Publications | University of Tübingen

From FAIR to CURE: Guidelines for Computational Models of Biological Systems

Herbert M. Sauro, Eran Agmon, Michael L. Blinov, John H. Gennari, Joe Hellerstein, Adel Heydarabadipour, Peter Hunter, Bartholomew E. Jardine, Elebeoba May, David P. Nickerson, Lucian P. Smith, Gary D. Bader, Frank T. Bergmann, Patrick M. Boyle, Andreas Dräger, James R. Faeder, Song Feng, Juliana Freire, Fabian Fröhlich, James A. Glazier, Thomas E. Gorochowski, Tomáš Helikar, Stefan Hoops, Princess Imoukhuede, Sarah M. Keating, Matthias König, Reinhard Laubenbacher, Leslie M. Loew, Carlos F. Lopez, William W. Lytton, Andrew McCulloch, Pedro Mendes, Chris J. Myers, Jerry G. Myers, Lealem Mulugeta, Anna Niarakis, David D. van Niekerk, Brett G. Olivier, Alexander A. Patrie, Ellen M. Quardokus, Nicole Radde, Johann M. Rohwer, Sven Sahle, James C. Schaff, T. J. Sego, Janis Shin, Jacky L. Snoep, Rajanikanth Vadigepalli, H. Steve Wiley, Dagmar Waltemath, and Ion Moraru
Arxiv, February, 21^st, 2025
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FROG Analysis Ensures the Reproducibility of Genome Scale Metabolic Models (Kopie 2)

Reihaneh Mostolizadeh, Finn Mier, and Andreas Dräger
BioRxiv, November, 22^nd, 2024
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FROG Analysis Ensures the Reproducibility of Genome Scale Metabolic Models

Karthik Raman, Miroslav Kratochvíl, Brett G. Olivier, Matthias König, Pratyay Sengupta, Dinesh Kumar Kuppa Baskaran, Tung V. N. Nguyen, Daniel Lobo, St Elmo Wilken, Krishna Kumar Tiwari, Aswathy K. Raghu, Indumathi Palanikumar, Lavanya Raajaraam, Maziya Ibrahim, Sanjaay Balakrishnan, Shreyanash Umale, Frank T. Bergmann, Tanisha Malpani, Venkata P. Satagopam, Reinhard Schneider, Moritz E. Beber, Sarah M. Keating, Mihail Anton, Alina Renz, Meiyappan Lakshmanan, Dong-Yup Lee, Lokanand Koduru, Reihaneh Mostolizadeh, Oscar Dias, Emanuel Cunha, Alexandre Oliveira, Yi Qing Lee, Karsten Zengler, Rodrigo Santibáñez-Palominos, Manish Kumar, Matteo Barberis, Bhanwar Lal Puniya, Tomáš Helikar, Hoang V. Dinh, Patrick F. Suthers, Costas D. Maranas, Isabella Casini, Seyed Babak Loghmani, Nadine Veith, Nantia Leonidou, Feiran Li, Yu Chen, Jens Nielsen, GaRyoung Lee, Sang Mi Lee, Gi Bae Kim, Pedro T. Monteiro, Miguel C. Teixeira, Hyun Uk Kim, Sang Yup Lee, Ulf W. Liebal, Lars M. Blank, Christian Lieven, Chaimaa Tarzi, Claudio Angione, Manga Enuh Blaise, Çelık Pinar Aytar, Mikhail Kulyashov, llya Akberdin, Dohyeon Kim, Sung Ho Yoon, Zhaohui Xu, Jyotshana Gautam, William T. Scott, Peter J. Schaap, Jasper J. Koehorst, Cristal Zuñiga, Gabriel Canto-Encalada, Sara Benito-Vaquerizo, Ivette Parera Olm, Maria Suarez-Diez, Qianquian Yuan, Hongwu Ma, Mohammad Mazharul Islam, Jason A. Papin, Francisco Zorrilla, Kiran Raosaheb Patil, Arianna Basile, Juan Nogales, Granado San León, Freddy Castillo-Alfonso, Roberto Olivares-Hernández, Gabriel Vigueras-Ramírez, Henning Hermjakob, Andreas Dräger, and Rahuman S. Malik-Sheriff
BioRxiv, September, 26^th, 2024
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Exploring the metabolic profile of A. baumannii for antimicrobial development using genome-scale modeling

Bioinformatics Advances

Perspectives on computational modeling of biological systems and the significance of the SysMod community

