@INCOLLECTION{GebKloDetRueKru2006,
  author = {J{\"o}rg Gebhardt and Aljoscha Klose and Heinz Detmer and Frank R{\"u}gheimer and Rudolf Kruse},
  editor = {Giacomo Della Riccia and Didier Dubois and Rudolf Kruse and Hans-Joachim Lenz},
  note = {contains papers read on the 7th Int. Workshop `Intelligent Agents: Decision-Support and Planning', Udine, Italy, 2004},
  number = {482},
  pages = {131--143},
  publisher = {Springer},
  series = {CISM Courses and Lectures},
  title = {Graphical Models for Industrial Planning on Complex Domains},
  url = {http://www.ruegheimer.org/publications/cism_04.pdf},
  booktitle = {Decision Theory and Multi-Agent Planning},
  year = {2006}
}

@INPROCEEDINGS{RueKru2005,
  author = {Frank R{\"u}gheimer and Rudolf Kruse},
  address = {Barcelona, Spain},
  booktitle = {Proc. of the Joint 4th EUSFLAT 11th LFA Conference 2005},
  publisher = {Universitat Polit{\`e}nica de Catalunya},
  title = {Information Miner -- a Data Analysis Platform},
  url = {http://www.ruegheimer.org/publications/eusflat05.pdf},
  year = {2005}
}

@INPROCEEDINGS{RueKru2005b,
  author = {Frank R{\"u}gheimer and Rudolf Kruse},
  address = {Karlsruhe, Germany},
  booktitle = {Proc. 15. Workshop Fuzzy-Systeme und Computational Intelligence},
  note = {in German},
  publisher = {Universit{\"a}tsverlag Karlsruhe},
  title = {Datenanalyse-Plattform InformationMiner},
  url = {http://www.ruegheimer.org/publications/bomm_05.pdf},
  editor = {Ralf Mikut and Markus Reischl},
  year = {2005}
}

@INPROCEEDINGS{RueGebDetKru2004,
  title = {Adaptable Markov Models in Industrial Planning},
  booktitle = {Proceedings of the 2004 IEEE International Conference on Fuzzy Systems (Budapest)},
  author = {J{\"o}rg Gebhardt and Frank R{\"u}gheimer and Heinz Detmer and Rudolf Kruse},
  publisher = {IEEE Press},
  address = {Piscataway, NJ, USA},
  url = {http://www.ruegheimer.org/publications/fieee_04.pdf},
  year = {2004}
}

@INPROCEEDINGS{KruGebRueDet2006,
  title = {Planning with Graphical Models},
  booktitle = {Proc. of the 2006 Conference on COGnitive systems with Interactive Sensors (COGIS'06), Paris, France},
  author = {Rudolf Kruse and J{\"o}rg Gebhardt and Frank R{\"u}gheimer and Heinz Detmer},
  year = {2006}
}

@ARTICLE{Rue2006,
  title = {15. Workshop Computational Intelligence (summary)},
  author = {Frank R{\"u}gheimer},
  journal = {at -- Automatisierungstechnik },
  volume = {54},
  month = MAR,
  note = {in German},
  publisher = {Oldenbourg Wissenschaftsverlag},
  address = {M{\"u}nchen, Germany},
  year = {2006}
}

@INPROCEEDINGS{Rue2003,
  title = {Data Mining with Graphical Models (extended abstract)},
  booktitle = {Soft-Computing in Wissenschaft und Wirtschaft, Tagungsband zum 6. G{\"o}ttinger Symposium Soft-Computing},
  author = {Frank R{\"u}gheimer},
  editor = {J. Biethan and J. Kuhl and A. Lackner},
  publisher = {AFN},
  address = {G{\"o}ttingen, Germany},
  note = {in German},
  year = {2003}
}

