Martin Kuiper

About

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).

Publications

2019

Vera-Ramos, Jose Antonio; Juanes-Cortes, Belen; Fernández-Breis, Jesualdo Tomás; Gaudet, Pascale; Kuiper, Martin; Lægreid, Astrid. (2019) An example of multimodal biological knowledge representation. CEUR Workshop Proceedings
Academic article
Carbon, Seth J.; Douglass, E; Dunn, N; Good, B; Harris, NL; Lewis, SE. (2019) The Gene Ontology Resource: 20 years and still GOing strong. Nucleic Acids Research (NAR)
Academic article
Perfetto, Livia; Acencio, Marcio Luis; Bradley, Glyn; Cesareni, Gianni; del Toro, Noemi; Fazekas, David. (2019) CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination . Bioinformatics
Academic article
Efstathiou, Sophia; Nydal, Rune; Lægreid, Astrid; Kuiper, Martin. (2019) Scientific knowledge in the age of computation: Explicated, computable and manageable?. Theoria. An international Journal of Theory, History and Foundations of Science
Academic article
Holmås, Stian; Riudavets Puig, Rafael; Acencio, Marcio Luis; Mironov, Vladimir; Kuiper, Martin. (2019) The Cytoscape BioGateway App: explorative network building from an RDF store. Bioinformatics
Academic article
Menden, Michael Patrick; Wang, Dennis; Mason, Mike J.; Szalai, Bence; Bulusu, Krishna C.; Guan, Yuanfang. (2019) Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen. Nature Communications
Academic article

2018

Vercruysse, Steven; Kuiper, Martin. (2018) The VSM-pages: How to Easily Plant Complex Ideas into Computers.
Website (informational material)

2017

Chawla, Konika; Kuiper, Martin. (2017) Discovering, analysing and taking care of knowledge. Norwegian University of Science and Technology
Doctoral dissertation

2016

Chawla, Konika; Kuiper, Martin. (2016) Genes2GO: A web application for querying gene sets for specific GO terms. Bioinformation
Academic article
Tripathi, Sushil; Vercruysse, Steven; Chawla, Konika; Christie, Karen R.; Blake, Judith A; Huntley, Rachael P.. (2016) Gene regulation knowledge commons: community action takes care of DNA binding transcription factors. Database: The Journal of Biological Databases and Curation
Academic article

2015

Skancke, Jørgen; Bar, Nadav; Kuiper, Martin; Hsu, Lilian M. (2015) Sequence-Dependent Promoter Escape Efficiency Is Strongly Influenced by Bias for the Pretranslocated State during Initial Transcription. Biochemistry
Academic article
Flobak, Åsmund; Baudot, Anaïs; Remy, Elisabeth; Thommesen, Liv; Thieffry, Denis; Kuiper, Martin. (2015) Discovery of Drug Synergies in Gastric Cancer Cells Predicted by Logical Modeling. PLoS Computational Biology
Academic article
Lægreid, Astrid; Kuiper, Martin. (2015) Health and the information commons.
Website (informational material)

2014

Gautam, Vinay Kumar; Czeizler, Eugen; Haddow, Pauline; Kuiper, Martin. (2014) Design of a Minimal System for Self-replication of Rectangular Patterns of DNA Tiles. Lecture Notes in Computer Science (LNCS)
Academic article
Venkatesan, Aravind; Tripathi, Sushil; Sanz de Galdeano, Alejandro; Blondé, Ward; Lægreid, Astrid; Mironov, Vladimir. (2014) Finding gene regulatory network candidates using the gene expression knowledge base. BMC Bioinformatics
Academic article
Blondé, Ward; Antezana, Erick; Mironov, Vladimir; Schulz, Stefan; Kuiper, Martin; De baets, Bernard. (2014) Using the relation ontology Metarel for modelling Linked Data as multi-digraphs. Semantic Web Journal
Academic article
Lægreid, Astrid; Kuiper, Martin. (2014) Å ta seg av kunnskap.
Website (informational material)
Mironov, Vladimir; Kuiper, Martin; Ekseth, Ole Kristian. (2014) OrthAgogue: An agile tool for the rapid prediction of orthology relations. Bioinformatics
Academic article

2013

Tripathi, Sushil; Christie, KR; Balakrishnan, Ravin; Huntley, R; Hill, DP; Thommesen, Liv. (2013) Gene Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a large-scale curation effort. Database: The Journal of Biological Databases and Curation
Academic article
Vercruysse, Steven; Kuiper, Martin. (2013) WordVis: JavaScript and Animation to Visualize the WordNet Relational Dictionary. Advances in Intelligent Systems and Computing
Academic article
Niehl, A; Zhang, Z.J.; Kuiper, Martin; Peck, SC; Heinlein, M. (2013) Label-Free Quantitative Proteomic Analysis of Systemic Responses to Local Wounding and Virus Infection in Arabidopsis thaliana. Journal of Proteome Research
Academic article
Chawla, Konika; Tripathi, Sushil; Thommesen, Liv; Lægreid, Astrid; Kuiper, Martin. (2013) TFcheckpoint: a curated compendium of specific DNA-binding RNA polymerase II transcription factors. Bioinformatics
Academic article
Antezana, Erick; Mironov, Vladimir; Kuiper, Martin. (2013) The emergence of Semantic Systems Biology. New Biotechnology
Academic article
Kuiper, Martin; Antezana, Erick; Mironov, Vladimir. (2013) Cell Cycle Ontology (CCO).
Website (informational material)

