Publications

Year of Publication: 2021

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 15th 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 19th 2021.
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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 8th 2021.
Details | DOIPreprint | PubMedPDF | BibTeX ]

The Systems Biology Simulation Core Library

Hemil Panchiwala, Shalin Shah, Hannes Planatscher, Mykola Zakharchuk, Matthias König, and Andreas Dräger.
Bioinformatics, btab669, September 23rd 2021.
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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, 24th 2021.
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Year of Publication: 2020

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

Alina RenzLina Widerspick, and Andreas Dräger.
Bioinformatics, Volume 36, Issue Supplement_2, December 29th 2020, Pages i813-i821.
Details | DOIZenodo | PubMed | YouTube | PDF | BibTeX ]

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 26th 2020.
Details | DOIMedRxiv | PDF | PubMed | BibTeX  ]

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 13th 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 28th 2020.
[ Details | DOI | PDF | PubMed | BibTeX ]

Clinical Applications of Metabolic Models in SBML Format

Alina Renz, Reihaneh Mostolizadeh, and Andreas Dräger
Reference Module in Biomedical Sciences, Elsevier, Januar 30th 2020
[ Details | DOI | PDF | PubMed | BibTeX ]

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 25th 2020
[ Details | DOI | PDF | PubMed | BibTeX ]


Year of Publication: 2019

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 7th 2019
[ Details | DOI | PDF | PubMed | BibTeX ]


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Year of Publication: 2007