@INPROCEEDINGS{RueNauKru2006,
  title = {Informationsfusion in Neuro-Fuzzy-Systemen},
  booktitle = {Informationsfusion in der Mess- und Sensortechnik},
  author = {Frank R{\"u}gheimer and Detlef Nauck and Rudolf Kruse},
  editor = {J. Beyerer and F. Puente Le{\'o}n and K.-D. Sommer},
  publisher = {Universit{\"a}tsverlag Karlsruhe},
  address = {Karlsruhe},
  pages = {113--125},
  isbn = {3-86644-053-7},
  note = {in German},
  year = {2006}
}

@INPROCEEDINGS{DelRue2007,
  title = {Discovering Linguistic Dependencies with Graphical Models},
  booktitle = {LWA 2007 Workshop Proceedings},
  author = {Ernesto William De~Luca and Frank R{\"u}gheimer},
  publisher = {Martin-Luther-University Halle-Wittenberg},
  location = {Halle},
  address = {Germany},
  pages = {119--125},
  month = SEP,
  keywords = {Graphical Models, MultiSemCor, MultiWordNet},
  remarks = {experiments on learning structure of graphical models from linguistic data only qualitative results due to small samples},
  year = {2007}
}

@INPROCEEDINGS{Rue2007,
  title = {A Condensed Representation for Distributions over Set-Valued Data},
  booktitle = {Proc. 17. Workshop Computational Intelligence},
  author = {Frank R{\"u}gheimer},
  editor = {Ralf Mikut and Markus Reischl},
  publisher = {Universit{\"a}tsverlag Karlsruhe},
  address = {Karlsruhe, Germany},
  year = {2007}
}

@INPROCEEDINGS{RueKru2008,
  title = {An Uncertainty Representation for Set-Valued Attributes with Hierarchical Domains},
  booktitle = {Proceedings of the 12th International Conference on Information Processing and Management of Uncertainty in Knowledge-Based Systems (IPMU 2008), M{\'a}laga, Spain},
  author = {Frank R{\"u}gheimer and Rudolf Kruse},
  url = {http://www.gimac.uma.es/ipmu08/proceedings/html/027.html},
  note = {published online},
  year = {2008}
}

@INBOOK{SteRueKru2008,
  title = {Computational Intelligence in Automotive Applications},
  series = {Studies in Computational Intelligence},
  author = {Matthias Steinbrecher and Frank R{\"u}gheimer and Rudolf Kruse},
  publisher = {Springer},
  address = {Berlin/Heidelberg},
  pages = {79--88},
  chapter = {Application of Graphical Models in the Automotive Industry},
  volume = {132/2008},
  year = {2008},
  isbn = {978-3-540-79256-7},
  keywords = {automotive industry, Bayesian Networks, Graphical Models, Markov Networks, planning},
  doi = {10.1007/978-3-540-79257-4_5},
  springer = {http://www.springerlink.com/content/v2g556403238145v/}
}

@INPROCEEDINGS{BocRueGuiGooCloSch2009,
  title = {Generalized Peptide Mass Fingerprinting on whole-cell {HPLC-MS} proteomics experiments},
  booktitle = {Proceedings of the Journ{\'e}es Ouvertes Biologie Informatique Math{\'e}matiques (JOBIM) 2009, Nantes},
  author = {Pascal Bochet and Frank R{\"u}gheimer and Tina Guina and David Goodlett and Peter Clote and Benno Schwikowski},
  publisher = {Soci{\'e}t{\'e} Fran\c{c}aise de Bioinformatique},
  pages = {129--130},
  year = {2009}
}

@INPROCEEDINGS{RueDel2009,
  title = {Condensed Random Sets for Efficient Quantitative Modelling of Gene Annotation Data},
  booktitle = {Proceedings of the Workshop Knowledge Discovery, Data Mining and Machine Learning (KDML) at the LWA 2009},
  author = {Frank R{\"u}gheimer and Ernesto William De~Luca},
  pages = {92--99},
  url = {http://lwa09.informatik.tu-darmstadt.de/pub/KDML/WebHome/KDML_Proceedings.pdf},
  publisher = {Gesellschaft f{\"u}r Informatik },
  note = {published online},
  year = {2009}
}

