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

2022

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. volum 1865 (1).
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. volum 13 (1).
Academic article
Kuiper, Martin; Bonello, Joseph; Fernández-Breis, Jesualdo Tomás; Bucher, Philipp; Futschik, Matthias E; Gaudet, Pascale; Kulakovskiy, Ivan V.; Licata, Luana; Logie, Colin; Lovering, Ruth C.; Makeev, Vsevolod J; Orchard, Sandra; Panni, Simona; Perfetto, Livia; Sant, David; Schulz, Stefan M.; Vercruysse, Steven; Zerbino, Daniel; Lægreid, Astrid. (2022) The gene regulation knowledge commons: the action area of GREEKC. Biochimica et Biophysica Acta. Gene Regulatory Mechanisms. volum 1865 (1).
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. volum 1865 (1).
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. volum 538.
Academic article

2021

Carbon, Seth J.; Douglass, Eric; Good, Benjamin M; Unni, Deepak R; Harris, Nomi L.; Mungall, Christopher J.; Basu, Siddartha; Chisholm, Rex L.; Dodson, Robert J.; Hartline, Eric; Fey, Petra; Thomas, Paul D.; Albou, Laurent-Philippe; Ebert, Dustin; Kesling, Michael J; Mi, Huaiyu; Muruganujan, Anushya; Huang, Xiaosong; Mushayahama, Tremayne; LaBonte, Sandra A.; Siegele, Deborah A.; Antonazzo, Giulia; Attrill, Helen; Brown, Nick H.; Garapati, Phani; Marygold, Steven J.; Trovisco, Vitor; dos Santos, Gil; Falls, Kathleen; Tabone, Christopher; Zhou, Pinglei; Goodman, Joshua L.; Strelets, Victor B.; Thurmond, Jim; Garmiri, Penelope; Ishtiaq, Rizwan; Rodríguez-López, Milagros; Acencio, Marcio Luis; Kuiper, Martin; Lægreid, Astrid; Logie, Colin; Lovering, Ruth C.; Kramarz, Barbara; Saverimuttu, Shirin C.C.; Pinheiro, Sandra M.; Gunn, Heather; Su, Renzhi; Thurlow, Katherine E.; Chibucos, Marcus; Giglio, Michelle; Nadendla, Suvarna; Munro, James; Jackson, Rebecca; Duesbury, Margaret J.; del-Toro, Noemi; Meldal, Birgit H.M.; Paneerselvam, Kalpana; Perfetto, Livia; Porras, Pablo; Orchard, Sandra; Shrivastava, Anjali. (2021) The Gene Ontology resource: enriching a GOld mine. Nucleic Acids Research (NAR).
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. volum 1864 (11-12).
Academic article
Juanes Cortés, Belén; Vera-Ramos, José Antonio; Lovering, Ruth C.; Gaudet, Pascale; Lægreid, Astrid; Logie, Colin; Schulz, Stefan; Roldán-García, María del Mar; Kuiper, Martin; Fernández-Breis, Jesualdo Tomás. (2021) Formalization of gene regulation knowledge using ontologies and gene ontology causal activity models. Biochimica et Biophysica Acta. Gene Regulatory Mechanisms. volum 1864 (11-12).
Academic article
Lovering, Ruth C.; Gaudet, Pascale; Acencio, Marcio Luis; Ignatchenko, Alex; Jolma, Arttu; Fornes, Oriol; Kuiper, Martin; Kulakovskiy, Ivan V.; Lægreid, Astrid; Martin, Maria J.; Logie, Colin. (2021) A GO catalogue of human DNA-binding transcription factors. Biochimica et Biophysica Acta. Gene Regulatory Mechanisms. volum 1864 (11-12).
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. volum 22 (4).
Academic literature review
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
Tsirvouli, Eirini; Ashcroft, Felicity; Johansen, Berit; Kuiper, Martin. (2021) Logical and experimental modeling of cytokine and eicosanoid signaling in psoriatic keratinocytes. iScience. volum 24.
Academic article

2020

Comte, Blandine; Baumbach, Jan; Benis, Arriel; Basílio, José; Debeljak, Nataša; Flobak, Åsmund; Franken, Christian; Harel, Nissim; He, Feng; Kuiper, Martin; Juan Albino Méndez, Pérez; Pujos-Guillot, Estelle; Režen, Tadeja; Rozman, Damjana; Schmid, Johannes A; Scerri, Jeanesse; Tieri, Paolo; Van Steen, Kristel; Sona, Vasudevan; Watterson, Steven; Schmidt, Harald H H W. (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
De Mulder, Wim; Kuiper, Martin. (2020) A foundation for reference models for drug combinations with an application to Loewe’s reference model. BMC Bioinformatics. volum 21 (460).
Academic article
Niarakis, Anna; Kuiper, Martin; Ostaszewski, Marek; Malik Sheriff, Rahuman; Casals-Casas, Cristina; Thieffry, Denis; Freeman, Tom; Thomas, Paul; Touré, Vasundra; Noel, Vincent; Stoll, Gautier; Saez-Rodriguez, Julio; Naldi, Aurélien; Oshurko, Eugenia; Xenarios, Ioannis; Soliman, Sylvain; Chaouiya, Claudine; Helikar, Tomas; Calzone, Laurence. (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
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
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. volum 72 (1).
Academic article
Touré, Vasundra; Vercruysse, Steven; Acencio, Marcio Luis; Lovering, Ruth C.; Orchard, Sandra; Bradley, Glyn; Casals-Casas, Cristina; Chaouiya, Claudine; del-Toro, Noemi; Flobak, Åsmund; Gaudet, Pascale; Hermjakob, Henning; Hoyt, Charles Tapley; Licata, Luana; Lægreid, Astrid; Mungall, Christopher; Niknejad, Anne; Panni, Simona; Perfetto, Livia; Porras, Pablo; Pratt, Dexter; Saez-Rodriguez, Julio; Thieffry, Denis; Thomas, Paul; Türei, Dénes; Kuiper, Martin. (2020) The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST). Bioinformatics.
Academic article
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. volum 7:502573.
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). volum 5 (53).
publications.INTERVJUSKRIFTL
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
Zobolas, John; Touré, Vasundra; Kuiper, Martin; Vercruysse, Steven. (2020) UniBioDicts: Unified access to biological dictionaries. Bioinformatics.
Academic article

