Martin Kuiper
Background and activities
Knowledge management - Semantic Web - BioGateway
Cytoscape App - BioGateway
Logical modelling - DrugLogics
Gene Regulation Consortium - GRECO and GREEKC
Text mining - curation: ExTRI and VSM
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The Kuiper lab focuses on the use of ontologies and semantic web technologies for the integration and exploration of biological knowledge.
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Martin Kuiper received a M.Sc. degree in Molecular Biology and Biochemistry (1982), and a PhD degree (1987) in Biology from the University of Groningen, Netherlands. He was a doctoral fellow of the Ohio State University, US (1987) and Utrecht University, Netherlands (1989). He then took a career change and went to industry, where he worked at KeyGene NV, the Netherlands; GenScope bvba / Celera West, Belgium / California; and Aventis CropScience, Belgium. After 9 years in industry he joined the VIB institute in Gent, Belgium, as PI in Computational Biology. He transferred to the Norwegian University of Science and Technology in 2008, where he now works as Professor in Systems Biology. His research interests include the development of approaches and tools for analysis of biological data, and the use of ontologies and semantic web technologies for integration of biological knowledge. Together with colleagues from the Faculty of Medicine and Faculty of Humanities he is involved in three sub-projects of the DrugLogics initiative (www.DrugLogics.eu), targeting Responsible Research and Innovation (RRI): Crossover Research 2.0; Rational development of anti-cancer drug combinations and the modeling of drug resistance in colon cancer (the ERACoSysMed project COLOSYS).
Courses
- BI3019 - Systems Biology: Resources, Standards and Tools
- BI8040 - Logical Modeling for Experimental Design in Biotechnology and Biomedicine
- BI8012 - Systems Biology: Examples from Current Literature
Scientific, academic and artistic work
A selection of recent journal publications, artistic productions, books, including book and report excerpts. See all publications in the database
Journal publications
- (2022) Dealing with different conceptions of pollution in the Gene Regulation Knowledge Commons. Biochimica et Biophysica Acta. Gene Regulatory Mechanisms. vol. 1865 (1).
- (2022) The gene regulation knowledge commons: the action area of GREEKC. Biochimica et Biophysica Acta. Gene Regulatory Mechanisms. vol. 1865 (1).
- (2022) ExTRI: Extraction of transcription regulation interactions from literature. Biochimica et Biophysica Acta. Gene Regulatory Mechanisms. vol. 1865 (1).
- (2022) Boolean function metrics can assist modelers to check and choose logical rules. Journal of Theoretical Biology. vol. 538.
- (2021) The Gene Ontology resource: enriching a GOld mine. Nucleic Acids Research (NAR).
- (2021) Gene Ontology representation for transcription factor functions. Biochimica et Biophysica Acta. Gene Regulatory Mechanisms. vol. 1864 (11-12).
- (2021) Formalization of gene regulation knowledge using ontologies and gene ontology causal activity models. Biochimica et Biophysica Acta. Gene Regulatory Mechanisms. vol. 1864 (11-12).
- (2021) A GO catalogue of human DNA-binding transcription factors. Biochimica et Biophysica Acta. Gene Regulatory Mechanisms. vol. 1864 (11-12).
- (2021) The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling. Briefings in Bioinformatics. vol. 22 (4).
- (2021) CausalBuilder: bringing the MI2CAST causal interaction annotation standard to the curator. Database: The Journal of Biological Databases and Curation.
- (2021) Logical and experimental modeling of cytokine and eicosanoid signaling in psoriatic keratinocytes. iScience. vol. 24.
- (2020) Network and Systems Medicine: Position Paper of the European Collaboration on Science and Technology Action on Open Multiscale Systems Medicine. Network and Systems Medicine.
- (2020) A foundation for reference models for drug combinations with an application to Loewe’s reference model. BMC Bioinformatics. vol. 21 (460).
- (2020) Setting the basis of best practices and standards for curation and annotation of logical models in biology—highlights of the [BC] 2 2019 CoLoMoTo/SysMod Workshop. Briefings in Bioinformatics.
- (2020) Silencing trust: confidence and familiarity in re-engineering knowledge infrastructures. Medicine, Health care and Philosophy.
- (2020) Network Building with the Cytoscape BioGateway App Explained in Five Use Cases. Current Protocols in Bioinformatics. vol. 72 (1).
- (2020) The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST). Bioinformatics.
- (2020) A middle-out modeling strategy to extend a colon cancer logical model improves drug synergy predictions in epithelial-derived cancer cell lines. Frontiers in Molecular Biosciences. vol. 7:502573.
- (2020) emba: R package for analysis and visualization of biomarkers in boolean model ensembles. Journal of Open Source Software (JOSS).
- (2020) UniBioDicts: Unified access to biological dictionaries. Bioinformatics.