Publications

Year of Publication: 2019

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.
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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 18th 2019.
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Year of Publication: 2018

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 21st 2018.
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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.
bioRxiv, September 26th 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 23rd 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, July 26th 2018.
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Memote: A community-driven effort towards a standardized genome-scale metabolic model test suite

Christian Lieven, Moritz Emanuel Beber, Brett G. Olivier, Frank T. Bergmann, Parizad Babaei, Jennifer A. Bartell, Lars M. Blank, Siddharth Chauhan, Kevin Correia, Christian Diener, Andreas Dräger, Birgitta Elisabeth Ebert, Janaka N. Edirisinghe, Ronan M. T. Fleming, Beatriz Garcia-Jimenez, Wout van Helvoirt, Christopher Henry, Henning Hermjakob, Markus J. Herrgård, Hyun Uk Kim, Zachary A. King, Jasper Jan Koehorst, Steffen Klamt, Edda Klipp, Meiyappan Lakshmanan, Nicolas Le Novère, Dong-Yup Lee, Sang Yup Lee, Sunjae Lee, Nathan E. Lewis, Hongwu Ma, Daniel Machado, Radhakrishnan Mahadevan, Paulo Maia, Adil Mardinoglu, Greg L. Medlock, Jonathan Monk, Jens Nielsen, Lars K. Nielsen, Juan Nogales, Intawat Nookaew, Osbaldo Resendis, Bernhard O. Palsson, Jason A. Papin, Kiran Raosaheb Patil, Nathan D. Price, Anne Richelle, Isabel Rocha, Peter Schaap, Rahuman S. Malik Sheriff, Saeed Shoaie, Nikolaus Sonnenschein, Bas Teusink, Paulo Vilaca, Jon Olav Vik, Judith A. Wodke, Joana C. Xavier, Qianqian Yuan, Maksim Zakhartsev, and Cheng Zhang.
BioRxiv, June 21st 2018.
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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, 26th 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. Danielsdottir, Almut Heinken, Alberto Noronha, Peter W. Rose, Stephen K. Burley, Ronan M. T. Fleming, Jens Nielsen, Ines Thiele, and Bernhard O. Palsson.
Nature Biotechnology, February 19th 2018.
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Year of Publication: 2017

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, October 2017.
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Year of Publication: 2016

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 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 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 2016.
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Year of Publication: 2015

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.
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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 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, September 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. Lia, Pep Charusantia, Ali Ebrahim, Colton J. Lloyd, James T. Yurkovich, Bin Du, Andreas Dräger, Alex Thomas, Yuekai Sun, Michael A. Saunders, and Bernhard O. Palsson.
Proceedings of the National Academy of Sciences, August 2015.
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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 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 2015.
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Year of Publication: 2014

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.
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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 2014.
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Year of Publication: 2013

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.
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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 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 2013.
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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.
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Parameter Estimation

Metabolic Network Modeling

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

Andreas Dräger and Hannes Planatscher.
Encyclopedia of Systems Biology, Kapitel 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 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 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 2013.
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Year of Publication: 2012

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.
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CySBML: a Cytoscape plugin for SBML

Matthias König, Andreas Dräger, and Hermann-Georg Holzhütter.
Bioinformatics, 28(18):2402-2403, July 2012.
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Year of Publication: 2011

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.
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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 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 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 2011.
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Computational Modeling of Biochemical Networks

Andreas Dräger
Ph.D. thesis, University of Tübingen, Tübingen, Germany, Verlag Dr. Hut, Munich. ISBN 978-3-86853-850-2, January 2011.
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Year of Publication: 2010

ProDGe: investigating protein-protein interactions at the domain level

Finja Büchel, Clemens Wrzodek, Florian Mittag, Andreas Dräger, Adrian Schröder, and Andreas Zell.
Technichal Report, Nature Precedings, August 2011.
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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.
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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.
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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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Year of Publication: 2009

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.
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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 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, April 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 2009.
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Year of Publication: 2008

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.
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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 2008.
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Year of Publication: 2007

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 (editors) 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 (Editoren) IEEE Congress on Evolutionary Computation (CEC 2007), pages 620-627, Singapore, September 2007.
IEEE Computational Intelligence Society, IEEE Press.
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Inferring gene regulatory networks by machine learning methods

Jochen Supper, Holger Fröhlich, Christian Spieth, Andreas Dräger, and Andreas Zell.
In David Sankoff, Lusheng Wang, and Francis Chin (editors) Proceedings of the 5th Asia-Pacific Bioinformatics Conference (APBC 2007), volume 5 of the 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.
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