2019

Carbon, Seth J.; Douglass, E; Dunn, N; Good, B; Harris, NL; Lewis, SE; Mungall, CJ; Basu, S; Chisholm, RL; Dodson, RJ; Hartline, E; Fey, P; Thomas, PD; Albou, LP; Ebert, D; Kesling, MJ; Mi, H; Muruganujan, A; Huang, X; Poudel, S; Mushayahama, T; Hu, JC; LaBonte, SA; Siegele, DA; Antonazzo, G; Attrill, H; Brown, NH; Fexova, S; Garapati, P; Jones, TEM; Marygold, SJ; Millburn, GH; Rey, AJ; Trovisco, V; Dos Santos, G; Emmert, DB; Falls, K; Zhou, P; Goodman, JL; Strelets, VB; Thurmond, J; Courtot, M; Osumi, DS; Parkinson, H; Roncaglia, P; Acencio, Marcio Luis; Kuiper, Martin; Lægreid, Astrid; Logie, C; Lovering, RC; Huntley, RP; Denny, P; Campbell, NH; Kramarz, B; Acquaah, V; Ahmad, SH; Chen, H; Rawson, JH; Chibucos, MC; Giglio, M; Nadendla, S; Tauber, R; Duesbury, MJ; Del, NT; Meldal, BHM; Perfetto, L; Porras, P; Orchard, S; Shrivastava, A; Xie, Z; Chang, HY; Finn, RD; Mitchell, AL; Rawlings, ND; Richardson, L; Sangrador-Vegas, A; Blake, JA; Christie, KR; Dolan, ME; Drabkin, HJ; Hill, DP; Ni, L; Sitnikov, D; Harris, MA; Oliver, SG; Rutherford, K; Wood, V; Hayles, J; Bahler, J; Lock, A; Bolton, ER; De Pons, J; Dwinell, M; Hayman, GT; Laulederkind, SJF; Shimoyama, M; Tutaj, M; Wang, SJ; D'Eustachio, P; Matthews, L; Balhoff, JP; Aleksander, SA; Binkley, G; Dunn, BL; Cherry, JM; Engel, SR; Gondwe, F; Karra, K; MacPherson, KA; Miyasato, SR; Nash, RS; Ng, PC; Sheppard, TK; Shrivatsav Vp, A; Simison, M; Skrzypek, MS; Weng, S; Wong, ED; Feuermann, M; Gaudet, P; Bakker, E; Berardini, TZ; Reiser, L; Subramaniam, S; Huala, E; Arighi, C; Auchincloss, A; Axelsen, K; Argoud, GP; Bateman, A; Bely, B; Blatter, MC; Boutet, E; Breuza, L; Bridge, A; Britto, R; Bye-A-Jee, H; Casals-Casas, C; Coudert, E; Estreicher, A; Famiglietti, L; Garmiri, P; Georghiou, G; Gos, A; Gruaz-Gumowski, N; Hatton-Ellis, E; Hinz, U; Hulo, C; Ignatchenko, A; Jungo, F; Keller, G; Laiho, K; Lemercier, P; Lieberherr, D; Lussi, Y; Mac-Dougall, A; Magrane, M; Martin, MJ; Masson, P; Natale, DA; Hyka, NN; Pedruzzi, I; Pichler, K; Poux, S; Rivoire, C; Rodriguez-Lopez, M; Sawford, T; Speretta, E; Shypitsyna, A; Stutz, A; Sundaram, S; Tognolli, M; Tyagi, N; Warner, K; Zaru, R; Wu, C; Chan, J; Cho, J; Gao, S; Grove, C; Harrison, MC; Howe, K; Lee, R; Mendel, J; Muller, HM; Raciti, D; Van Auken, K; Berriman, M; Stein, L; Sternberg, PW; Howe, D; Toro, S; Westerfield, Monte. (2019) The Gene Ontology Resource: 20 years and still GOing strong. Nucleic Acids Research (NAR). volum 47 (gky1055).
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. volum 34 (2).
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; Flobak, Åsmund; Kuiper, Martin; Lægreid, Astrid; Thommesen, Liv. (2019) Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen. Nature Communications. volum 10 (2674).
Academic article
Perfetto, Livia; Acencio, Marcio Luis; Bradley, Glyn; Cesareni, Gianni; del Toro, Noemi; Fazekas, David; Hermjakob, Henning; Korcsmaros, Tamas; Kuiper, Martin; Lægreid, Astrid; Lo Surdo, Prisca; Lovering, Ruth C.; Orchard, Sandra; Porras, Pablo; Thomas, Paul; Touré, Vasundra; Zobolas, John; Licata, Luana. (2019) CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination. Bioinformatics. volum 35 (19).
Academic article
Vera-Ramos, Jose Antonio; Juanes-Cortes, Belen; Fernández-Breis, Jesualdo Tomás; Gaudet, Pascale; Kuiper, Martin; Lægreid, Astrid; Logie, Colin; Roldan-Garcia, Maria del Mar; Schulz, Stefan. (2019) An example of multimodal biological knowledge representation. CEUR Workshop Proceedings. volum 2518.
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. 2017. ISBN 978-82-326-2316-7.
Doctoral dissertation