2012

Vercruysse, Steven; Venkatesan, Aravind; Kuiper, Martin. (2012) OLSVis: an animated, interactive visual browser for bio-ontologies. BMC Bioinformatics
Academic article
Kuiper, Martin; Venkatesan, Aravind; Antezana, Erick; Vercruysse, Steven; Mironov, Vladimir; Blondé, Ward. (2012) Putting Semantics in Systems Biology. META
Article in business/trade/industry journal
Mironov, Vladimir; Seethappan, Nirmala; Blondé, Ward; Antezana, Erick; Splendiani, Andrea; Kuiper, Martin. (2012) Gauging triple stores with actual biological data. BMC Bioinformatics
Academic article
Vercruysse, Steven; Kuiper, Martin. (2012) Jointly creating digital abstracts: dealing with synonymy and polysemy. BMC Research Notes
Academic article

2011

Beisvag, Vidar; Kauffmann, Audrey; Malone, James; Foy, Carole; Salit, Marc; Schimmel, H. (2011) Contributions of the EMERALD project to assessing and improving microarray data quality. BioTechniques
Academic article
Blondé, Ward; Mironov, Vladimir; Venkatesan, Aravind; Antezana, Erick; De baets, Bernard; Kuiper, Martin. (2011) Reasoning with bio-ontologies: using relational closure rules to enable practical querying. Bioinformatics
Academic article
Mironov, Vladimir; Antezana, Erick; Egaña, Mikel; Blondé, Ward; De baets, Bernard; Kuiper, Martin. (2011) Flexibility and utility of the cell cycle ontology. Applied Ontology
Academic article
Chawla, Konika; Barah, Pankaj; Kuiper, Martin; Bones, Atle M.. (2011) Systems Biology: a Promising Tool to Study Abiotic Stress Responses. Bentham eBooks
Academic chapter/article/Conference paper
Hu, QA; Hollunder, Jens; Niehl, A; Körner, Camilla J; Gereige, Dalya; Windels, David. (2011) Specific Impact of Tobamovirus Infection on the Arabidopsis Small RNA Profile. PLOS ONE
Academic article

2010

Antezana, Erick; Venkatesan, Aravind; Mungall, Chris; Mironov, Vladimir; Kuiper, Martin. (2010) ONTO-ToolKit: enabling bio-ontology engineering via Galaxy. BMC Bioinformatics
Academic article
De Mulder, Wim; Kuiper, Martin; Boel, Rene. (2010) Clustering of gene expression profiles: creating initialization-independent clusterings by eliminating unstable genes. Journal of Integrative Bioinformatics (JIB)
Academic article
Egaña, Mikel; Stevens, Robert; Antezana, Erick; Fernández-Breis, Jesualdo Tomás; Kuiper, Martin; Mironov, Vladimir. (2010) Technologies and best practices for building bio-ontologies. John Wiley & Sons
Academic chapter/article/Conference paper
Laukens, K; Hollunder, J; Thanh, HD; De Jaeger, G; Kuiper, Martin; Witters, E. (2010) Flexible network reconstruction from relational databases with Cytoscape and CytoSQL. BMC Bioinformatics
Academic article

2009

Antezana, E; Kuiper, Martin; Mironov, Vladimir. (2009) Biological knowledge management: the emerging role of the Semantic Web technologies. Briefings in Bioinformatics
Academic literature review
Antezana, Erick; Egaña, Mikel; Blondé, Ward; Illarramendi, Aitzol; Bilbao, Inaki; De baets, Bernard. (2009) The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process. Genome Biology
Academic literature review
Antezana, Erick; Blondé, Ward; Egaña, Mikel; Rutherford, Alistair; Stevens, Robert; De baets, Bernard. (2009) BioGateway: A Semantic Systems Biology Tool for the Life Sciences. BMC Bioinformatics
Academic article
Naouar, Naira; Vandepoele, Klaas; Lammens, Tim; Casneuf, Tineke; Zeller, Georg; Van Hummelen, Paul. (2009) Quantitative RNA expression analysis with Affymetrix Tiling 1.0R arrays identifies new E2F target genes. The Plant Journal
Academic article
Wabnik, K; Hvidsten, TR; Kedzierska, A; Van Leene, J; De Jaeger, G; Beemster, GTS. (2009) Gene expression trends and protein features effectively complement each other in gene function prediction. Bioinformatics
Academic article

2008

Taylor, CF; Field, D; Sansone, SA; Aerts, J; Apweiler, R; Ashburner, M. (2008) Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nature Biotechnology
Editorial
Wabnik, Krysztof; Hvidsten, Torgeir Rhoden; Kedzierska, Anna; Van Leene, Jelle; De Jaeger, Geert; Beemster, Gerrit. (2008) Gene expression trends and protein features effectively complement each other in gene function prediction. Bioinformatics
Academic article

