See also google.scholar and dblp.

2022

CNApy: a CellNetAnalyzer GUI in Python for analyzing and designing metabolic networks, Sven Thiele, Axel von Kamp, Pavlos Stephanos Bekiaris, Philipp Schneider, Steffen Klamt, Bioinformatics, 38(5), 2022.

2019

Designing optimal experiments to discriminate interaction graph models, Sven Thiele, Sandra Heise, Wiebke Hessenkemper, Hannes Bongartz, Melissa Fensky, Fred Schaper, Steffen Klamt, IEEE/ACM Trans. Comput. Biol. Bioinform, 16(3), 2019.

2017

Use of CellNetAnalyzer in biotechnology and metabolic engineering, Axel von Kamp, Sven Thiele, Oliver Hädicke, Steffen Klamt, Journal of Biotechnology, 2017.

Meneco, a Topology-Based Gap-Filling Tool Applicable to Degraded Genome-Wide Metabolic Networks, Sylvain Prigent, Clémence Frioux, Simon M Dittami, Sven Thiele, Abdelhalim Larhlimi, Guillaume Collet, Fabien Gutknecht, Jeanne Got, Damien Eveillard, Jérémie Bourdon, Frédéric Plewniak, Thierry Tonon, Anne Siegel, PLOS Computational Biology, 2017.

2016

Putative bacterial interactions from metagenomic knowledge with an integrative systems ecology approach, Philippe Bordron, Mauricio Latorre, Maria-Paz Cortés, Mauricio González, Sven Thiele, Anne Siegel, Alejandro Maass, Damien Eveillard, MicrobiologyOpen, 2016.

2015

Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies, Sven Thiele, Luca Cerone, Julio Saez-Rodriguez, Anne Siegel, Carito Guziołowski, and Steffen Klamt, BMC Bioinformatics, 16(345), 2015.

Learning Boolean logic models of signaling networks with ASP, Santiago Videla, Carito Guziołowski, Federica Eduati, Sven Thiele, Martin Gebser, Jacques Nicolas, Julio Saez-Rodriguez, Torsten Schaub, and Anne Siegel, Theoretical Computer Science, 599, pages 79–101, Advances in Computational Methods in Systems Biology, 2015.

2014

The genome-scale metabolic network of Ectocarpus siliculosus (EctoGEM): a resource to study brown algal physiology and beyond, Sylvain Prigent, Guillaume Collet, Simon M. Dittami, Ludovic Delage, Floriane Ethis de Corny, Olivier Dameron, Damien Eveillard, Sven Thiele, Jeanne Cambefort, Catherine Boyen, Anne Siegel, and Thierry Tonon, The Plant Journal, 80(2), pages 367–381, 2014.

2013

Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming, Carito Guziołowski, Santiago Videla, Federica Eduati, Sven Thiele, Thomas Cokelaer, Anne Siegel, and Julio Saez-Rodriguez, Bioinformatics, 29(18), pages 2320-2326, 2013.

An ASP Application in Integrative Biology: Identification of Functional Gene Units, Philippe Bordron, Damien Eveillard, Alejandro Maass, Anne Siegel, and Sven Thiele, Proceedings of the Twelfth International Conference on Logic Programming and Nonmonotonic Reasoning, volume 8148 of Lecture Notes in Computer Science, pages 206-218, Springer, 2013.

Extending the Metabolic Network of Ectocarpus Siliculosus Using Answer Set Programming, Guillaume Collet, Damien Eveillard, Martin Gebser, Sylvain Prigent, Torsten Schaub, Anne Siegel, and Sven Thiele, Proceedings of the Twelfth International Conference on Logic Programming and Nonmonotonic Reasoning, volume 8148 of Lecture Notes in Computer Science, pages 245-256, Springer, 2013.

2012

Revisiting the Training of Logic Models of Protein Signaling Networks with ASP, Santiago Videla, Carito Guziołowski, Federica Eduati, Sven Thiele, Niels Grabe, Julio Saez-Rodriguez, and Anne Siegel, Proceedings of the Tenth International Conference on Computational Methods in Systems Biology (CMSB’12), volume 7605 of Lecture Notes in Computer Science, pages 342-361, Springer, 2012.

Modeling biological systems with Answer Set Programming, Sven Thiele, PhD thesis, Universitätsbibliothek, 2012.

2011

Detecting Inconsistencies in Large Biological Networks with Answer Set Programming, Martin Gebser, Torsten Schaub, Sven Thiele, and Philippe Veber, Theory and Practice of Logic Programming, 11(2-3), pages 323-360, 2011.