2016

Chawla, Konika; Kuiper, Martin. (2016) Genes2GO: A web application for querying gene sets for specific GO terms. Bioinformation. volum 12 (3).
Academic article
Tripathi, Sushil; Vercruysse, Steven; Chawla, Konika; Christie, Karen R.; Blake, Judith A; Huntley, Rachael P.; Orchard, Sandra; Hermjakob, Henning; Thommesen, Liv; Lægreid, Astrid; Kuiper, Martin. (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

Flobak, Åsmund; Baudot, Anaïs; Remy, Elisabeth; Thommesen, Liv; Thieffry, Denis; Kuiper, Martin; Lægreid, Astrid. (2015) Discovery of Drug Synergies in Gastric Cancer Cells Predicted by Logical Modeling. PLoS Computational Biology. volum 11 (8).
Academic article
Lægreid, Astrid; Kuiper, Martin. (2015) Health and the information commons.
Website (informational material)
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. volum 54 (28).
Academic article

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). volum 8890.
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. volum 5 (2).
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. volum 30 (5).
Academic article
Venkatesan, Aravind; Tripathi, Sushil; Sanz de Galdeano, Alejandro; Blondé, Ward; Lægreid, Astrid; Mironov, Vladimir; Kuiper, Martin. (2014) Finding gene regulatory network candidates using the gene expression knowledge base. BMC Bioinformatics. volum 15 (1).
Academic article

2013

Antezana, Erick; Mironov, Vladimir; Kuiper, Martin. (2013) The emergence of Semantic Systems Biology. New Biotechnology. volum 30 (3).
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. volum 29 (19).
Academic article
Kuiper, Martin; Antezana, Erick; Mironov, Vladimir. (2013) Cell Cycle Ontology (CCO).
Website (informational material)
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. volum 12 (6).
Academic article
Tripathi, Sushil; Christie, KR; Balakrishnan, Ravin; Huntley, R; Hill, DP; Thommesen, Liv; Blake, JA; Kuiper, Martin; Lægreid, Astrid. (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. volum 179.
Academic article

2012

Kuiper, Martin; Venkatesan, Aravind; Antezana, Erick; Vercruysse, Steven; Mironov, Vladimir; Blondé, Ward. (2012) Putting Semantics in Systems Biology. META. volum 2012 (3).
Article
Mironov, Vladimir; Seethappan, Nirmala; Blondé, Ward; Antezana, Erick; Splendiani, Andrea; Kuiper, Martin. (2012) Gauging triple stores with actual biological data. BMC Bioinformatics. volum 13.
Academic article
Vercruysse, Steven; Kuiper, Martin. (2012) Jointly creating digital abstracts: dealing with synonymy and polysemy. BMC Research Notes. volum 5 (601).
Academic article
Vercruysse, Steven; Venkatesan, Aravind; Kuiper, Martin. (2012) OLSVis: an animated, interactive visual browser for bio-ontologies. BMC Bioinformatics. volum 13.
Academic article

2011

Beisvag, Vidar; Kauffmann, Audrey; Malone, James; Foy, Carole; Salit, Marc; Schimmel, H; Bongcam-Rudloff, Eric; Landegren, Ulf; Parkinson, Helen; Huber, Wolfgang; Brazma, Alvis; Sandvik, Arne Kristian; Kuiper, Martin. (2011) Contributions of the EMERALD project to assessing and improving microarray data quality. BioTechniques. volum 50 (1).
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. volum 27 (11).
Academic article
Chawla, Konika; Barah, Pankaj; Kuiper, Martin; Bones, Atle M.. (2011) Systems Biology: a Promising Tool to Study Abiotic Stress Responses. Omics and Plant Abiotic Stress Tolerance.
Academic chapter/article/Conference paper
Hu, QA; Hollunder, Jens; Niehl, A; Körner, Camilla J; Gereige, Dalya; Windels, David; Arnold, Andreas; Kuiper, Martin; Vazquez, Frank; Pooggin, M; Heinlein, M. (2011) Specific Impact of Tobamovirus Infection on the Arabidopsis Small RNA Profile. PLOS ONE. volum 6 (5).
Academic article
Mironov, Vladimir; Antezana, Erick; Egaña, Mikel; Blondé, Ward; De baets, Bernard; Kuiper, Martin; Stevens, Robert. (2011) Flexibility and utility of the cell cycle ontology. Applied Ontology. volum 6 (3).
Academic article