Journal publications

Tsirvouli, Eirini; Noël, Vincent; Flobak, Åsmund; Calzone, Laurence; Kuiper, Martin. (2024) Dynamic Boolean modeling of molecular and cellular interactions in psoriasis predicts drug target candidates. iScience
Academic article
Niarakis, Anna; Ostaszewski, Marek; Mazein, Alexander; Kuperstein, Inna; Kutmon, Martina; Gillespie, Marc E.. (2024) Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches. Frontiers in Immunology
Academic article
Mulero-Hernández, Juan; Mironov, Vladimir; Miñarro-Giménez, José Antonio; Kuiper, Martin; Fernández-Breis, Jesualdo Tomás. (2024) Integration of chromosome locations and functional aspects of enhancers and topologically associating domains in knowledge graphs enables versatile queries about gene regulation. Nucleic Acids Research (NAR)
Academic article
Heck, Kathleen; Lindholm, Håvard Takle; Niederdorfer, Barbara; Tsirvouli, Eirini; Kuiper, Martin; Flobak, Åsmund. (2023) Characterisation of Colorectal Cancer Cell Lines through Proteomic Profiling of Their Extracellular Vesicles. Proteomes
Academic article
Acencio, Marcio Luis; Vázquez, Miguel; Chawla, Konika; Lægreid, Astrid Renner; Kuiper, Martin. (2023) TFCheckpoint database update, a cross-referencing system for transcription factors from human, mouse and rat. Nucleic Acids Research (NAR)
Academic article
Flobak, Åsmund; Zobolas, John; Vázquez, Miguel; Steigedal, Tonje S.; Thommesen, Liv; Grislingås, Asle Andreas. (2023) Fine tuning a logical model of cancer cells to predict drug synergies: combining manual curation and automated parameterization. Frontiers in Systems Biology
Academic article
Chatterjee, Anamika; Swierstra, Tsjalling; Kuiper, Martin. (2022) Dealing with different conceptions of pollution in the Gene Regulation Knowledge Commons. Biochimica et Biophysica Acta. Gene Regulatory Mechanisms
Academic article
Kuiper, Martin; Bonello, Joseph; Fernández-Breis, Jesualdo Tomás; Bucher, Philipp; Futschik, Matthias E; Gaudet, Pascale. (2022) The gene regulation knowledge commons: the action area of GREEKC. Biochimica et Biophysica Acta. Gene Regulatory Mechanisms
Academic article
Vazquez Garcia, Miguel; Krallinger, Martin; Leitner, Florian; Kuiper, Martin; Valencia, Alfonso; Lægreid, Astrid. (2022) ExTRI: Extraction of transcription regulation interactions from literature. Biochimica et Biophysica Acta. Gene Regulatory Mechanisms
Academic article
Zobolas, John; Monteiro, Pedro T.; Kuiper, Martin; Flobak, Åsmund. (2022) Boolean function metrics can assist modelers to check and choose logical rules. Journal of Theoretical Biology
Academic article
Hadzic, Maida; Sun, Yitong; Tomic, Nikolina; Tsirvouli, Eirini; Kuiper, Martin; Pojskic, Lejla. (2022) Halogenated boroxine increases propensity to apoptosis in leukemia (UT-7) but not non-tumor cells in vitro. FEBS Open Bio
Academic article
Gaudet, Pascale; Logie, Colin; Lovering, Ruth C.; Kuiper, Martin; Lægreid, Astrid; Thomas, Paul D.. (2021) Gene Ontology representation for transcription factor functions. Biochimica et Biophysica Acta. Gene Regulatory Mechanisms
Academic article
Lovering, Ruth C.; Gaudet, Pascale; Acencio, Marcio Luis; Ignatchenko, Alex; Jolma, Arttu; Fornes, Oriol. (2021) A GO catalogue of human DNA-binding transcription factors. Biochimica et Biophysica Acta. Gene Regulatory Mechanisms
Academic article
Juanes Cortés, Belén; Vera-Ramos, José Antonio; Lovering, Ruth C.; Gaudet, Pascale; Lægreid, Astrid; Logie, Colin. (2021) Formalization of gene regulation knowledge using ontologies and gene ontology causal activity models. Biochimica et Biophysica Acta. Gene Regulatory Mechanisms
Academic article
Tsirvouli, Eirini; Ashcroft, Felicity; Johansen, Berit; Kuiper, Martin. (2021) Logical and experimental modeling of cytokine and eicosanoid signaling in psoriatic keratinocytes. iScience
Academic article
Touré, Vasundra; Zobolas, John; Kuiper, Martin; Vercruysse, Steven. (2021) CausalBuilder: bringing the MI2CAST causal interaction annotation standard to the curator. Database: The Journal of Biological Databases and Curation
Academic article
Touré, Vasundra; Flobak, Asmund; Niarakis, Anna; Vercruysse, Steven; Kuiper, Martin. (2021) The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling. Briefings in Bioinformatics
Academic literature review
Carbon, Seth J.; Douglass, Eric; Good, Benjamin M; Unni, Deepak R; Harris, Nomi L.; Mungall, Christopher J.. (2021) The Gene Ontology resource: enriching a GOld mine. Nucleic Acids Research (NAR)
Academic article
Puig, Rafael Riudavets; Holmås, Stian; Mironov, Vladimir; Kuiper, Martin. (2020) Network Building with the Cytoscape BioGateway App Explained in Five Use Cases . Current Protocols in Bioinformatics
Academic article
Nydal, Rune; Bennett, Gaymon; Kuiper, Martin; Lægreid, Astrid. (2020) Silencing trust: confidence and familiarity in re-engineering knowledge infrastructures. Medicine, Health care and Philosophy
Academic article
Touré, Vasundra; Vercruysse, Steven; Acencio, Marcio Luis; Lovering, Ruth C.; Orchard, Sandra; Bradley, Glyn. (2020) The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST). Bioinformatics
Academic article
Zobolas, John; Kuiper, Martin; Flobak, Åsmund. (2020) emba: R package for analysis and visualization of biomarkers in boolean model ensembles. Journal of Open Source Software (JOSS)
Academic article
De Mulder, Wim; Kuiper, Martin. (2020) A foundation for reference models for drug combinations with an application to Loewe’s reference model. BMC Bioinformatics
Academic article
Zobolas, John; Kuiper, Martin; Flobak, Åsmund. (2020) emba: R package for analysis and visualization of biomarkers in boolean model ensembles. Journal of Open Source Software (JOSS)
Interview Journal
Zobolas, John; Touré, Vasundra; Kuiper, Martin; Vercruysse, Steven. (2020) UniBioDicts: Unified access to biological dictionaries. Bioinformatics
Academic article
Comte, Blandine; Baumbach, Jan; Benis, Arriel; Basílio, José; Debeljak, Nataša; Flobak, Åsmund. (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
Academic literature review
Tsirvouli, Eirini; Touré, Vasundra; Niederdorfer, Barbara; Vazquez Garcia, Miguel; Flobak, Åsmund; Kuiper, Martin. (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
Academic article
Niarakis, Anna; Kuiper, Martin; Ostaszewski, Marek; Malik Sheriff, Rahuman; Casals-Casas, Cristina; Thieffry, Denis. (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
Academic article
Vera-Ramos, Jose Antonio; Juanes-Cortes, Belen; Fernández-Breis, Jesualdo Tomás; Gaudet, Pascale; Kuiper, Martin; Lægreid, Astrid. (2019) An example of multimodal biological knowledge representation. CEUR Workshop Proceedings
Academic article
Carbon, Seth J.; Douglass, E; Dunn, N; Good, B; Harris, NL; Lewis, SE. (2019) The Gene Ontology Resource: 20 years and still GOing strong. Nucleic Acids Research (NAR)
Academic article
Perfetto, Livia; Acencio, Marcio Luis; Bradley, Glyn; Cesareni, Gianni; del Toro, Noemi; Fazekas, David. (2019) CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination . Bioinformatics
Academic article
