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
2024
-
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
-
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
2023
-
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
-
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
-
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
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
Academic article
-
Garcia, Miguel Vazquez;
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
-
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
-
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
-
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
2021
-
Tsirvouli, Eirini;
Ashcroft, Felicity;
Johansen, Berit;
Kuiper, Martin.
(2021)
Logical and experimental modeling of cytokine and eicosanoid signaling in psoriatic keratinocytes.
iScience
Academic article
-
Cortés, Belén Juanes;
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
-
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
-
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
-
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
-
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
-
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
2020
-
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
-
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
Academic article
-
Tsirvouli, Eirini;
Touré, Vasundra;
Niederdorfer, Barbara;
Garcia, Miguel Vazquez;
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
-
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
-
Niarakis, Anna;
Kuiper, Martin;
Ostaszewski, Marek;
Sheriff, Rahuman Malik;
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
-
Mulder, Wim De;
Kuiper, Martin.
(2020)
A foundation for reference models for drug combinations with an application to Loewe’s reference model.
BMC Bioinformatics
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;
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.
(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;
Toro, Noemi del;
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
-
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
-
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
-
Holmås, Stian;
Puig, Rafael Riudavets;
Acencio, Marcio Luis;
Mironov, Vladimir;
Kuiper, Martin.
(2019)
The Cytoscape BioGateway App: explorative network building from an RDF store.
Bioinformatics
Academic article
2017
-
Chawla, Konika;
Kuiper, Martin.
(2017)
Discovering, analysing and taking care of knowledge.
Norges teknisk-naturvitenskapelige universitet
Norges teknisk-naturvitenskapelige universitet
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
-
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
-
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
2014
-
Mironov, Vladimir;
Kuiper, Martin;
Ekseth, Ole Kristian.
(2014)
OrthAgogue: An agile tool for the rapid prediction of orthology relations.
Bioinformatics
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
-
Blondé, Ward;
Antezana, Erick;
Mironov, Vladimir;
Schulz, Stefan;
Kuiper, Martin;
baets, Bernard De.
(2014)
Using the relation ontology Metarel for modelling Linked Data as multi-digraphs.
Semantic Web – Interoperability, Usability, Applicability
Academic article
-
Venkatesan, Aravind;
Tripathi, Sushil;
Galdeano, Alejandro Sanz de;
Blondé, Ward;
Lægreid, Astrid;
Mironov, Vladimir.
(2014)
Finding gene regulatory network candidates using the gene expression knowledge base.
BMC Bioinformatics
Academic article
2013
-
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
-
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
-
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
-
Vercruysse, Steven;
Kuiper, Martin.
(2013)
WordVis: JavaScript and Animation to Visualize the WordNet Relational Dictionary.
Advances in Intelligent Systems and Computing
Academic article
-
Antezana, Erick;
Mironov, Vladimir;
Kuiper, Martin.
(2013)
The emergence of Semantic Systems Biology.
New Biotechnology
Academic article
2012
-
Vercruysse, Steven;
Kuiper, Martin.
(2012)
Jointly creating digital abstracts: dealing with synonymy and polysemy.
BMC Research Notes
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
-
Vercruysse, Steven;
Venkatesan, Aravind;
Kuiper, Martin.
(2012)
OLSVis: an animated, interactive visual browser for bio-ontologies.
BMC Bioinformatics
Academic article
-
Mironov, Vladimir;
Seethappan, Nirmala;
Blondé, Ward;
Antezana, Erick;
Splendiani, Andrea;
Kuiper, Martin.
(2012)
Gauging triple stores with actual biological data.
BMC Bioinformatics
Academic article
2011
-
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
-
Chawla, Konika;
Barah, Pankaj;
Kuiper, Martin;
Bones, Atle M..
(2011)
Systems Biology: a Promising Tool to Study Abiotic Stress Responses.
Academic chapter/article/Conference paper
-
Blondé, Ward;
Mironov, Vladimir;
Venkatesan, Aravind;
Antezana, Erick;
baets, Bernard De;
Kuiper, Martin.
(2011)
Reasoning with bio-ontologies: using relational closure rules to enable practical querying.
Bioinformatics
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
-
Mironov, Vladimir;
Antezana, Erick;
Egaña, Mikel;
Blondé, Ward;
baets, Bernard De;
Kuiper, Martin.
(2011)
Flexibility and utility of the cell cycle ontology.