2010

Antezana, Erick; Venkatesan, Aravind; Mungall, Chris; Mironov, Vladimir; Kuiper, Martin. (2010) ONTO-ToolKit: enabling bio-ontology engineering via Galaxy. BMC Bioinformatics. volum 11.
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). volum 7 (3).
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. Knowledge-based bioinformatics : from analysis to interpretation.
Academic chapter/article/Conference paper
Laukens, K; Hollunder, J; Thanh, HD; De Jaeger, G; Kuiper, Martin; Witters, E; Verschoren, A; Van Leemput, K. (2010) Flexible network reconstruction from relational databases with Cytoscape and CytoSQL. BMC Bioinformatics. volum 11.
Academic article

2009

Antezana, E; Kuiper, Martin; Mironov, Vladimir. (2009) Biological knowledge management: the emerging role of the Semantic Web technologies. Briefings in Bioinformatics. volum 10 (4).
Academic literature review
Antezana, Erick; Blondé, Ward; Egaña, Mikel; Rutherford, Alistair; Stevens, Robert; De baets, Bernard; Mironov, Vladimir; Kuiper, Martin. (2009) BioGateway: A Semantic Systems Biology Tool for the Life Sciences. BMC Bioinformatics. volum 10 (S11).
Academic article
Antezana, Erick; Egaña, Mikel; Blondé, Ward; Illarramendi, Aitzol; Bilbao, Inaki; De baets, Bernard; Stevens, Robert; Mironov, Vladimir; Kuiper, Martin. (2009) The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process. Genome Biology. volum 10 (5).
Academic literature review
Naouar, Naira; Vandepoele, Klaas; Lammens, Tim; Casneuf, Tineke; Zeller, Georg; Van Hummelen, Paul; Weigel, Detlef; Ratsch, Gunnar; Inze, Dirk; Kuiper, Martin; De Veylder, Lieven; Vuylsteke, Marnik. (2009) Quantitative RNA expression analysis with Affymetrix Tiling 1.0R arrays identifies new E2F target genes. The Plant Journal. volum 57 (1).
Academic article
Wabnik, K; Hvidsten, TR; Kedzierska, A; Van Leene, J; De Jaeger, G; Beemster, GTS; Komorowski, J; Kuiper, Martin. (2009) Gene expression trends and protein features effectively complement each other in gene function prediction. Bioinformatics. volum 25 (3).
Academic article

2008

Taylor, CF; Field, D; Sansone, SA; Aerts, J; Apweiler, R; Ashburner, M; Ball, CA; Binz, PA; Bogue, M; Booth, T; Brazma, A; Brinkman, RR; Clark, AM; Deutsch, EW; Fiehn, O; Fostel, J; Ghazal, P; Gibson, F; Gray, T; Grimes, G; Hancock, JM; Hardy, NW; Hermjakob, H; Julian, RK; Kane, M; Kettner, C; Kinsinger, C; Kolker, E; Kuiper, Marius Tremen Roelof; Le Novere, N; Leebens-Mack, J; Lewis, SE; Lord, P; Mallon, AM; Marthandan, N; Masuya, H; McNally, R; Mehrle, A; Morrison, N; Orchard, S; Quackenbush, J; Reecy, JM; Robertson, DG; Rocca-Serra, P; Rodriguez, H; Rosenfelder, H; Santoyo-Lopez, J; Scheuermann, RH; Schober, D; Smith, B; Snape, J; Stoeckert, CJ; Tipton, K; Sterk, P; Untergasser, A; Vandesompele, J; Wiemann, S. (2008) Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nature Biotechnology. volum 26 (8).
Editorial
Wabnik, Krysztof; Hvidsten, Torgeir Rhoden; Kedzierska, Anna; Van Leene, Jelle; De Jaeger, Geert; Beemster, Gerrit; Komorowski, Jan; Kuiper, Martin. (2008) Gene expression trends and protein features effectively complement each other in gene function prediction. Bioinformatics.
Academic article