Efstathiou, Sophia; Nydal, Rune; Lægreid, Astrid; Kuiper, Martin. (2019) Scientific knowledge in the age of computation: Explicated, computable and manageable?. Theoria. An international Journal of Theory, History and Foundations of Science
Academic article
Holmås, Stian; Riudavets Puig, Rafael; Acencio, Marcio Luis; Mironov, Vladimir; Kuiper, Martin. (2019) The Cytoscape BioGateway App: explorative network building from an RDF store. Bioinformatics
Academic article
Menden, Michael Patrick; Wang, Dennis; Mason, Mike J.; Szalai, Bence; Bulusu, Krishna C.; Guan, Yuanfang. (2019) Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen. Nature Communications
Academic article
Chawla, Konika; Kuiper, Martin. (2016) Genes2GO: A web application for querying gene sets for specific GO terms. Bioinformation
Academic article
Tripathi, Sushil; Vercruysse, Steven; Chawla, Konika; Christie, Karen R.; Blake, Judith A; Huntley, Rachael P.. (2016) Gene regulation knowledge commons: community action takes care of DNA binding transcription factors. Database: The Journal of Biological Databases and Curation
Academic article
Skancke, Jørgen; Bar, Nadav; Kuiper, Martin; Hsu, Lilian M. (2015) Sequence-Dependent Promoter Escape Efficiency Is Strongly Influenced by Bias for the Pretranslocated State during Initial Transcription. Biochemistry
Academic article
Flobak, Åsmund; Baudot, Anaïs; Remy, Elisabeth; Thommesen, Liv; Thieffry, Denis; Kuiper, Martin. (2015) Discovery of Drug Synergies in Gastric Cancer Cells Predicted by Logical Modeling. PLoS Computational Biology
Academic article
Gautam, Vinay Kumar; Czeizler, Eugen; Haddow, Pauline; Kuiper, Martin. (2014) Design of a Minimal System for Self-replication of Rectangular Patterns of DNA Tiles. Lecture Notes in Computer Science (LNCS)
Academic article
Venkatesan, Aravind; Tripathi, Sushil; Sanz de Galdeano, Alejandro; Blondé, Ward; Lægreid, Astrid; Mironov, Vladimir. (2014) Finding gene regulatory network candidates using the gene expression knowledge base. BMC Bioinformatics
Academic article
Blondé, Ward; Antezana, Erick; Mironov, Vladimir; Schulz, Stefan; Kuiper, Martin; De baets, Bernard. (2014) Using the relation ontology Metarel for modelling Linked Data as multi-digraphs. Semantic Web Journal
Academic article
Mironov, Vladimir; Kuiper, Martin; Ekseth, Ole Kristian. (2014) OrthAgogue: An agile tool for the rapid prediction of orthology relations. Bioinformatics
Academic article
Tripathi, Sushil; Christie, KR; Balakrishnan, Ravin; Huntley, R; Hill, DP; Thommesen, Liv. (2013) Gene Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a large-scale curation effort. Database: The Journal of Biological Databases and Curation
Academic article
Vercruysse, Steven; Kuiper, Martin. (2013) WordVis: JavaScript and Animation to Visualize the WordNet Relational Dictionary. Advances in Intelligent Systems and Computing
Academic article
Niehl, A; Zhang, Z.J.; Kuiper, Martin; Peck, SC; Heinlein, M. (2013) Label-Free Quantitative Proteomic Analysis of Systemic Responses to Local Wounding and Virus Infection in Arabidopsis thaliana. Journal of Proteome Research
Academic article
Chawla, Konika; Tripathi, Sushil; Thommesen, Liv; Lægreid, Astrid; Kuiper, Martin. (2013) TFcheckpoint: a curated compendium of specific DNA-binding RNA polymerase II transcription factors. Bioinformatics
Academic article
Antezana, Erick; Mironov, Vladimir; Kuiper, Martin. (2013) The emergence of Semantic Systems Biology. New Biotechnology
Academic article
Vercruysse, Steven; Venkatesan, Aravind; Kuiper, Martin. (2012) OLSVis: an animated, interactive visual browser for bio-ontologies. BMC Bioinformatics
Academic article
Kuiper, Martin; Venkatesan, Aravind; Antezana, Erick; Vercruysse, Steven; Mironov, Vladimir; Blondé, Ward. (2012) Putting Semantics in Systems Biology. META
Article in business/trade/industry journal
Mironov, Vladimir; Seethappan, Nirmala; Blondé, Ward; Antezana, Erick; Splendiani, Andrea; Kuiper, Martin. (2012) Gauging triple stores with actual biological data. BMC Bioinformatics
Academic article
Vercruysse, Steven; Kuiper, Martin. (2012) Jointly creating digital abstracts: dealing with synonymy and polysemy. BMC Research Notes
Academic article
Beisvag, Vidar; Kauffmann, Audrey; Malone, James; Foy, Carole; Salit, Marc; Schimmel, H. (2011) Contributions of the EMERALD project to assessing and improving microarray data quality. BioTechniques
Academic article
Blondé, Ward; Mironov, Vladimir; Venkatesan, Aravind; Antezana, Erick; De baets, Bernard; Kuiper, Martin. (2011) Reasoning with bio-ontologies: using relational closure rules to enable practical querying. Bioinformatics
Academic article
Mironov, Vladimir; Antezana, Erick; Egaña, Mikel; Blondé, Ward; De baets, Bernard; Kuiper, Martin. (2011) Flexibility and utility of the cell cycle ontology. Applied Ontology
Academic article
Hu, QA; Hollunder, Jens; Niehl, A; Körner, Camilla J; Gereige, Dalya; Windels, David. (2011) Specific Impact of Tobamovirus Infection on the Arabidopsis Small RNA Profile. PLOS ONE
Academic article
Antezana, Erick; Venkatesan, Aravind; Mungall, Chris; Mironov, Vladimir; Kuiper, Martin. (2010) ONTO-ToolKit: enabling bio-ontology engineering via Galaxy. BMC Bioinformatics
Academic article
De Mulder, Wim; Kuiper, Martin; Boel, Rene. (2010) Clustering of gene expression profiles: creating initialization-independent clusterings by eliminating unstable genes. Journal of Integrative Bioinformatics (JIB)
Academic article
Laukens, K; Hollunder, J; Thanh, HD; De Jaeger, G; Kuiper, Martin; Witters, E. (2010) Flexible network reconstruction from relational databases with Cytoscape and CytoSQL. BMC Bioinformatics
Academic article
Antezana, E; Kuiper, Martin; Mironov, Vladimir. (2009) Biological knowledge management: the emerging role of the Semantic Web technologies. Briefings in Bioinformatics
Academic literature review
Antezana, Erick; Egaña, Mikel; Blondé, Ward; Illarramendi, Aitzol; Bilbao, Inaki; De baets, Bernard. (2009) The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process. Genome Biology
Academic literature review
Antezana, Erick; Blondé, Ward; Egaña, Mikel; Rutherford, Alistair; Stevens, Robert; De baets, Bernard. (2009) BioGateway: A Semantic Systems Biology Tool for the Life Sciences. BMC Bioinformatics
Academic article
Naouar, Naira; Vandepoele, Klaas; Lammens, Tim; Casneuf, Tineke; Zeller, Georg; Van Hummelen, Paul. (2009) Quantitative RNA expression analysis with Affymetrix Tiling 1.0R arrays identifies new E2F target genes. The Plant Journal
Academic article
Wabnik, K; Hvidsten, TR; Kedzierska, A; Van Leene, J; De Jaeger, G; Beemster, GTS. (2009) Gene expression trends and protein features effectively complement each other in gene function prediction. Bioinformatics
Academic article
Taylor, CF; Field, D; Sansone, SA; Aerts, J; Apweiler, R; Ashburner, M. (2008) Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nature Biotechnology
Editorial
Wabnik, Krysztof; Hvidsten, Torgeir Rhoden; Kedzierska, Anna; Van Leene, Jelle; De Jaeger, Geert; Beemster, Gerrit. (2008) Gene expression trends and protein features effectively complement each other in gene function prediction. Bioinformatics
Academic article