@INPROCEEDINGS{DelRue2009,
  title = {The Sense Folder Approach for Generic and Domain-Specific Retrieval Tasks},
  booktitle = {Proceedings of the Workshop Information Retrieval (WIR) at the LWA 2009},
  pages = {44--51},
  author = {Ernesto William De~Luca and Frank R{\"u}gheimer},
  publisher = {Gesellschaft f{\"u}r Informatik},
  url = {http://lwa09.informatik.tu-darmstadt.de/pub/IR/WebHome/LWA_Proceedings.pdf},
  note = {published online},
  year = {2009}
}

@INBOOK{Rue2010,
  title = {Information Processing and Management of Uncertainty in Knowledge-Based Systems. Applications},
  series = {Communications in Computer and Information Science},
  author = {Frank R{\"u}gheimer},
  editor = {Eyke H{\"u}llermeier and Rudolf Kruse and Frank Hoffmann},
  publisher = {Springer},
  address = {Heidelberg},
  chapter = {Using Enriched Ontology Structure for Improving Statistical Models of Gene Annotation Sets},
  pages = {55--64},
  volume = {81},
  year = {2010},
  isbn = {978-3-642-14057-0},
  keywords = {Gene Ontology, set-valued},
  url = {http://www.ruegheimer.org/publications/Rue_IPMU2010_Springer.pdf},
  doi = {10.1007/978-3-642-14058-7},
  springer = {http://www.springerlink.com/content/g366h6980175r04p/}
}

@ARTICLE{BocRueGuiGooCloSch2011,
  title = {Fragmentation-free {LC-MS} can identify hundreds of proteins},
  author = {Pascal Bochet and Frank R{\"u}gheimer and Tina Guina and Peter Brooks and David Goodlett and Peter Clote and Benno Schwikowski},
  journal = {Proteomics},
  year = {2011},
  issn = {1615-9861},
  keywords = {mass spectrometry, probabilisitic model, protein identification},
  url = {http://onlinelibrary.wiley.com/doi/10.1002/pmic.200900765/pdf},
  doi = {10.1002/pmic.200900765},
  pages = {22--32},
  number = {1},
  month = JAN,
  volume = {11}
}

@INPROCEEDINGS{RueAnaSch2011,
  title = {A Software architecture for \textit{De Novo} Induction of Regulatory Networks from Expression Data},
  booktitle = {Proceedings of the Journ{\'e}es Ouvertes Biologie Informatique Math{\'e}matiques (JOBIM) 2011, Paris},
  author = {Frank R{\"u}gheimer and Ashish Anand and Benno Schwikowski},
  pages = {295--296},
  year = {2011},
  keywords = {expression data, regulatory network induction},
  url = {http://www.ruegheimer.org/publications/Rue_jobim_2011.pdf}
}

@ARTICLE{BueLieJul2012,
  title = {Global network reorganization during dynamic adaptation of \textit{Bacillus subtilis} metabolism},
  author = {Joerg Martin Buescher and Wolfram Liebermeister and Matthieu Jules and Markus Uhr and Jan Muntel and Eric Botella and Bernd Hessling and Roelco Jacobus Kleijn and Ludovic {Le Chat} and Fran\c{c}ois Lecointe and Ulrike M{\"a}der and Pierre Nicolas and Sjouke Piersma and Frank R{\"u}gheimer and D{\"o}rte Becher and Philippe Bessieres and Elena Bidnenko and Emma L. Denham and Entienne Dervyn and Kevin M. Devine and Geoff Doherty and Samuel Drulhe and Liza Felicori and Mark J. Fogg and Anne Goelzer and Annette Hansen and Colin R. Harwood and Michael Hecker and Sebastian Hubner and Claus Hultschig and Hanne Jarmer and Edda Klipp and Aur{\'e}lie Leduc and Peter Lewis and Frank Molina and Philippe Noirot and Sabine Peres and Nathalie Pigeonneau and Susanne Pohl and Simon Rasmussen and Bernd Rinn and Marc Schaffer and Julian Schnidder and Benno Schwikowski and Jan Maarten van Dijl and Patrick Veiga and Sean Walsh and Anthony J. Wilkinson and J{\"o}rg Stelling and St{\'e}phane Aymerich and Uwe Sauer},
  journal = {Science},
  year = {2012},
  month = MAR,
  volume = {335},
  number = {6072},
  pages = {1099--1103},
  url = {http://www.sciencemag.org/content/335/6072/1099.full.pdf},
  doi = {10.1126/science.1206871 }
}