Journal publications

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. volum 1865 (1).
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. volum 13 (1).
Academic article
Kuiper, Martin; Bonello, Joseph; Fernández-Breis, Jesualdo Tomás; Bucher, Philipp; Futschik, Matthias E; Gaudet, Pascale; Kulakovskiy, Ivan V.; Licata, Luana; Logie, Colin; Lovering, Ruth C.; Makeev, Vsevolod J; Orchard, Sandra; Panni, Simona; Perfetto, Livia; Sant, David; Schulz, Stefan M.; Vercruysse, Steven; Zerbino, Daniel; Lægreid, Astrid. (2022) The gene regulation knowledge commons: the action area of GREEKC. Biochimica et Biophysica Acta. Gene Regulatory Mechanisms. volum 1865 (1).
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. volum 1865 (1).
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. volum 538.
Academic article
Carbon, Seth J.; Douglass, Eric; Good, Benjamin M; Unni, Deepak R; Harris, Nomi L.; Mungall, Christopher J.; Basu, Siddartha; Chisholm, Rex L.; Dodson, Robert J.; Hartline, Eric; Fey, Petra; Thomas, Paul D.; Albou, Laurent-Philippe; Ebert, Dustin; Kesling, Michael J; Mi, Huaiyu; Muruganujan, Anushya; Huang, Xiaosong; Mushayahama, Tremayne; LaBonte, Sandra A.; Siegele, Deborah A.; Antonazzo, Giulia; Attrill, Helen; Brown, Nick H.; Garapati, Phani; Marygold, Steven J.; Trovisco, Vitor; dos Santos, Gil; Falls, Kathleen; Tabone, Christopher; Zhou, Pinglei; Goodman, Joshua L.; Strelets, Victor B.; Thurmond, Jim; Garmiri, Penelope; Ishtiaq, Rizwan; Rodríguez-López, Milagros; Acencio, Marcio Luis; Kuiper, Martin; Lægreid, Astrid; Logie, Colin; Lovering, Ruth C.; Kramarz, Barbara; Saverimuttu, Shirin C.C.; Pinheiro, Sandra M.; Gunn, Heather; Su, Renzhi; Thurlow, Katherine E.; Chibucos, Marcus; Giglio, Michelle; Nadendla, Suvarna; Munro, James; Jackson, Rebecca; Duesbury, Margaret J.; del-Toro, Noemi; Meldal, Birgit H.M.; Paneerselvam, Kalpana; Perfetto, Livia; Porras, Pablo; Orchard, Sandra; Shrivastava, Anjali. (2021) The Gene Ontology resource: enriching a GOld mine. Nucleic Acids Research (NAR).
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. volum 1864 (11-12).
Academic article
Juanes Cortés, Belén; Vera-Ramos, José Antonio; Lovering, Ruth C.; Gaudet, Pascale; Lægreid, Astrid; Logie, Colin; Schulz, Stefan; Roldán-García, María del Mar; Kuiper, Martin; Fernández-Breis, Jesualdo Tomás. (2021) Formalization of gene regulation knowledge using ontologies and gene ontology causal activity models. Biochimica et Biophysica Acta. Gene Regulatory Mechanisms. volum 1864 (11-12).
Academic article
Lovering, Ruth C.; Gaudet, Pascale; Acencio, Marcio Luis; Ignatchenko, Alex; Jolma, Arttu; Fornes, Oriol; Kuiper, Martin; Kulakovskiy, Ivan V.; Lægreid, Astrid; Martin, Maria J.; Logie, Colin. (2021) A GO catalogue of human DNA-binding transcription factors. Biochimica et Biophysica Acta. Gene Regulatory Mechanisms. volum 1864 (11-12).
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. volum 22 (4).
Academic literature review
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
Tsirvouli, Eirini; Ashcroft, Felicity; Johansen, Berit; Kuiper, Martin. (2021) Logical and experimental modeling of cytokine and eicosanoid signaling in psoriatic keratinocytes. iScience. volum 24.
Academic article
Comte, Blandine; Baumbach, Jan; Benis, Arriel; Basílio, José; Debeljak, Nataša; Flobak, Åsmund; Franken, Christian; Harel, Nissim; He, Feng; Kuiper, Martin; Juan Albino Méndez, Pérez; Pujos-Guillot, Estelle; Režen, Tadeja; Rozman, Damjana; Schmid, Johannes A; Scerri, Jeanesse; Tieri, Paolo; Van Steen, Kristel; Sona, Vasudevan; Watterson, Steven; Schmidt, Harald H H W. (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
De Mulder, Wim; Kuiper, Martin. (2020) A foundation for reference models for drug combinations with an application to Loewe’s reference model. BMC Bioinformatics. volum 21 (460).
Academic article
Niarakis, Anna; Kuiper, Martin; Ostaszewski, Marek; Malik Sheriff, Rahuman; Casals-Casas, Cristina; Thieffry, Denis; Freeman, Tom; Thomas, Paul; Touré, Vasundra; Noel, Vincent; Stoll, Gautier; Saez-Rodriguez, Julio; Naldi, Aurélien; Oshurko, Eugenia; Xenarios, Ioannis; Soliman, Sylvain; Chaouiya, Claudine; Helikar, Tomas; Calzone, Laurence. (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
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
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. volum 72 (1).
Academic article
Touré, Vasundra; Vercruysse, Steven; Acencio, Marcio Luis; Lovering, Ruth C.; Orchard, Sandra; Bradley, Glyn; Casals-Casas, Cristina; Chaouiya, Claudine; del-Toro, Noemi; Flobak, Åsmund; Gaudet, Pascale; Hermjakob, Henning; Hoyt, Charles Tapley; Licata, Luana; Lægreid, Astrid; Mungall, Christopher; Niknejad, Anne; Panni, Simona; Perfetto, Livia; Porras, Pablo; Pratt, Dexter; Saez-Rodriguez, Julio; Thieffry, Denis; Thomas, Paul; Türei, Dénes; Kuiper, Martin. (2020) The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST). Bioinformatics.
Academic article
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. volum 7:502573.
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). volum 5 (53).
publications.INTERVJUSKRIFTL
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