Part of book/report

Chawla, Konika; Barah, Pankaj; Kuiper, Martin; Bones, Atle M.. (2011) Systems Biology: a Promising Tool to Study Abiotic Stress Responses. Bentham eBooks
Academic chapter/article/Conference paper
Egaña, Mikel; Stevens, Robert; Antezana, Erick; Fernández-Breis, Jesualdo Tomás; Kuiper, Martin; Mironov, Vladimir. (2010) Technologies and best practices for building bio-ontologies. John Wiley & Sons
Academic chapter/article/Conference paper

Report

Chawla, Konika; Kuiper, Martin. (2017) Discovering, analysing and taking care of knowledge. Norwegian University of Science and Technology
Doctoral dissertation

INFORMASJONSMATR

Vercruysse, Steven; Kuiper, Martin. (2018) The VSM-pages: How to Easily Plant Complex Ideas into Computers.
Website (informational material)
Lægreid, Astrid; Kuiper, Martin. (2015) Health and the information commons.
Website (informational material)
Lægreid, Astrid; Kuiper, Martin. (2014) Å ta seg av kunnskap.
Website (informational material)
Kuiper, Martin; Antezana, Erick; Mironov, Vladimir. (2013) Cell Cycle Ontology (CCO).
Website (informational material)

Teaching

Courses

Knowledge Transfer

2020

Academic lecture

Bermúdez, Viviam; Fariñas, Marco; Tsirvouli, Eirini; Kuiper, Martin. (2020) From COVID-19 Disease Map molecular mechanisms to executable cell-specific logical models. Anna Niarakis, Univ Evry, University of Paris-Saclay; FR 2020 Disease Maps Community Meeting , Luxembourg 2020-11-12 - 2020-11-14
Lecture