Applied Ontology
Academic article
2010
-
Egaña, Mikel;
Stevens, Robert;
Antezana, Erick;
Fernández-Breis, Jesualdo Tomás;
Kuiper, Martin;
Mironov, Vladimir.
(2010)
Technologies and best practices for building bio-ontologies.
Academic chapter/article/Conference paper
-
Laukens, K;
Hollunder, J;
Thanh, HD;
Jaeger, G De;
Kuiper, Martin;
Witters, E.
(2010)
Flexible network reconstruction from relational databases with Cytoscape and CytoSQL.
BMC Bioinformatics
Academic article
-
Mulder, Wim De;
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
-
Antezana, Erick;
Venkatesan, Aravind;
Mungall, Chris;
Mironov, Vladimir;
Kuiper, Martin.
(2010)
ONTO-ToolKit: enabling bio-ontology engineering via Galaxy.
BMC Bioinformatics
Academic article
2009
-
Antezana, Erick;
Egaña, Mikel;
Blondé, Ward;
Illarramendi, Aitzol;
Bilbao, Inaki;
baets, Bernard De.
(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;
baets, Bernard De.
(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;
Hummelen, Paul Van.
(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;
Leene, J Van;
Jaeger, G De;
Beemster, GTS.
(2009)
Gene expression trends and protein features effectively complement each other in gene function prediction.
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
2008
-
Wabnik, Krysztof;
Hvidsten, Torgeir Rhoden;
Kedzierska, Anna;
Leene, Jelle Van;
Jaeger, Geert De;
Beemster, Gerrit.
(2008)
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
Journal publications
-
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
-
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
-
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
-
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
-
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
-
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
-
Garcia, Miguel Vazquez;
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
-
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
-
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
-
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
-
Tsirvouli, Eirini;
Ashcroft, Felicity;
Johansen, Berit;
Kuiper, Martin.
(2021)
Logical and experimental modeling of cytokine and eicosanoid signaling in psoriatic keratinocytes.
iScience
Academic article
-
Cortés, Belén Juanes;
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
Academic article
-
Tsirvouli, Eirini;
Touré, Vasundra;
Niederdorfer, Barbara;
Garcia, Miguel Vazquez;
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
-
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
-
Niarakis, Anna;
Kuiper, Martin;
Ostaszewski, Marek;
Sheriff, Rahuman Malik;
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
-
Mulder, Wim De;
Kuiper, Martin.
(2020)
A foundation for reference models for drug combinations with an application to Loewe’s reference model.
BMC Bioinformatics
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;
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.
(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;
Toro, Noemi del;
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
-
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
-
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
-
Holmås, Stian;
Puig, Rafael Riudavets;
Acencio, Marcio Luis;
Mironov, Vladimir;
Kuiper, Martin.
(2019)
The Cytoscape BioGateway App: explorative network building from an RDF store.
Bioinformatics
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
-
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
-
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
-
Mironov, Vladimir;
Kuiper, Martin;
Ekseth, Ole Kristian.
(2014)
OrthAgogue: An agile tool for the rapid prediction of orthology relations.
Bioinformatics
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
-
Blondé, Ward;
Antezana, Erick;
Mironov, Vladimir;
Schulz, Stefan;
Kuiper, Martin;
baets, Bernard De.
(2014)
Using the relation ontology Metarel for modelling Linked Data as multi-digraphs.
Semantic Web – Interoperability, Usability, Applicability
Academic article
-
Venkatesan, Aravind;
Tripathi, Sushil;
Galdeano, Alejandro Sanz de;
Blondé, Ward;
Lægreid, Astrid;
Mironov, Vladimir.
(2014)
Finding gene regulatory network candidates using the gene expression knowledge base.
BMC Bioinformatics
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
-
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
-
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
-
Vercruysse, Steven;
Kuiper, Martin.
(2013)
WordVis: JavaScript and Animation to Visualize the WordNet Relational Dictionary.
Advances in Intelligent Systems and Computing
Academic article
-
Antezana, Erick;
Mironov, Vladimir;
Kuiper, Martin.
(2013)
The emergence of Semantic Systems Biology.
New Biotechnology
Academic article
-
Vercruysse, Steven;
Kuiper, Martin.
(2012)
Jointly creating digital abstracts: dealing with synonymy and polysemy.