Zobolas, John; Touré, Vasundra; Kuiper, Martin; Vercruysse, Steven. (2020) UniBioDicts: Unified access to biological dictionaries. Bioinformatics.
Academic article
Carbon, Seth J.; Douglass, E; Dunn, N; Good, B; Harris, NL; Lewis, SE; Mungall, CJ; Basu, S; Chisholm, RL; Dodson, RJ; Hartline, E; Fey, P; Thomas, PD; Albou, LP; Ebert, D; Kesling, MJ; Mi, H; Muruganujan, A; Huang, X; Poudel, S; Mushayahama, T; Hu, JC; LaBonte, SA; Siegele, DA; Antonazzo, G; Attrill, H; Brown, NH; Fexova, S; Garapati, P; Jones, TEM; Marygold, SJ; Millburn, GH; Rey, AJ; Trovisco, V; Dos Santos, G; Emmert, DB; Falls, K; Zhou, P; Goodman, JL; Strelets, VB; Thurmond, J; Courtot, M; Osumi, DS; Parkinson, H; Roncaglia, P; Acencio, Marcio Luis; Kuiper, Martin; Lægreid, Astrid; Logie, C; Lovering, RC; Huntley, RP; Denny, P; Campbell, NH; Kramarz, B; Acquaah, V; Ahmad, SH; Chen, H; Rawson, JH; Chibucos, MC; Giglio, M; Nadendla, S; Tauber, R; Duesbury, MJ; Del, NT; Meldal, BHM; Perfetto, L; Porras, P; Orchard, S; Shrivastava, A; Xie, Z; Chang, HY; Finn, RD; Mitchell, AL; Rawlings, ND; Richardson, L; Sangrador-Vegas, A; Blake, JA; Christie, KR; Dolan, ME; Drabkin, HJ; Hill, DP; Ni, L; Sitnikov, D; Harris, MA; Oliver, SG; Rutherford, K; Wood, V; Hayles, J; Bahler, J; Lock, A; Bolton, ER; De Pons, J; Dwinell, M; Hayman, GT; Laulederkind, SJF; Shimoyama, M; Tutaj, M; Wang, SJ; D'Eustachio, P; Matthews, L; Balhoff, JP; Aleksander, SA; Binkley, G; Dunn, BL; Cherry, JM; Engel, SR; Gondwe, F; Karra, K; MacPherson, KA; Miyasato, SR; Nash, RS; Ng, PC; Sheppard, TK; Shrivatsav Vp, A; Simison, M; Skrzypek, MS; Weng, S; Wong, ED; Feuermann, M; Gaudet, P; Bakker, E; Berardini, TZ; Reiser, L; Subramaniam, S; Huala, E; Arighi, C; Auchincloss, A; Axelsen, K; Argoud, GP; Bateman, A; Bely, B; Blatter, MC; Boutet, E; Breuza, L; Bridge, A; Britto, R; Bye-A-Jee, H; Casals-Casas, C; Coudert, E; Estreicher, A; Famiglietti, L; Garmiri, P; Georghiou, G; Gos, A; Gruaz-Gumowski, N; Hatton-Ellis, E; Hinz, U; Hulo, C; Ignatchenko, A; Jungo, F; Keller, G; Laiho, K; Lemercier, P; Lieberherr, D; Lussi, Y; Mac-Dougall, A; Magrane, M; Martin, MJ; Masson, P; Natale, DA; Hyka, NN; Pedruzzi, I; Pichler, K; Poux, S; Rivoire, C; Rodriguez-Lopez, M; Sawford, T; Speretta, E; Shypitsyna, A; Stutz, A; Sundaram, S; Tognolli, M; Tyagi, N; Warner, K; Zaru, R; Wu, C; Chan, J; Cho, J; Gao, S; Grove, C; Harrison, MC; Howe, K; Lee, R; Mendel, J; Muller, HM; Raciti, D; Van Auken, K; Berriman, M; Stein, L; Sternberg, PW; Howe, D; Toro, S; Westerfield, Monte. (2019) The Gene Ontology Resource: 20 years and still GOing strong. Nucleic Acids Research (NAR). volum 47 (gky1055).
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. volum 34 (2).
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; Flobak, Åsmund; Kuiper, Martin; Lægreid, Astrid; Thommesen, Liv. (2019) Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen. Nature Communications. volum 10 (2674).
Academic article
Perfetto, Livia; Acencio, Marcio Luis; Bradley, Glyn; Cesareni, Gianni; del Toro, Noemi; Fazekas, David; Hermjakob, Henning; Korcsmaros, Tamas; Kuiper, Martin; Lægreid, Astrid; Lo Surdo, Prisca; Lovering, Ruth C.; Orchard, Sandra; Porras, Pablo; Thomas, Paul; Touré, Vasundra; Zobolas, John; Licata, Luana. (2019) CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination. Bioinformatics. volum 35 (19).
Academic article
Vera-Ramos, Jose Antonio; Juanes-Cortes, Belen; Fernández-Breis, Jesualdo Tomás; Gaudet, Pascale; Kuiper, Martin; Lægreid, Astrid; Logie, Colin; Roldan-Garcia, Maria del Mar; Schulz, Stefan. (2019) An example of multimodal biological knowledge representation. CEUR Workshop Proceedings. volum 2518.
Academic article
Chawla, Konika; Kuiper, Martin. (2016) Genes2GO: A web application for querying gene sets for specific GO terms. Bioinformation. volum 12 (3).
Academic article
Tripathi, Sushil; Vercruysse, Steven; Chawla, Konika; Christie, Karen R.; Blake, Judith A; Huntley, Rachael P.; Orchard, Sandra; Hermjakob, Henning; Thommesen, Liv; Lægreid, Astrid; Kuiper, Martin. (2016) Gene regulation knowledge commons: community action takes care of DNA binding transcription factors. Database: The Journal of Biological Databases and Curation.
Academic article
Flobak, Åsmund; Baudot, Anaïs; Remy, Elisabeth; Thommesen, Liv; Thieffry, Denis; Kuiper, Martin; Lægreid, Astrid. (2015) Discovery of Drug Synergies in Gastric Cancer Cells Predicted by Logical Modeling. PLoS Computational Biology. volum 11 (8).
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. volum 54 (28).
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). volum 8890.
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. volum 5 (2).
Academic article
Mironov, Vladimir; Kuiper, Martin; Ekseth, Ole Kristian. (2014) OrthAgogue: An agile tool for the rapid prediction of orthology relations. Bioinformatics. volum 30 (5).
Academic article
Venkatesan, Aravind; Tripathi, Sushil; Sanz de Galdeano, Alejandro; Blondé, Ward; Lægreid, Astrid; Mironov, Vladimir; Kuiper, Martin. (2014) Finding gene regulatory network candidates using the gene expression knowledge base. BMC Bioinformatics. volum 15 (1).
Academic article
Antezana, Erick; Mironov, Vladimir; Kuiper, Martin. (2013) The emergence of Semantic Systems Biology. New Biotechnology. volum 30 (3).