Bermúdez, Viviam; Tsirvouli, Eirini; Fariñas, Marco; Sridhar, Arun; Johansen, Berit; Pestana, Carolina. (2020) Modelo lógico de la activación de macrófagos y la asociación del metabolismo de ecosanoides en la polarización de los distintos fenotipos. Universidad Técnica de Manabí Cuarta Convención Científica Internacional de la Universidad Técnica de Manabí , University of Manabi, Ecuador 2020-10-21 - 2020-10-23

2019

Poster

Zobolas, John; Vázquez, Miguel; Kuiper, Martin; Flobak, Åsmund. (2019) DrugLogics: An ensemble model analysis related to drug prediction performance [version 1; not peer reviewed]. F1000Research 2019, 8:113 (poster). Norwegian Biochemical Society NBS 2019 , Røros 2019-01-24 - 2019-01-27
Poster

Vercruysse, Steven; Zobolas, John; Touré, Vasundra; Kuiper, Martin. (2019) VSM-box: the general-purpose curation interface as an open-source web-component [version 1; not peer reviewed]. F1000Research 2019, 8:442 (poster). The 12th International Biocuration Conference 2019 2019-04-12 -
Academic lecture

Acencio, Marcio Luis; Touré, Vasundra; Kuiper, Martin. (2019) MICAST Curation Guidelines: example of application for the causal relationships between DNA binding transcription factors and target genes . Biocuration 2019: Developing the Gene Regulation Knowledge Commons 2019-04-07 - 2019-04-07
Poster

Vercruysse, Steven; Zobolas, John; Touré, Vasundra; Kuiper, Martin. (2019) VSM-box: the general-purpose curation interface as an open-source web-component. Biocuration 2019 2019-04-08 - 2019-04-11
Poster

Holmås, Stian; Mironov, Vladimir; Kuiper, Martin. (2019) Network building in Cytoscape using the BioGateway App. Albert Burger, Ronald Cornet SWAT4(HC)LS 2019: Semantic Web Applications and Tools for Healthcare and Life Sciences , Edinburgh 2019-12-09 - 2019-12-12
Academic lecture

Kuiper, Martin. (2019) Towards a curation platform for causal interaction statements. Anna Niarakis, Univ Evry, University of Paris-Saclay; FR Basel Life 2019 Workshop , Basel 2019-09-09 - 2019-09-09

2018

Poster

Touré, Vasundra; Flobak, Åsmund; Lægreid, Astrid; Kuiper, Martin. (2018) Knowledge management and standard representation of causal statements for systems modeling. JOBIM 2018 , Marseille 2018-07-03 - 2018-07-06
Lecture

Niederdorfer, Barbara; Vázquez, Miguel; Thommesen, Liv; Kuiper, Martin; Lægreid, Astrid; Flobak, Åsmund. (2018) Logical model simulations predict drug synergies across different cancer cell lines. International Society for Computational Biology ISMB 2018 , Chicago 2018-07-06 - 2018-07-10
Academic lecture

Nydal, Rune; Lægreid, Astrid; Kuiper, Martin; Gabrielsen, Ane Møller. (2018) Introduction. Visions for Life Science Knowledge Commons. Crossover project Visions for Life Science Knowledge Commons , Trondheim 2018-05-23 - 2018-05-24
Academic lecture

Kuiper, Martin; Holmås, Stian. (2018) Network building in Cytoscape using the BioGateway App: benefits of hiding the SPARQL from your eyes. Daniel Zerbino, ENSEMBL PI, EMBL-EBI Invited seminar at the European Bioinformatics Institute (EBI) , Hinxton, Cambridge 2018-11-20 - 2018-11-20
Popular scientific lecture

Kuiper, Martin. (2018) In Silico Clinical Trials. Rob Diemel & Simone de Graaf, ZonMw - ERACoSysMed Invited seminar at the ERACoSysMed meeting in Paris, June 2018 , Paris 2018-06-15 - 2018-06-15
Academic lecture

Acencio, Marcio Luis; Krallinger, Martin; Kuiper, Martin; Lægreid, Astrid. (2018) Mining DbTF-TG causal interactions from biomedical literature. GREEKC CA15205: Ontologies for the Gene Regulation Knowledge Commons, and Database 'FAIRness' Short description: 2018-10-01 - 2018-10-02

2017

Lecture

Acencio, Marcio Luis; Lægreid, Astrid; Kuiper, Martin; Thommesen, Liv; Leitner, Florian; Krallinger, Martin. (2017) NTNU DbTF Curation: current status and Mining Transcription Regulation Information from Literature. Short Research Stay at the European Bioinformatics Institute (EBI) , Hinxton, Cambridge 2017-05-08 - 2017-05-10
Academic lecture

Acencio, Marcio Luis; Vázquez, Miguel; Kuiper, Martin; Lægreid, Astrid. (2017) DbTF-TG interactions and regulatory relationships: a survey. Curation workshop on molecular and causal interactions 2017-12-05 - 2017-12-07
Lecture

Kuiper, Martin. (2017) The logical way to tackle cancer. Ministry of Education, Science and Sport (MIZS) Slovenia Systems Medicine Conference in Slovenia , Ljubljana 2017-06-08 - 2017-06-09

2016

Academic lecture

Nydal, Rune; Lægreid, Astrid; Kuiper, Martin. (2016) Curation strategeis of NTNU project. EBI and Crossover Workshop upstart crossover at EBI , EBI 2016-04-22 - 2016-04-23
Lecture

Acencio, Marcio Luis; Lægreid, Astrid; Kuiper, Martin. (2016) Knowledge Commons digitalization - curation . Crossover Seminar 2016-04-14 - 2016-04-15
Lecture

Acencio, Marcio Luis; Lægreid, Astrid; Kuiper, Martin. (2016) Causal statements for Gene Regulation & Signal Transduction: what can be done in PSI-MI. HUPO-PSI meeting 2016 2016-04-18 - 2016-04-20

