Systems Biology



Publications in peer reviewed journals



  • Mironov V, Antezana E, Egaña M, Blondé W, De Baets B, Kuiper M and Stevens R (2011) Flexibility and utility of the cell cycle ontology. Applied Ontology 6:247-261
  • Hu Q, Hollunder J, Niehl A, Kørner CJ, Gereige D, Windels D, Arnold A, Kuiper M, Vazquez F, Pooggin M, Heinlein M (2011) Specific impact of tobamovirus infection on the Arabidopsis small RNA profile. PLoS One 6:e19549.
  • Blondé W, Mironov V, Venkatesan A, Antezana E, De Baets B and Kuiper M (2011) Reasoning with bio-ontologies: using relational closure rules to enable practical querying. Bioinformatics 27:1562-1568. Epub 2011 Apr 5.
  • Antezana E, Blondé W, Venkatesan A, De Baets B, Mironov M, Kuiper M (2011). Semantic SB: enabling integrative biology via SW technologies. Proceedings of the International Conference on Web Intelligence, Mining and Semantics, ACM, New York, NY, USA (doi>10.1145/1988688.1988756).
  • Venkatesan A, Blondé W, Antezana E, Skillingstad M, Marshall MS, De Baets B, Mironov M, Kuiper M (2011). The RDF Foundry: Call for an initiative to build enhanced RDF resources for biological data integration. Proceedings of the International Conference on Web Intelligence, Mining and Semantics, ACM,  New York, NY, USA (doi>10.1145/1988688.1988757).
  • Beisvåg V, Kauffmann A, Malone J, Foy C, Salit M, Schimmel H, Bongcam-Rudloff E, Landegren U, Parkinson H, Huber W, Brazma A, Sandvik AK, Kuiper M (2011). Contributions of the EMERALD project to assessing and improving microarray data quality. Biotechniques 50:27-31


  • Mironov V, Seethappan N, Blondé W, Antezana E, Lindi B, Kuiper M (2010). Benchmarking triple stores with biological data. SWAT4LS-2010 Proceedings.
  • Antezana E, Venkatesan A, Mungall C, Mironov V, Kuiper M (2010). ONTO-ToolKit: enabling bio-ontology engineering via Galaxy. BMC Bioinformatics 11(Suppl 12):S8
  • Van Leene J, Hollunder J, Eeckhout D, Persiau G, Van De Slijke E, Stals H, Van Isterdael G, Verkest A, Neirynck S, Buffel Y, De Bodt S, Maere S, Laukens K, Pharazyn A, Ferreira PCG, Eloy N, Renne C, Meyer C, Faure J-D, Steinbrenner J, Beynon J, Larkin JC, Van de Peer Y, Hilson P, Kuiper M, De Veylder L, Van Onckelen H, Inzé D, Witters E and De Jaeger G (2010). Targeted interactomics reveals a complex core cell cycle machinery in Arabidopsis thaliana. Mol Syst Biol 6:397
  • Laukens K, Hollunder J, Dang TH, De Jaeger G, Kuiper M, Witters E, Verschoren A, Van Leemput K (2010). Flexible network reconstruction from relational databases with Cytoscape and CytoSQL. BMC Bioinformatics 11:360
  • De Mulder W, Kuiper M, and Boel R. Clustering of gene expression profiles: creating initialization-independent clusterings by eliminating unstable genes (2010). J Integr Bioinform 7, issue 3.
  • Hollunder J, Friedel M, Kuiper M and Wilhelm P (2010) DASS-GUI: a user interface for identification and analysis of significant patterns in non-sequential data. Bioinformatics 26:987-989