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. volum 29 (19).
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. volum 12 (6).
Academic article
Tripathi, Sushil; Christie, KR; Balakrishnan, Ravin; Huntley, R; Hill, DP; Thommesen, Liv; Blake, JA; Kuiper, Martin; Lægreid, Astrid. (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. volum 179.
Academic article
Kuiper, Martin; Venkatesan, Aravind; Antezana, Erick; Vercruysse, Steven; Mironov, Vladimir; Blondé, Ward. (2012) Putting Semantics in Systems Biology. META. volum 2012 (3).
Article
Mironov, Vladimir; Seethappan, Nirmala; Blondé, Ward; Antezana, Erick; Splendiani, Andrea; Kuiper, Martin. (2012) Gauging triple stores with actual biological data. BMC Bioinformatics. volum 13.
Academic article
Vercruysse, Steven; Kuiper, Martin. (2012) Jointly creating digital abstracts: dealing with synonymy and polysemy. BMC Research Notes. volum 5 (601).
Academic article
Vercruysse, Steven; Venkatesan, Aravind; Kuiper, Martin. (2012) OLSVis: an animated, interactive visual browser for bio-ontologies. BMC Bioinformatics. volum 13.
Academic article
Beisvag, Vidar; Kauffmann, Audrey; Malone, James; Foy, Carole; Salit, Marc; Schimmel, H; Bongcam-Rudloff, Eric; Landegren, Ulf; Parkinson, Helen; Huber, Wolfgang; Brazma, Alvis; Sandvik, Arne Kristian; Kuiper, Martin. (2011) Contributions of the EMERALD project to assessing and improving microarray data quality. BioTechniques. volum 50 (1).
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. volum 27 (11).
Academic article
Hu, QA; Hollunder, Jens; Niehl, A; Körner, Camilla J; Gereige, Dalya; Windels, David; Arnold, Andreas; Kuiper, Martin; Vazquez, Frank; Pooggin, M; Heinlein, M. (2011) Specific Impact of Tobamovirus Infection on the Arabidopsis Small RNA Profile. PLOS ONE. volum 6 (5).
Academic article
Mironov, Vladimir; Antezana, Erick; Egaña, Mikel; Blondé, Ward; De baets, Bernard; Kuiper, Martin; Stevens, Robert. (2011) Flexibility and utility of the cell cycle ontology. Applied Ontology. volum 6 (3).
Academic article
Antezana, Erick; Venkatesan, Aravind; Mungall, Chris; Mironov, Vladimir; Kuiper, Martin. (2010) ONTO-ToolKit: enabling bio-ontology engineering via Galaxy. BMC Bioinformatics. volum 11.
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). volum 7 (3).
Academic article
Laukens, K; Hollunder, J; Thanh, HD; De Jaeger, G; Kuiper, Martin; Witters, E; Verschoren, A; Van Leemput, K. (2010) Flexible network reconstruction from relational databases with Cytoscape and CytoSQL. BMC Bioinformatics. volum 11.
Academic article
Antezana, E; Kuiper, Martin; Mironov, Vladimir. (2009) Biological knowledge management: the emerging role of the Semantic Web technologies. Briefings in Bioinformatics. volum 10 (4).
Academic literature review
Antezana, Erick; Blondé, Ward; Egaña, Mikel; Rutherford, Alistair; Stevens, Robert; De baets, Bernard; Mironov, Vladimir; Kuiper, Martin. (2009) BioGateway: A Semantic Systems Biology Tool for the Life Sciences. BMC Bioinformatics. volum 10 (S11).
Academic article
Antezana, Erick; Egaña, Mikel; Blondé, Ward; Illarramendi, Aitzol; Bilbao, Inaki; De baets, Bernard; Stevens, Robert; Mironov, Vladimir; Kuiper, Martin. (2009) The Cell Cycle Ontology: an application ontology for the representation and integrated analysis of the cell cycle process. Genome Biology. volum 10 (5).
Academic literature review
Naouar, Naira; Vandepoele, Klaas; Lammens, Tim; Casneuf, Tineke; Zeller, Georg; Van Hummelen, Paul; Weigel, Detlef; Ratsch, Gunnar; Inze, Dirk; Kuiper, Martin; De Veylder, Lieven; Vuylsteke, Marnik. (2009) Quantitative RNA expression analysis with Affymetrix Tiling 1.0R arrays identifies new E2F target genes. The Plant Journal. volum 57 (1).
Academic article
Wabnik, K; Hvidsten, TR; Kedzierska, A; Van Leene, J; De Jaeger, G; Beemster, GTS; Komorowski, J; Kuiper, Martin. (2009) Gene expression trends and protein features effectively complement each other in gene function prediction. Bioinformatics. volum 25 (3).
Academic article
Taylor, CF; Field, D; Sansone, SA; Aerts, J; Apweiler, R; Ashburner, M; Ball, CA; Binz, PA; Bogue, M; Booth, T; Brazma, A; Brinkman, RR; Clark, AM; Deutsch, EW; Fiehn, O; Fostel, J; Ghazal, P; Gibson, F; Gray, T; Grimes, G; Hancock, JM; Hardy, NW; Hermjakob, H; Julian, RK; Kane, M; Kettner, C; Kinsinger, C; Kolker, E; Kuiper, Marius Tremen Roelof; Le Novere, N; Leebens-Mack, J; Lewis, SE; Lord, P; Mallon, AM; Marthandan, N; Masuya, H; McNally, R; Mehrle, A; Morrison, N; Orchard, S; Quackenbush, J; Reecy, JM; Robertson, DG; Rocca-Serra, P; Rodriguez, H; Rosenfelder, H; Santoyo-Lopez, J; Scheuermann, RH; Schober, D; Smith, B; Snape, J; Stoeckert, CJ; Tipton, K; Sterk, P; Untergasser, A; Vandesompele, J; Wiemann, S. (2008) Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nature Biotechnology. volum 26 (8).
Editorial
Wabnik, Krysztof; Hvidsten, Torgeir Rhoden; Kedzierska, Anna; Van Leene, Jelle; De Jaeger, Geert; Beemster, Gerrit; Komorowski, Jan; Kuiper, Martin. (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. Omics and Plant Abiotic Stress Tolerance.
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. Knowledge-based bioinformatics : from analysis to interpretation.
Academic chapter/article/Conference paper