2015

Lecture

Kuiper, Martin. (2015) Keynote lecture: Taking care of knowledge to enable systems analysis. AB3C President: Glória R Franco (UFMG) X-Meeting 2015 - 11th International Conference of th AB3C + Brazilian Symposium of Bioinformatics , University of São Paulo 2015-11-03 - 2015-11-06

2014

Lecture

Kuiper, Martin. (2014) Keynote lecture: Networks for Knowledge. IEEE - University of Ulster IEEE International Conference Bioinformatics and Biomedicine 2014 , Belfast 2014-11-02 - 2014-11-05
Lecture

Kuiper, Martin. (2014) Augmenting the human brain. Crossover research group NTNU Knowledge management and the futures of our society, a Virtual Physiological Human 2014 Satellite Workshop , Trondheim 2014-09-08 - 2014-09-09
Lecture

Nydal, Rune; Efstathiou, Sophia; Lægreid, Astrid; Kuiper, Martin. (2014) Setting the stage: Tragedy of the knowledge commons. Crossover research group NTNU Knowledge management and the futures of our society, a Virtual Physiological Human 2014 Satellite Workshop , Trondheim 2014-09-08 - 2014-09-09
Poster

Kuiper, Martin; Mironov, Vladimir; Venkatesan, Aravind; Tripathi, Sushil; Blondé, Ward; Sanz de Galdeano, Alejandro. (2014) The gene expression knowledge base. Stig Omholt / VPH consortium Virtual Physiological Human Conference 2014 , Trondheim 2014-09-09 - 2014-09-12
Poster

Flobak, Åsmund; Baudot, Anaïs; Remy, Elisabeth; Thommesen, Liv; Thieffry, Denis; Kuiper, Martin. (2014) Drug synergies in a gastric cancer cell line discovered by signal transduction modeling. Stig Omholt / VPH consortium Virtual Physiological Human Conference 2014 , Trondheim 2014-09-09 - 2014-09-12
Poster

Kuiper, Martin; Lægreid, Astrid. (2014) The GRECO initiative: taking care of Gene Regulation knowledge. Stig Omholt / VPH consortium Virtual Physiological Human Conference 2014 , Trondheim 2014-09-09 - 2014-09-12
Lecture

De Mulder, Wim; Zavareh, Zahra; Chawla, Konika; Kuiper, Martin. (2014) Experimental Verification of the Quality of Clusterings Produced by Hard Clustering Algorithms After the Removal of Unstable Data Elements. International Academy, Research and Industry Association BIOTECHNO 2014, DBKDA 2014 , Chamonix 2014-04-20 - 2014-04-24

2013

Academic lecture

Gautam, Vinay Kumar; Haddow, Pauline; Kuiper, Martin. (2013) Reliable Self-assembly by Self-triggered Activation of Enveloped DNA Tiles. Lecture Notes in Computer Science 2nd International Conference on the Theory and Practice of Natural Computing , Cáceres 2013-12-03 - 2013-12-05
Lecture

Kuiper, Martin. (2013) It's all semantics for the user. Jin-Dong Kim and Fabio Rinaldi LBM 2013 – International Symposium on Languages in Biology and Medicine , Tokyo 2013-12-12 - 2013-12-13

2012

Academic lecture

Kuiper, Martin. (2012) The Emergence of Semantic Systems Biology. Rune Nydal The Ethos of Integrative Research:The case of systems biology , Trondheim 2012-11-26 - 2012-11-27
Academic lecture

Efstathiou, Sophia; Carusi, Annamaria; Kuiper, Martin; Lægreid, Astrid; Nydal, Rune. (2012) Research Systems for Systems Biology. Austrian Society for Cybernetic Studies European Meetings on Cybernetics and Systems Research , Vienna 2012-04-10 - 2012-04-13
Academic lecture

Efstathiou, Sophia; Nydal, Rune; Carusi, Annamaria; Kuiper, Martin; Lægreid, Astrid. (2012) Well-constructed systems biology: Integrating socio-humanist research. European Meetings on Cybernetics and Systems Research , AUSTRIA 2012-04-12 - 2012-04-14
Academic lecture

Efstathiou, Sophia; Nydal, Rune; Kuiper, Martin; Lægreid, Astrid; Carusi, Annamaria. (2012) When ‘Knowledge’ Becomes Something to Manage. Society for the Study of Nanoscience and Emerging Technologies 2012-10-23 - 2012-10-25
Academic lecture

Venkatesan, Aravind; Mironov, Vladimir; Kuiper, Martin. (2012) Towards an integrated knowledge system for capturing gene expression events. Stefan Schulz, Catalina Martínez, Markus Kreuzthaler 3rd International Conference on Biomedical Ontology (ICBO 2012) , Graz 2012-07-21 - 2012-07-25
Poster

Hollunder, Jens; Mironov, Vladimir; Antezana, Erick; Hoehndorf, Robert; Kuiper, Martin. (2012) Profiling of Semantically Annotated Proteins. SWAT4LS Semantic Web Applications and Tools for Life Sciences 2012 , Paris 2012-11-28 - 2012-11-30
Poster

Venkatesan, Aravind; Antezana, Erick; Blondé, Ward; Vercruysse, Steven; Mironov, Vladimir; Kuiper, Martin. (2012) Putting Semantics in Systems Biology. Norwegian Bioinformatics Forum NTNU Bioinformatics Network Seminar 2012 Norwegian Bioinformatics Forum 2012 , Trondheim 2012-10-18 - 2012-10-19

