List of Publications

Oriol Guitart-Pla, Manjunath Kustagi, Frank Rügheimer, Andrea Califano and Benno Schwikowski:
The Cyni framework for network inference in Cytoscape.
Bioinformatics, Dec. 2014, (advance access online version).
[ bib | DOI | http ]

Frank Rügheimer:
Computational Intelligence in Intelligent Data Analysis, vol. 445 of Studies in Computational Intelligence, chap. Applications of Intelligent Data Analysis for the Discovery of Gene Regulatory Networks, pp. 251-262, Springer, Berlin Heidelberg, Jan. 2013.
[ bib | DOI | springerlink ]

Joerg Martin Buescher, Wolfram Liebermeister, Matthieu Jules, Markus Uhr, Jan Muntel, Eric Botella, Bernd Hessling, Roelco Jacobus Kleijn, Ludovic Le Chat, François Lecointe, Ulrike Mäder, Pierre Nicolas, Sjouke Piersma, Frank Rügheimer, Dörte Becher, Philippe Bessieres, Elena Bidnenko, Emma L. Denham, Entienne Dervyn, Kevin M. Devine, Geoff Doherty, Samuel Drulhe, Liza Felicori, Mark J. Fogg, Anne Goelzer, Annette Hansen, Colin R. Harwood, Michael Hecker, Sebastian Hubner, Claus Hultschig, Hanne Jarmer, Edda Klipp, Aurélie Leduc, Peter Lewis, Frank Molina, Philippe Noirot, Sabine Peres, Nathalie Pigeonneau, Susanne Pohl, Simon Rasmussen, Bernd Rinn, Marc Schaffer, Julian Schnidder, Benno Schwikowski, Jan Maarten van Dijl, Patrick Veiga, Sean Walsh, Anthony J. Wilkinson, Jörg Stelling, Stéphane Aymerich and Uwe Sauer:
Global network reorganization during dynamic adaptation of Bacillus subtilis metabolism.
Science, 335(6072):1099-1103, Mar. 2012.
[ bib | DOI | .pdf ]

Pierre Nicolas, Ulrike Mäder, Entienne Dervyn, Tatiana Rochat, Aurélie Leduc, Nathalie Pigeonneau, Elena Bidnenko, Elodie Marchadier, Mark Hoebeke, Stéphane Aymerich, Dörte Becher, Paola Biscicchia, Eric Botella, Olivier Delumeau, Geoff Doherty, Emma L. Denham, Mark J. Fogg, Vincent Fromion, Anne Goelzer, Annette Hansen, Elisabeth Härtig, Colin R Harwood, Georg Homuth, Hanne Jarmer, Matthieu Jules, Edda Klipp, Ludovic Le Chat, François Lecointe, Peter Lewis, Wolfram Liebermeister, Anika March, Ruben A. T. Mars, Priyanka Nannapaneni, David Noone, Susanne Pohl, Bernd Rinn, Frank Rügheimer, Praveen K. Sappa, Franck Samson, Marc Schaffer, Benno Schwikowski, Leif Steil, Jörg Stülke, Thomas Wiegert, Kevin M. Devine, Anthony J. Wilkinson, Jan Maarten van Dijl, Michael Hecker, Uwe Völker, Philippe Bessières and Philippe Noirot:
Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis.
Science, 335(6072):1103-1106, Mar. 2012.
[ bib | DOI | .pdf ]

Frank Rügheimer:
Knowledge representation with condensed set-valued attributes, Ph.D. thesis, Fakultät für Informatik, Otto-von-Guericke Universität Magdeburg, Magdeburg, 2012.
[ bib | http ]

Pascal Bochet, Frank Rügheimer, Tina Guina, Peter Brooks, David Goodlett, Peter Clote and Benno Schwikowski:
Fragmentation-free LC-MS can identify hundreds of proteins.
Proteomics, 11(1):22-32, Jan. 2011.
[ bib | DOI | http ]

Frank Rügheimer, Ashish Anand and Benno Schwikowski:
A Software architecture for De Novo Induction of Regulatory Networks from Expression Data.
In Proceedings of the Journées Ouvertes Biologie Informatique Mathématiques (JOBIM) 2011, Paris, pp. 295-296, 2011.
[ bib | .pdf ]

Frank Rügheimer:
Information Processing and Management of Uncertainty in Knowledge-Based Systems. Applications, vol. 81 of Communications in Computer and Information Science, chap. Using Enriched Ontology Structure for Improving Statistical Models of Gene Annotation Sets, pp. 55-64, Springer, Heidelberg, 2010.
[ bib | DOI | springerlink | .pdf ]

Pascal Bochet, Frank Rügheimer, Tina Guina, David Goodlett, Peter Clote and Benno Schwikowski:
Generalized Peptide Mass Fingerprinting on whole-cell HPLC-MS proteomics experiments.
In Proceedings of the Journées Ouvertes Biologie Informatique Mathématiques (JOBIM) 2009, Nantes, pp. 129-130, Société Française de Bioinformatique, 2009.
[ bib ]