BMC Research Notes
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
-
Vercruysse, Steven;
Venkatesan, Aravind;
Kuiper, Martin.
(2012)
OLSVis: an animated, interactive visual browser for bio-ontologies.
BMC Bioinformatics
Academic article
-
Mironov, Vladimir;
Seethappan, Nirmala;
Blondé, Ward;
Antezana, Erick;
Splendiani, Andrea;
Kuiper, Martin.
(2012)
Gauging triple stores with actual biological data.
BMC Bioinformatics
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
-
Blondé, Ward;
Mironov, Vladimir;
Venkatesan, Aravind;
Antezana, Erick;
baets, Bernard De;
Kuiper, Martin.
(2011)
Reasoning with bio-ontologies: using relational closure rules to enable practical querying.
Bioinformatics
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
-
Mironov, Vladimir;
Antezana, Erick;
Egaña, Mikel;
Blondé, Ward;
baets, Bernard De;
Kuiper, Martin.
(2011)
Flexibility and utility of the cell cycle ontology.
Applied Ontology
Academic article
-
Laukens, K;
Hollunder, J;
Thanh, HD;
Jaeger, G De;
Kuiper, Martin;
Witters, E.
(2010)
Flexible network reconstruction from relational databases with Cytoscape and CytoSQL.
BMC Bioinformatics
Academic article
-
Mulder, Wim De;
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
-
Antezana, Erick;
Venkatesan, Aravind;
Mungall, Chris;
Mironov, Vladimir;
Kuiper, Martin.
(2010)
ONTO-ToolKit: enabling bio-ontology engineering via Galaxy.
BMC Bioinformatics
Academic article
-
Antezana, Erick;
Egaña, Mikel;
Blondé, Ward;
Illarramendi, Aitzol;
Bilbao, Inaki;
baets, Bernard De.
(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;
baets, Bernard De.
(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;
Hummelen, Paul Van.
(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;
Leene, J Van;
Jaeger, G De;
Beemster, GTS.
(2009)
Gene expression trends and protein features effectively complement each other in gene function prediction.
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
-
Wabnik, Krysztof;
Hvidsten, Torgeir Rhoden;
Kedzierska, Anna;
Leene, Jelle Van;
Jaeger, Geert De;
Beemster, Gerrit.
(2008)
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
Part of book/report
-
Chawla, Konika;
Barah, Pankaj;
Kuiper, Martin;
Bones, Atle M..
(2011)
Systems Biology: a Promising Tool to Study Abiotic Stress Responses.
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.
Academic chapter/article/Conference paper
Report
-
Chawla, Konika;
Kuiper, Martin.
(2017)
Discovering, analysing and taking care of knowledge.
Norges teknisk-naturvitenskapelige universitet
Norges teknisk-naturvitenskapelige universitet
Doctoral dissertation
Outreach
2020
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LectureBermúdez, 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. Cuarta Convención Científica Internacional de la Universidad Técnica de Manabí , University of Manabi, Ecuador 21.10.2020 - 23.10.2020
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Academic lectureBermúdez, 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 , Luxembourg 12.11.2020 - 14.11.2020
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InterviewZobolas, 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) Journal of Open Source Software (JOSS) [Journal]
2019
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Academic lectureAcencio, 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 07.04.2019 - 07.04.2019
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PosterHolmås, 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 , Edinburgh 09.12.2019 - 12.12.2019
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PosterVercruysse, Steven; Zobolas, John; Touré, Vasundra; Kuiper, Martin. (2019) VSM-box: the general-purpose curation interface as an open-source web-component. Biocuration 2019 08.04.2019 - 11.04.2019
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PosterZobolas, 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 , Røros 24.01.2019 - 27.01.2019
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PosterVercruysse, 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 12.04.2019 -
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Academic lectureKuiper, Martin. (2019) Towards a curation platform for causal interaction statements. Basel Life 2019 Workshop , Basel 09.09.2019 - 09.09.2019
2018
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Academic lectureAcencio, 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: 01.10.2018 - 02.10.2018
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Academic lectureKuiper, 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) , Hinxton, Cambridge 20.11.2018 - 20.11.2018
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PosterTouré, Vasundra; Flobak, Åsmund; Lægreid, Astrid; Kuiper, Martin. (2018) Knowledge management and standard representation of causal statements for systems modeling. JOBIM 2018 , Marseille 03.07.2018 - 06.07.2018
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LectureNiederdorfer, 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 , Chicago 06.07.2018 - 10.07.2018
