Martin Kuiper

Steven Vercruysse, Aravind Venkatesan, Martin Kuiper: OLSVis: an animated, interactive visual browser for bio-ontologies. BMC Bioinformatics 13: 116 (2012)

Vladimir Mironov, Nirmala Seethappan, Ward Blondé, Erick Antezana, Andrea Splendiani, Martin Kuiper: Gauging triple stores with actual biological data. BMC Bioinformatics 13(S-1): S3 (2012)

Aravind Venkatesan, Vladimir Mironov, Martin Kuiper: Towards an integrated knowledge system for capturing gene expression events. ICBO 2012

Jens Hollunder, Vladimir Mironov, Erick Antezana, Robert Hoehndorf, Martin Kuiper: Profiling of Semantically Annotated Proteins. SWAT4LS 2012

Vladimir Mironov, Erick Antezana, Mikel Egaña, Ward Blondé, Bernard De Baets, Martin Kuiper, Robert Stevens: Flexibility and utility of the cell cycle ontology. Applied Ontology 6(3): 247-261 (2011)

Ward Blondé, Vladimir Mironov, Aravind Venkatesan, Erick Antezana, Bernard De Baets, Martin Kuiper: Reasoning with bio-ontologies: using relational closure rules to enable practical querying. Bioinformatics 27(11): 1562-1568 (2011)

Erick Antezana, Ward Blondé, Aravind Venkatesan, Bernard De Baets, Vladimir Mironov, Martin Kuiper: Semantic systems biology: enabling integrative biology via semantic web technologies. WIMS 2011: 58

Aravind Venkatesan, Ward Blondé, Erick Antezana, Mats Skillingstad, M. Scott Marshall, Bernard De Baets, Vladimir Mironov, Martin Kuiper: The RDF foundry: call for an initiative to build enhanced RDF resources for biological data integration. WIMS 2011: 59

Jens Hollunder, Maik Friedel, Martin Kuiper, Thomas Wilhelm: DASS-GUI: a user interface for identification and analysis of significant patterns in non-sequential data. Bioinformatics 26(7): 987-989 (2010)

Kris Laukens, Jens Hollunder, Thanh Hai Dang, Geert De Jaeger, Martin Kuiper, Erwin Witters, Alain Verschoren, Koenraad Van Leemput: Flexible network reconstruction from relational databases with Cytoscape and CytoSQL. BMC Bioinformatics 11: 360 (2010)

Erick Antezana, Aravind Venkatesan, Chris Mungall, Vladimir Mironov, Martin Kuiper: ONTO-ToolKit: enabling bio-ontology engineering via Galaxy. BMC Bioinformatics 11(S-12): S8 (2010)

Wim De Mulder, Martin Kuiper, René K. Boel: Clustering of gene expression profiles: creating initialization-independent clusterings by eliminating unstable genes. J. Integrative Bioinformatics 7(3) (2010)

Vladimir Mironov, Nirmala Seethappan, Ward Blondé, Erick Antezana, Bjorn Lindi, Martin Kuiper: Benchmarking Triple Stores with Biological Data. SWAT4LS 2010

Vladimir Mironov, Nirmala Seethappan, Ward Blondé, Erick Antezana, Bjorn Lindi, Martin Kuiper: Benchmarking triple stores with biological data. CoRR abs/1012.1632 (2010)

Erick Antezana, Martin Kuiper, Vladimir Mironov: Biological knowledge management: the emerging role of the Semantic Web technologies. Briefings in Bioinformatics 10(4): 392-407 (2009)

Krzysztof Wabnik, Torgeir R. Hvidsten, Anna M. Kedzierska, Jelle Van Leene, Geert De Jaeger, Gerrit T. S. Beemster, Henryk Jan Komorowski, Martin T. R. Kuiper: Gene expression trends and protein features effectively complement each other in gene function prediction. Bioinformatics 25(3): 322-330 (2009)

Erick Antezana, Ward Blondé, Mikel Egaña, Alistair Rutherford, Robert Stevens, Bernard De Baets, Vladimir Mironov, Martin Kuiper: BioGateway: a semantic systems biology tool for the life sciences. BMC Bioinformatics 10(S-10): 11 (2009)

Erick Antezana, Mikel Egaña, Bernard De Baets, Martin Kuiper, Vladimir Mironov: ONTO-PERL: An API for supporting the development and analysis of bio-ontologies. Bioinformatics 24(6): 885-887 (2008)

Mikel Egaña Aranguren, Erick Antezana, Martin Kuiper, Robert Stevens: Ontology Design Patterns for bio-ontologies: a case study on the Cell Cycle Ontology. BMC Bioinformatics 9(S-5) (2008)

Wim De Mulder, Stefan Schliebs, René K. Boel, Martin Kuiper: Initialization Dependence of Clustering Algorithms. ICONIP (2) 2008: 615-622

Tom Michoel, Steven Maere, Eric Bonnet, Anagha Joshi, Yvan Saeys, Tim Van den Bulcke, Koenraad Van Leemput, Piet van Remortel, Martin Kuiper, Kathleen Marchal, Yves Van de Peer: Validating module network learning algorithms using simulated data. BMC Bioinformatics 8(S-2) (2007)

Gert Sclep, Joke Allemeersch, Robin Liechti, Björn De Meyer, Jim Beynon, Rishikesh Bhalerao, Yves Moreau, Wilfried Nietfeld, Jean-Pierre Renou, Philippe Reymond, Martin T. R. Kuiper, Pierre Hilson: CATMA, a comprehensive genome-scale resource for silencing and transcript profiling of Arabidopsis genes. BMC Bioinformatics 8 (2007)

Erick Antezana, Elena Tsiporkova, Vladimir Mironov, Martin Kuiper: A Cell-Cycle Knowledge Integration Framework. DILS 2006: 19-34

Steven Vercruysse, Martin Kuiper: Simulating genetic networks made easy: network construction with simple building blocks. Bioinformatics 21(2): 269-271 (2005)

Steven Maere, Karel Heymans, Martin Kuiper: BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks. Bioinformatics 21(16): 3448-3449 (2005)