Report

Chawla, Konika; Kuiper, Martin. (2017) Discovering, analysing and taking care of knowledge. 2017. ISBN 978-82-326-2316-7.
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

Media

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. 2020 Disease Maps Community Meeting . Anna Niarakis, Univ Evry, University of Paris-Saclay; FR; Luxembourg. 2020-11-12 - 2020-11-14.
Lecture

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

2019

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

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

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

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.
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). NBS 2019 . Norwegian Biochemical Society; Røros. 2019-01-24 - 2019-01-27.

2018

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.
Popular scientific lecture

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

Kuiper, Martin; Holmås, Stian. (2018) Network building in Cytoscape using the BioGateway App: benefits of hiding the SPARQL from your eyes. Invited seminar at the European Bioinformatics Institute (EBI) . Daniel Zerbino, ENSEMBL PI, EMBL-EBI; Hinxton, Cambridge. 2018-11-20 - 2018-11-20.
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. ISMB 2018 . International Society for Computational Biology; 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. Visions for Life Science Knowledge Commons . Crossover project; Trondheim. 2018-05-23 - 2018-05-24.
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.

2017

Lecture

Acencio, Marcio Luis; Lægreid, Astrid; Kuiper, Martin; Thommesen, Liv; Leitner, Florian; Krallinger, Martin; Lourenço, Analia; Vázquez, Miguel; Valencia, Alfonso. (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. Systems Medicine Conference in Slovenia . Ministry of Education, Science and Sport (MIZS) Slovenia; Ljubljana. 2017-06-08 - 2017-06-09.

2016

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.
Lecture

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

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

2015

Lecture

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

2014

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. BIOTECHNO 2014, DBKDA 2014 . International Academy, Research and Industry Association; Chamonix. 2014-04-20 - 2014-04-24.
Poster

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

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

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

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

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

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

2013

Academic lecture

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

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

2012

Academic lecture

Efstathiou, Sophia; Carusi, Annamaria; Kuiper, Martin; Lægreid, Astrid; Nydal, Rune. (2012) Research Systems for Systems Biology. European Meetings on Cybernetics and Systems Research . Austrian Society for Cybernetic Studies; 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.
Poster

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

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

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

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

2011

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

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.
Poster

Tripathi, Sushil; Venkatesan, Aravind; Egaña, Mikel; Zavareh, Zahra; Chawla, Konika; Mironov, Vladimir; Thommesen, Liv; Bruland, Torunn; Kuiper, Martin; Lægreid, Astrid. (2011) Automated Assessment of High Throughput Hypotheses on Gene Regulatory Mechanisms Involved in the Gastrin Response. Bio-Ontologies 2011 . ISMB 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; Mironov, Vladimir; Kuiper, Martin. (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

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.

2010

Academic lecture

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

2009

Poster

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

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

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

Kuiper, Martin. (2009) BioGateway: an overture to Semantic Systems Biology. NBS Contact meeting – 2009 . NBS; Roros. 2009-01-29 - 2009-02-01.
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. Semantic Web User Interaction . Duane Degler; Washington DC. 2009-10-25 - 2009-10-25.

2008

Poster

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

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

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

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

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

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

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Martin Kuiper

Martin Kuiper

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