@ARTICLE{NicMaeDer2012,
  title = {Condition-dependent transcriptome reveals high-level regulatory architecture in \textit{Bacillus subtilis}},
  author = {Pierre Nicolas and Ulrike M{\"a}der and Entienne Dervyn and Tatiana Rochat and Aur{\'e}lie Leduc and Nathalie Pigeonneau and Elena Bidnenko and Elodie Marchadier and Mark Hoebeke and St{\'e}phane Aymerich and D{\"o}rte Becher and Paola Biscicchia and Eric Botella and Olivier Delumeau and Geoff Doherty and Emma L. Denham and Mark J. Fogg and Vincent Fromion and Anne Goelzer and Annette Hansen and Elisabeth H{\"a}rtig and Colin R Harwood and Georg Homuth and Hanne Jarmer and Matthieu Jules and Edda Klipp and Ludovic {Le Chat} and Fran\c{c}ois Lecointe and Peter Lewis and Wolfram Liebermeister and Anika March and Ruben A. T. Mars and Priyanka Nannapaneni and David Noone and Susanne Pohl and Bernd Rinn and Frank R{\"u}gheimer and Praveen K. Sappa and Franck Samson and Marc Schaffer and Benno Schwikowski and Leif Steil and J{\"o}rg St{\"u}lke and Thomas Wiegert and Kevin M. Devine and Anthony J. Wilkinson and Jan Maarten van Dijl and Michael Hecker and Uwe V{\"o}lker and Philippe Bessi{\`e}res and Philippe Noirot},
  journal = {Science},
  year = {2012},
  month = MAR,
  volume = {335},
  number = {6072},
  pages = {1103--1106},
  url = {http://www.sciencemag.org/content/335/6072/1103.full.pdf},
  doi = {10.1126/science.1206848 }
}

@INBOOK{Rue2013,
  title = {Computational Intelligence in Intelligent Data Analysis},
  series = {Studies in Computational Intelligence},
  author = {Frank R{\"u}gheimer},
  editor = {Christian Moewes and Andreas N{\"u}rnberger},
  publisher = {Springer},
  address = {Berlin Heidelberg},
  pages = {251--262},
  chapter = {Applications of Intelligent Data Analysis for the Discovery of Gene Regulatory Networks},
  volume = {445},
  month = JAN,
  year = {2013},
  isbn = {978-3-642-32377-5},
  keywords = {expression data, regulatory network induction},
  doi = {10.1007/978-3-642-32378-2_17},
  springer = {http://link.springer.com/chapter/10.1007/978-3-642-32378-2_17}
}

@PHDTHESIS{Rue2012,
  title = {Knowledge representation with condensed set-valued attributes},
  author = {Frank R{\"u}gheimer},
  school = {Fakult{\"a}t f{\"u}r Informatik, Otto-von-Guericke Universit{\"a}t Magdeburg},
  address = {Magdeburg},
  year = {2012},
  url = {http://edoc2.bibliothek.uni-halle.de/hs/urn/urn:nbn:de:gbv:ma9:1-2855},
  urn = {urn:nbn:de:gbv:ma9:1-2855}
}

@ARTICLE{GuiKusRueCalSch2014,
  title = {The {C}yni framework for network inference in {C}ytoscape},
  author = {Oriol Guitart-Pla and Manjunath Kustagi and Frank R{\"u}gheimer and Andrea Califano and Benno Schwikowski},
  journal = {Bioinformatics},
  month = DEC,
  year = {2014},
  doi = {10.1093/bioinformatics/btu812},
  url = {http://bioinformatics.oxfordjournals.org/content/early/2015/01/20/bioinformatics.btu812.abstract},
  note = {advance access online version}
}