2011

Poster

Tripathi, Sushil; Venkatesan, Aravind; Egaña, Mikel; Zavareh, Zahra; Chawla, Konika; Mironov, Vladimir. (2011) Automated Assessment of High Throughput Hypotheses on Gene Regulatory Mechanisms Involved in the Gastrin Response. ISMB 2011 Bio-Ontologies 2011 , Vienna 2011-07-15 - 2011-07-16
Academic lecture

Venkatesan, Aravind; Blondé, Ward; Antezana, Erick; Skillingstad, Mats Gløer Løkås; Marshall, Scott M; De baets, Bernard. (2011) The RDF Foundry: Call for an initiative to build enhanced RDF resources for biological data integration. WIMS: International Conferences on Web Intelligence, Mining and Semantics. , Sogndal 2011-05-25 - 2011-05-27
Academic lecture

Antezana, Erick; Blondé, Ward; Venkatesan, Aravind; De baets, Bernard; Mironov, Vladimir; Kuiper, Martin. (2011) Semantic SB: enablng integrative biology via SW technologies. WIMS: International Conferences on Web Intelligence, Mining and Semantics. , Sogndal 2011-05-25 - 2011-05-27
Academic lecture

Vercruysse, Steven; Kuiper, Martin. (2011) WordVis: JavaScript and Animation to Visualize the WordNet Relational Dictionary. IHCI 2011: Third International Conference on Intelligent Human Computer Interaction , Faculty of Mathematics and Physics of the Charles University 2011-08-29 - 2011-08-31
Academic lecture

Mironov, Vladimir; Venkatesan, Aravind; Kuiper, Martin. (2011) RDF Foundry - a call for a community effort to harmonize triple store practices. BioHackathon 2011 , Kyoto University 2011-08-20 - 2011-08-26

2010

Academic lecture

Mironov, Vladimir; Seethappan, Nirmala; Blondé, Ward; Antezana, Erick; Lindi, Bjørn; Kuiper, Martin. (2010) Benchmarking triple stores with biological data. Adrian Paschke, Corporate Semantic Web, Freie Universitaet Semantic Web Applications and Tools for Life Sciences , Berlin 2010-12-10 - 2010-12-10

2009

Academic lecture

Kuiper, Martin; Splendiani, Andrea; Rawlings, Chris. (2009) Toward a New Paradigm for User Interaction on the Semantic Web to Support Life Sciences Investigation. Duane Degler Semantic Web User Interaction , Washington DC 2009-10-25 - 2009-10-25
Academic lecture

Kuiper, Martin. (2009) BioGateway: an overture to Semantic Systems Biology. NBS NBS Contact meeting – 2009 , Roros 2009-01-29 - 2009-02-01
Academic lecture

Blondé, Ward; Antezana, Erick; De baets, Bernard; Mironov, Vladimir; Kuiper, Martin. (2009) Metarel: an ontology to support the inferencing of semantic web relations within biomedical ontologies. International Conference on Biomedical Ontology , Buffalo 2009-07-20 - 2009-07-23
Poster

Beisvag, Vidar; Sandvik, Arne Kristian; Kuiper, Martin. (2009) EMERALD – Enhancing Microarray Data Quality. Microarray Gene expression and Data Society MGED12 , Phoenix, Arizona 2009-10-05 - 2009-10-08
Poster

Beisvag, Vidar; Sandvik, Arne Kristian; Kuiper, Martin. (2009) EMERALD – Enhancing Microarray Data Quality. Select Bioscineces The 5th Advinces in Microarray Technology 2009 , Stockholm 2009-05-18 - 2009-05-20
Poster

Beisvag, Vidar; Sandvik, Arne Kristian; Kuiper, Martin. (2009) EMERALD – Enhancing Microarray Data Quality. Norsk Biokjemisk Selskap Norsk Biokjemisk Selskap Kontaktmøte 2009 , Røros 2009-01-29 - 2009-01-31

2008

Academic lecture

Kuiper, Martin. (2008) The Cell Cycle Ontology: an overture to Semantic Systems Biology. Pascal Kahlem - ENFIN Systems Biology Approaches to Study the Cell Cycle , Malaga 2008-10-20 - 2008-10-21
Poster

Beisvåg, Vidar; Sandvik, Arne Kristian; Kuiper, Marius Tremen Roelof. (2008) EMERALD – Enhancing Microarray Data Quality. the Microarray and Gene Expression Data Society 11th International Meeting of MGED , Riva Del Garda 2008-09-01 - 2008-09-06
Poster

Beisvåg, Vidar; Sandvik, Arne Kristian; Kuiper, Marius Tremen Roelof. (2008) EMERALD – Enhancing Microarray Data Quality. CAMDA The eigth international conference for the Critical Assessment of Microarray Data Analysis (CAMDA 2008) , Vien 2008-12-04 - 2008-12-06
Poster

Beisvåg, Vidar; Sandvik, Arne Kristian; Kuiper, Marius Tremen Roelof. (2008) EMERALD – Enhancing Microarray Data Quality. European Molecular Biology Organisation (EMBO) 4th EMBO Conference: From Functional Genomics to Systems Biology , EMBL, Heidelberg 2008-11-15 - 2008-11-18
Poster

Beisvåg, Vidar; Sandvik, Andreas; Kuiper, Marius Tremen Roelof. (2008) EMERALD – Enhancing Microarray Data Quality. The Consortium of European project PROUST: the Temporal Dime Genes at work on time , Torina 2008-10-15 - 2008-10-18
Poster

Beisvåg, Vidar; Kuiper, Marius Tremen Roelof; Sandvik, Arne Kristian. (2008) EMERALD – Enhancing Microarray Data Quality. European Scinece Foundation 3rd ESF Conference on Functional Genomics and Disease , Innsbruck 2008-10-01 - 2008-10-04

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Martin Kuiper

Martin Kuiper

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