Bhanwar Lal Puniya, Meghna Verma, Chiara Damiani, Shaimaa Bakr, and Andreas Dräger
Bioinformatics Advances, 26^th 2024
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Microbiology Spectrum

Genome-scale model of Rothia mucilaginosa predicts gene essentialities and reveals metabolic capabilities

Genome-scale metabolic model of Staphylococcus epidermidis ATCC 12228 matches in vitro conditions

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, Nantia Leonidou, Filipe Cabreiro, Andreas Dräger, Michael Schindler, and Christoph Kaleta
Preprints 2023, November, 30^th 2023.
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Genome-scale metabolic models consistently predict in vitro characteristics of Corynebacterium striatum

An integrated systems-biology approach reveals differences in formate metabolism in the genus Methanothermobacter

Isabella 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, and Bastian Molitor
iScience, September 22^nd, 2023
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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, and Berna Sarıyar Akbulut
OMICS: A Journal of Integrative Biology, 27:9, September 14^th, 2023.
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Advancements in Computational Modelling of Biological Systems: seventh annual SysMod meeting

Bhanwar Lal Puniya and Andreas Dräger
Bioinformatics, 14. September 2023.
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SBOannotator: a Python Tool for the Automated Assignment of Systems Biology Ontology Terms

New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells

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
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Genome-scale model of Pseudomonas aeruginosa metabolism unveils virulence and drug potentiation

Hierarchical modelling of microbial communities

Manuel Glöckler, Andreas Dräger, and Reihaneh Mostolizadeh
Bioinformatics, January 17^th, 2023.
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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, October 11^th, 2022
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Computational modelling in health and disease. Highlights of the 6th 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.
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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
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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.
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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.
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The Systems Biology Simulation Core Library

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.
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COVID19 Disease Map, a computational knowledge repository of 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.
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SBMLWebApp: Web-based Simulation, Steady-State Analysis, and Parameter Estimation of Systems Biology Models

An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism

Curating and Comparing 114 Strain-Specific Genome-Scale Metabolic Models of Staphylococcus aureus

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, 24^th 2021.
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Genome-Scale Metabolic Model of Infection with SARS-CoV-2 Mutants Confirms Guanylate Kinase as Robust Potential Antiviral Target

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
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FBA reveals guanylate kinase as a potential target for antiviral therapies against SARS-CoV-2

Computational Model Informs Effective Control Interventions against Y. enterocolitica Co-Infection

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.
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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.
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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.
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Community standards to facilitate development and address challenges in metabolic modeling

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, Michael Hucka and the SBML Level 3 community: 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.
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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.
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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.
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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.
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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.
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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.
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Clinical Applications of Metabolic Models in SBML Format

Alina Renz, Reihaneh Mostolizadeh, and Andreas Dräger
Reference Module in Biomedical Sciences, Elsevier, Januar 30^th 2020
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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, Januar 25^th 2020
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BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree

Charles J. Norsigian, Neha Pusarla, John Luke McConn, James T. Yurkovich, Andreas Dräger, Bernhard O. Palsson, and Zachary King
Nucleic Acids Research, gkz1054, November 7^th 2019
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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.
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Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0

Adrien Rougny, Vasundra Touré, Stuart Moodie, 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, Juni 13^th, 2019.
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Insights into Dynamic Network States Using Metabolomic Data

Reihaneh Mostolizadeh, Andreas Dräger, and Neema Jamshidi.
In: Angelo D’Alessandro (Editor) High-Throughput Metabolomics.
Methods in Molecular Biology, Volumne 1978, chapter, pages 243-258. Humana, New York, NY, May 23^rd, 2019.
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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.
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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 21^st, 2018.
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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^rd, 2018.
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Hopf bifurcation in a model for adult T‐cell leukemia

Reihaneh Mostolizadeh and Zahra Afsharnezhad.
Mathematical Methods in the Applied Sciences, Juli 26^th, 2018.
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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.
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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.
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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. Danielsdóttir, 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.
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A Padawan Programmer's Guide to Developing Academic Software Libraries

James T. Yurkovich, Benjamin J. Yurkovich, Andreas Dräger, Bernhard O. Palsson, and Zachary A. King.
Cell Systems, November 22^nd, 2017.
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Evaluation of rate law approximations in bottom-up kinetic models of metabolism