2010

Repair and Prediction (Under Inconsistency) in Large Biological Networks with Answer Set Programming, Martin Gebser, Carito Guziołowski, Mihail Ivanchev, Torsten Schaub, Anne Siegel, Sven Thiele, and Philippe Veber, Proceedings of the Twelfth International Conference on the Principles of Knowledge Representation and Reasoning (KR’10), AAAI Press, 2010.

xpanda: A (Simple) Preprocessor for Adding Multi-Valued Propositions to ASP, Martin Gebser, Henrik Hinrichs, Torsten Schaub, and Sven Thiele, Proceedings of the Twenty-third Workshop on (Constraint) Logic Programming (WLP’09), page 51, Universitätsverlag Potsdam, 2010.

The BioASP Library: ASP Solutions for Systems Biology, Martin Gebser, Arne König, Torsten Schaub, Sven Thiele, and Philippe Veber, Proceedings of the Twenty-second International Conference on Tools with Artificial Intelligence (ICTAI’10), volume 1, pages 383-389, IEEE Computer Society, 2010.

2009

Metabolic Network Expansion with Answer Set Programming, Torsten Schaub and Sven Thiele, Proceedings of the Twenty-fifth International Conference on Logic Programming (ICLP’09), volume 5649 of Lecture Notes in Computer Science, pages 312-326, Springer, 2009.

On the Input Language of ASP Grounder Gringo, Martin Gebser, Roland Kaminski, Max Ostrowski, Torsten Schaub, and Sven Thiele, Proceedings of the Tenth International Conference on Logic Programming and Nonmonotonic Rea- soning (LPNMR’09), volume 5753 of Lecture Notes in Computer Science, pages 502-508, Springer, 2009.

2008

Detecting Inconsistencies in Large Biological Networks with Answer Set Programming, Martin Gebser, Torsten Schaub, Sven Thiele, Björn Usadel, and Philippe Veber, Proceedings of the Twenty-fourth International Conference on Logic Programming (ICLP’08), volume 5366 of Lecture Notes in Computer Science, pages 130-144, Springer, 2008.

Engineering an Incremental ASP Solver, Martin Gebser, Roland Kaminski, Benjamin Kaufmann, Max Ostrowski, Torsten Schaub, and Sven Thiele, Proceedings of the Twenty-fourth International Conference on Logic Programming (ICLP’08), volume 5366 of Lecture Notes in Computer Science, pages 190-205, Springer, 2008.

A Versatile Intermediate Language for Answer Set Programming, Martin Gebser, Tomi Janhunen, Max Ostrowski, Torsten Schaub, and Sven Thiele, Proceedings of the Twelfth International Workshop on Nonmonotonic Reasoning (NMR’08), number UNSW-CSE-TR-0819 in School of Computer Science and Engineering, The University of New South Wales, Technical Report Series, pages 150-159, 2008.

2007

Gringo : A New Grounder for Answer Set Programming, Martin Gebser, Torsten Schaub, and Sven Thiele, Proceedings of the Ninth International Conference on Logic Programming and Nonmonotonic Reasoning (LPNMR’07), volume 4483 of Lecture Notes in Computer Science, pages 266-271, Springer, 2007.

COBA 2.0: A Consistency-Based Belief Change System, James P. Delgrande, Daphne H. Liu, Torsten Schaub, and Sven Thiele, Proceedings of the Ninth European Conference on Symbolic and Quantitative Approaches to Reasoning with Uncertainty (ECSQARU’07), volume 4724 of Lecture Notes in Computer Science, pages 78-90. Springer, 2007.

2006

On Probing and Multi-Threading in Platypus, Jean Gressmann, Tomi Janhunen, Robert E. Mercer, Torsten Schaub, Sven Thiele, and Richard Tichy, Proceedings of the Seventeenth European Conference on Artificial Intelligence (ECAI’06), volume 141 of Frontiers in Artificial Intelligence and Applications, pages 392-396, IOS Press, 2006.

2005

Platypus: A Platform for Distributed Answer Set Solving, Jean Gressmann, Tomi Janhunen, Robert E. Mercer, Torsten Schaub, Sven Thiele, and Richard Tichy, Proceedings of the Eighth International Conference on Logic Programming and Nonmonotonic Reasoning (LPNMR’05), volume 3662 of Lecture Notes in Computer Science, pages 227-239, Springer, 2005.