, USA (March 25^th 2019)
13. 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 10^th 2018)
14. 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 11^th 2018)
15. 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
    COMBINE 2018, Boston, MA, USA (October 11^th 2018)
16. 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)
17. Visualization and Creation of Biochemical Networks with Escher
    Andreas Dräger, Zachary A. King, James T. Yurkovich, Christoph M. Blessing, Devesh Khandelwal, Ali Ebrahim, Nikolaus Sonnenschein, Nathan E. Lewis, and Bernhard O. Palsson
    COMBINE 2017, Mailand, Italien (October 11^th 2017).
18. 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 Dräger
    COMBINE 2017, Milan, Italy (October 10^th 2017).
19. Visualization and Creation of Biochemical Networks with Escher
    Andreas Dräger, Zachary A. King, James T. Yurkovich, Christoph M. Blessing, Devesh Khandelwall, Ali Ebrahim, Nikolaus Sonnenschein, Nathan E. Lewis, Bernhard O. Palsson
    BioVis Special Interest Group meeting during ISMB 2017 in Prag, Czech Republic (July 24^th 2017).
20. The ZBIT Systems Biology Software and Web-Service Collection
    Andreas Dräger
    Invited talk, Helmholtz Center Munich, Germany (November 15^th 2016).
21. The ZBIT Systems Biology Software and Web-Service Collection
    Andreas Dräger
    COMBINE 2016, Newcastle, UK (Setember 21^st 2016)
    [ Folien ]
22. The ZBIT Systems Biology Software and Web-Service Collection
    Andreas Dräger
    Invited talk, University of Luxembourg, Esch Belval, Luxembourg (September 1^st 2016).
23. Biochemical Pathways and Large-Scale Metabolic Networks
    Andreas Dräger and Nathan E. Lewis
    Lecture day on reconstruction and modeling of metabolic systems at genome-scale Summer School
    Invited talk, SIB Siwss Institute for Bioinformatics, Lausanne, Switzerland (August 30^th 2016).
24. Recent Software and Services to Support the SBML Community
    Michael Hucka, Frank T. Bergmann, Andreas Dräger, Harold F. Gómez, Sarah M. Keating, Nicolas Rodriguez, Lucian P. Smith
    First SysMod Special Interest Group meeting during ISMB 2016, Orlando, FL, USA (July 9^th 2016).
    [ DOI ]
25. The ZBIT systems biology software and web service collection
    Andreas Dräger​​​​​​​.
    First SysMod Special Interest Group meeting during ISMB 2016, Orlando, FL, USA (July 9^th 2016).
    [ DOI | Slides ]
26. 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 13^th 2015)
    [ Slides ]
27. SED-ML in the simulation core library
    Andreas Dräger​​​​​​​​​​​​​​
    COMBINE 2013, Paris, Frankreich.
28. From KEGG to dynamic pathway models: a collection of tools to facilitate the modeling of biochemical networks
    Andreas Dräger​​​​​​​​​​​​​​. COMBINE 2011, Heidelberg, Deutschland.
29. JSBML—The SBML Java™ library
    Andreas Dräger​​​​​​​​​​​​​​ and Nicolas Rodriguez
    HARMONY Workshop 2011, invited talk, New York, USA (April 18^th 2011).
30. 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 9^th 2010).
    [ Slides​​​​​​​ ]
31. Inferring Genetic Networks from Gene Expression Data
    Andreas Dräger​​​​​​​​​​​​​​, Nora Speer, Christian Spieth, Jochen Supper, and Andreas Zell
    Biotechnica 2009, International Trade Fair for Biotechnology, invited talk, Hannover, Germany (October 8^th 2009).
32. 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 2009, 29. international exhibition congress for chemical technique, environmental protection and biotechnology, invited talk, Frankfurt (Main), Deutschland (May 13^th 2009).

1. Model-driven Elucidation of Antiviral Drug Targets
   Mirjam Hohner, Maximilian Breitenbach, Alina Renz, Jonathan Josephs-Spaulding, Lena Best, Georgios Marinos, Johanna Dürrwald, Andreas Dräger​​​​​​​, Christoph Kaleta, Michael Schindler
   DZIF autumn school, Lübeck, September 2022
2. MCC: The automated curation of Mass and Charge Curation in genome-scale metabolic reconstruction
   Reihaneh Mostolizadeh, Finn Mier​​​​​​​ und Andreas Dräger
   7^th Annual SysMod Meeting as part of the ISMB 2022 at July 11^th 2022 in Madison, Wisconsin, USA, 
3. New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells
   Nantia Leonidou, Alina Renz, Reihaneh Mostolizadeh und Andreas Dräger
   7^th Annual SysMod Meeting as part of the ISMB 2022 at July 11^th 2022 in Madison, Wisconsin, USA, 
4. Computationally Modeling the Human Microbiome of the Respiratory Tract
   Andreas Dräger
   Joint Annual DZIF Meeting 2022, Stuttgart, Germany, June 1^st-3^rd
5. The Systems Biology Simulation Core Library
   Hemil Panchiwala, Shalin Shah, Hannes Planatscher, Mykola Zakharchuk, Matthias König, and Andreas Dräger
   ISMB/ECCB 2021, virtual conference
   [ Link ]
6. Curating and Comparing 114 Strain-Specific Genome-Scale Metabolic Models of Staphylococcus aureus
   Alina Renz and Andreas Dräger
   ISMB/ECCB 2021, virtual conference
   [ Link ]
7. FBA reveals potential targets for antiviral therapies against SARS-CoV-2
   Alina Renz, Lina Widerspick, and Andreas Dräger
   7^th Conference on Constraint-Based Reconstruction and Analysis (COBRA 2021), virtual, March 1-2, 2021.