Frank Rügheimer and Ernesto William De Luca:
Condensed Random Sets for Efficient Quantitative Modelling of Gene Annotation Data.
In Proceedings of the Workshop Knowledge Discovery, Data Mining and Machine Learning (KDML) at the LWA 2009, pp. 92-99, Gesellschaft für Informatik, 2009, (published online).
[ bib | .pdf ]

Ernesto William De Luca and Frank Rügheimer:
The Sense Folder Approach for Generic and Domain-Specific Retrieval Tasks.
In Proceedings of the Workshop Information Retrieval (WIR) at the LWA 2009, pp. 44-51, Gesellschaft für Informatik, 2009, (published online).
[ bib | .pdf ]

Frank Rügheimer and Rudolf Kruse:
An Uncertainty Representation for Set-Valued Attributes with Hierarchical Domains.
In Proceedings of the 12th International Conference on Information Processing and Management of Uncertainty in Knowledge-Based Systems (IPMU 2008), Málaga, Spain, 2008, (published online).
[ bib | .html ]

Matthias Steinbrecher, Frank Rügheimer and Rudolf Kruse:
Computational Intelligence in Automotive Applications, vol. 132/2008 of Studies in Computational Intelligence, chap. Application of Graphical Models in the Automotive Industry, pp. 79-88, Springer, Berlin/Heidelberg, 2008.
[ bib | DOI | springerlink ]

Ernesto William De Luca and Frank Rügheimer:
Discovering Linguistic Dependencies with Graphical Models.
In LWA 2007 Workshop Proceedings, pp. 119-125, Martin-Luther-University Halle-Wittenberg, Germany, Sep. 2007.
[ bib ]

Frank Rügheimer:
A Condensed Representation for Distributions over Set-Valued Data.
In Ralf Mikut and Markus Reischl, eds.:
Proc. 17. Workshop Computational Intelligence, Universitätsverlag Karlsruhe, Karlsruhe, Germany, 2007.
[ bib ]

Frank Rügheimer:
15. Workshop Computational Intelligence (summary).
at - Automatisierungstechnik, 54, Mar. 2006, (in German).
[ bib ]

Jörg Gebhardt, Aljoscha Klose, Heinz Detmer, Frank Rügheimer and Rudolf Kruse:
Graphical Models for Industrial Planning on Complex Domains.
In Giacomo Della Riccia, Didier Dubois, Rudolf Kruse and Hans-Joachim Lenz, eds.:
Decision Theory and Multi-Agent Planning, no. 482 In CISM Courses and Lectures, pp. 131-143, Springer, 2006, (contains papers read on the 7th Int. Workshop `Intelligent Agents: Decision-Support and Planning', Udine, Italy, 2004).
[ bib | .pdf ]

Rudolf Kruse, Jörg Gebhardt, Frank Rügheimer and Heinz Detmer:
Planning with Graphical Models.
In Proc. of the 2006 Conference on COGnitive systems with Interactive Sensors (COGIS'06), Paris, France, 2006.
[ bib ]

Frank Rügheimer, Detlef Nauck and Rudolf Kruse:
Informationsfusion in Neuro-Fuzzy-Systemen.
In J. Beyerer, F. Puente León and K.-D. Sommer, eds.:
Informationsfusion in der Mess- und Sensortechnik, pp. 113-125, Universitätsverlag Karlsruhe, Karlsruhe, 2006, (in German).
[ bib ]

Frank Rügheimer and Rudolf Kruse:
Information Miner - a Data Analysis Platform.
In Proc. of the Joint 4th EUSFLAT 11th LFA Conference 2005, Universitat Politènica de Catalunya, Barcelona, Spain, 2005.
[ bib | .pdf ]

Frank Rügheimer and Rudolf Kruse:
Datenanalyse-Plattform InformationMiner.
In Ralf Mikut and Markus Reischl, eds.:
Proc. 15. Workshop Fuzzy-Systeme und Computational Intelligence, Universitätsverlag Karlsruhe, Karlsruhe, Germany, 2005, (in German).
[ bib | .pdf ]

Jörg Gebhardt, Frank Rügheimer, Heinz Detmer and Rudolf Kruse:
Adaptable Markov Models in Industrial Planning.
In Proceedings of the 2004 IEEE International Conference on Fuzzy Systems (Budapest), IEEE Press, Piscataway, NJ, USA, 2004.
[ bib | .pdf ]

Frank Rügheimer:
Data Mining with Graphical Models (extended abstract).
In J. Biethan, J. Kuhl and A. Lackner, eds.:
Soft-Computing in Wissenschaft und Wirtschaft, Tagungsband zum 6. Göttinger Symposium Soft-Computing, AFN, Göttingen, Germany, 2003, (in German).
[ bib ]

(Bibliography generated using bibtex2html 1.85.)