Bin Du, Daniel C. Zielinski, Andreas Dräger, Justin Tan, Zhen Zhang, Kayla Ruggiero, Garry Arzumanyan, and Bernhard O. Palsson.
BMC Systems Biology, 10(1):1-15, June 6^th, 2016.
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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.
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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 16^th, 2016.
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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 4^th, 2016.
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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 17^th, 2015.
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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 14^th, 2015.
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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, October 9^th, 2015.
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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.
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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 10^th, 2015.
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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 27^th, 2015.
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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 16^th, 2015.
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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 18^th, 2014.
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Improving collaboration by standardization efforts in systems biology

Andreas Dräger and Bernhard Ø. Palsson.
Frontiers in Bioengineering and Biotechnology, 2(61), December 8^th, 2014.
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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 10^th, 2013.
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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 12^th, 2013.
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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 6^th, 2013.
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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 1^st, 2013.
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Parameter Estimation

Metabolic Network Modeling

Andreas Dräger and Hannes Planatscher.
Encyclopedia of Systems Biology, chapter Metabolic Network Modeling, pages 1627-1631. Springer-Verlag, Springer New York Heidelberg Dorodrecht London, August 2013.
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Metabolic Networks

Metabolic Network Modeling

Andreas Dräger and Hannes Planatscher.
Encyclopedia of Systems Biology, chapter Metabolic Network Modeling, pages 1249-1251. Springer-Verlag, Springer New York Heidelberg Dorodrecht London, August 2013.
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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 5^th, 2013.
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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 26^th, 2013.
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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 21^st, 2013.
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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 24^th, 2012.
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CySBML: a Cytoscape plugin for SBML

Matthias König, Andreas Dräger, and Hermann-Georg Holzhütter.
Bioinformatics, 28(18):2402-2403, July 24^th, 2012.
[ Details | DOI | PubMed | BibTeX ]

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, October 25^th, 2011.
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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 14^th, 2011.
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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.
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KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats

Clemens Wrzodek, Andreas Dräger, and Andreas Zell.
Bioinformatics, 27(16):2314-2315, June 23^rd, 2011.
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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 22^nd, 2011.
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Computational Modeling of Biochemical Networks

Andreas Dräger
Ph.D. thesis, Eberhard Karls University of Tübingen, Tübingen, Germany, Verlag Dr. Hut, München. ISBN 978-3-86853-850-2, January 2011.
[ Details | Link | BibTeX ]

ProDGe: investigating protein-protein interactions at the domain level

Finja Büchel, Clemens Wrzodek, Florian Mittag, Andreas Dräger, Adrian Schröder, and Andreas Zell.
Technischer Bericht, Nature Precedings, August 4^th, 2011.
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Automating mathematical modeling of biochemical reaction networks

Andreas Dräger, Adrian Schröder, and Andreas Zell.
Systems Biology for Signaling Networks, vol. 1 of Systems Biology, chapter, pages 159-205. Springer-Verlag, August 5^th, 2010.
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International Conference on Bioinformatics and Computational Biology, BIOCOMP 2010

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 (eds.) International Conference on Bioinformatics and Computational Biology, BIOCOMP 2010, vol. 2, pages 734-742. CSREA Press, July 2010.
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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.
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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 (eds.), German Conference on Bioinformatics (GCB 2009), vol. P-157 of the Lecture Notes in Informatics, pages 191-200, Halle (Saale), Germany, September 2009. German Society for Computer Science.
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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 30^th, 2009.
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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, March 23^rd, 2009.
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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 14^th, 2009.
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BioJava: an open-source framework for bioinformatics

https://doi.org/10.1093/bioinformatics/btn397

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 8^th, 2008.
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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 30^th, 2008.
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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 and Lipo Wang (Editoren) IEEE Congress on Evolutionary Computation (CEC 2007), pages 896-903, Singapore, September 2007. IEEE Computational Intelligence Society, IEEE Press.
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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 (eds.) IEEE Congress on Evolutionary Computation (CEC 2007), pages 620-627, Singapore, September 2007.
IEEE Computational Intelligence Society, IEEE Press.
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Proceedings of the 5th Asia-Pacific Bioinformatics Conference (APBC 2007)

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 (eds.) Proceedings of the 5th Asia-Pacific Bioinformatics Conference (APBC 2007), vol. 5 of the Series on Advances in Bioinformatics and Computational Biology, pages 247-256, 57 Shelton Street, Govent Garden, London WC2H 9HE, UK, January 2007. Imperial College Press.
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