   [ Link ]
8. Computational Model Informs Effective Control Interventions Against Y. enterocolitica Co-Infection
   Reihaneh Mostolizadeh and Andreas Dräger
   7^th Conference on Constraint-Based Reconstruction and Analysis (COBRA 2021), virtual, March 1-2, 2021.
   [ Link ]
9. Tissue-specific reconstruction of constraint-based metabolic models based on ReconX
   Nantia Leonidou, Alina Renz, Reihaneh Mostolizadeh, and Andreas Dräger
   7^th Conference on Constraint-Based Reconstruction and Analysis (COBRA 2021), virtual, March 1-2, 2021.
   [ Link ]
10. Modeling the Microbiome of the Human Respiratory Tract to Combat Infections
    Andreas Dräger
    7^th Conference on Constraint-Based Reconstruction and Analysis (COBRA 2021), virtual, March 1-2, 2021.
    [ Link ]
11. High-quality genome-scale reconstruction of Corynebacterium glutamicum ATCC 13032
    Martina Feierabend, Alina Renz, Elisabeth Zelle, Katharina Nöh, Wolfgang Wiechert, and Andreas Dräger
    7^th Conference on Constraint-Based Reconstruction and Analysis (COBRA 2021), virtual, March 1-2, 2021.
    [ Link ]
12. Integration of Systems Biology and Metabolic Modeling for Power-to-Gas Applications with Methanothermobacter spp.
    Isabella Casini, Timothy Mc Cubbin, Andreas Dräger, Esteban Marcellin, Largus T. Angernent, and Bastian Molitor
    7^th Conference on Constraint-Based Reconstruction and Analysis (COBRA 2021), virtual, March 1-2, 2021.
    [ Link ]
13. A Web-based Visual Analytics Application for Biological Networks
    Michael Krone, Andreas Dräger, Ebru Cobanoglu, Manuel O. Harke, Miriam Hoene, Cora Weigert, and Rainer Lehmann.
    EUROVIS 2020, virtual conference. Editors: J. Byška and S. Jänicke.
    [ DOI | YouTube | PDF | BibTeX ]
14. Building a reference map of the interaction network in the human nasal microbial community
    Reihaneh Mostolizadeh, Alina Renz, Anastasia Grekova, and Andreas Dräger
    ISMB 2020, virtual conference
15. FBA reveals guanylate kinase as a potential target against SARS-CoV-2
    Alina Renz, Lina Widerspick, Andreas Dräger.
    ISMB 2020, virtual conference
    [ YouTube ]
16. 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 Dräger.
    Internationale Konferenz zur Systembiologie (ICSB), Okinawa, Japan
17. The Systems Biology Graphical Notation: a standardised representation of biological maps
    Vasundra Touré, Alexander Mazein, Adrien Rougny, Andreas Dräger, Ugur Dogrusoz, Michael Blinov, and Augustin Luna
    Internationale Konferenz zur Systembiologie (ICSB), Okinawa, Japan
18. 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
19. 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
20. 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
21. 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.
22. 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 ]
23. 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, 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 ]
24. 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 ]
25. Support for Flux Balance Constraints Models in JSBML
    Nicolas Rodriguez, Alex Thomas, Michael Hucka, Nicolas Le Novère, Bernhard Ø Palsson, and Andreas Dräger. 3^rd Conference on Constraint-Based Reconstruction and Analysis, Charlottesville, VA, USA (20.-23. Mai 2014). 
26. 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. 20^th International Symposium on Microsomes and Drug Oxidations, 2014. [ link ]
27. 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. 4^th Conference on Systems Biology of Mammalian Cells (SBMC), 2012. [ PDF ]
28. 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 ]
29. A Tool for Interactive Comparative Sequence Analysis
    Andreas Dräger, Dietrich H. Nies, and Stefan Posch. German Conference on Bioinformatics (GCB) 2006, Tübingen, Germany. [ PDF ]