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Academic lectureNydal, Rune; Lægreid, Astrid; Kuiper, Martin; Gabrielsen, Ane Møller. (2018) Introduction. Visions for Life Science Knowledge Commons. Visions for Life Science Knowledge Commons , Trondheim 23.05.2018 - 24.05.2018
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LectureKuiper, Martin. (2018) In Silico Clinical Trials. Invited seminar at the ERACoSysMed meeting in Paris, June 2018 , Paris 15.06.2018 - 15.06.2018
2017
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LectureKuiper, Martin. (2017) The logical way to tackle cancer. Systems Medicine Conference in Slovenia , Ljubljana 08.06.2017 - 09.06.2017
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Academic lectureAcencio, Marcio Luis; Vázquez, Miguel; Kuiper, Martin; Lægreid, Astrid. (2017) DbTF-TG interactions and regulatory relationships: a survey. Curation workshop on molecular and causal interactions 05.12.2017 - 07.12.2017
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LectureAcencio, 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 08.05.2017 - 10.05.2017
2016
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Academic lectureNydal, Rune; Lægreid, Astrid; Kuiper, Martin. (2016) Curation strategeis of NTNU project. Workshop upstart crossover at EBI , EBI 22.04.2016 - 23.04.2016
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LectureAcencio, Marcio Luis; Lægreid, Astrid; Kuiper, Martin. (2016) Knowledge Commons digitalization - curation. Crossover Seminar 14.04.2016 - 15.04.2016
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LectureAcencio, 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 18.04.2016 - 20.04.2016
2015
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LectureKuiper, 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 , University of São Paulo 03.11.2015 - 06.11.2015
2014
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PosterKuiper, Martin; Lægreid, Astrid. (2014) The GRECO initiative: taking care of Gene Regulation knowledge. Virtual Physiological Human Conference 2014 , Trondheim 09.09.2014 - 12.09.2014
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LectureKuiper, Martin. (2014) Keynote lecture: Networks for Knowledge. IEEE International Conference Bioinformatics and Biomedicine 2014 , Belfast 02.11.2014 - 05.11.2014
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PosterFlobak, 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. Virtual Physiological Human Conference 2014 , Trondheim 09.09.2014 - 12.09.2014
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LectureKuiper, Martin. (2014) Augmenting the human brain. Knowledge management and the futures of our society, a Virtual Physiological Human 2014 Satellite Workshop , Trondheim 08.09.2014 - 09.09.2014
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PosterKuiper, Martin; Mironov, Vladimir; Venkatesan, Aravind; Tripathi, Sushil; Blondé, Ward; Galdeano, Alejandro Sanz de. (2014) The gene expression knowledge base. Virtual Physiological Human Conference 2014 , Trondheim 09.09.2014 - 12.09.2014
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LectureNydal, 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 , Trondheim 08.09.2014 - 09.09.2014
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LectureMulder, Wim De; 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 , Chamonix 20.04.2014 - 24.04.2014
2013
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Academic lectureGautam, 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 , Cáceres 03.12.2013 - 05.12.2013
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LectureKuiper, Martin. (2013) It's all semantics for the user. LBM 2013 – International Symposium on Languages in Biology and Medicine , Tokyo 12.12.2013 - 13.12.2013
2012
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Academic lectureVenkatesan, Aravind; Mironov, Vladimir; Kuiper, Martin. (2012) Towards an integrated knowledge system for capturing gene expression events. 3rd International Conference on Biomedical Ontology (ICBO 2012) , Graz 21.07.2012 - 25.07.2012
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PosterHollunder, Jens; Mironov, Vladimir; Antezana, Erick; Hoehndorf, Robert; Kuiper, Martin. (2012) Profiling of Semantically Annotated Proteins. Semantic Web Applications and Tools for Life Sciences 2012 , Paris 28.11.2012 - 30.11.2012
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Academic lectureEfstathiou, Sophia; Carusi, Annamaria; Kuiper, Martin; Lægreid, Astrid; Nydal, Rune. (2012) Research Systems for Systems Biology. European Meetings on Cybernetics and Systems Research , Vienna 10.04.2012 - 13.04.2012
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Academic lectureEfstathiou, 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 12.04.2012 - 14.04.2012
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Academic lectureEfstathiou, 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 23.10.2012 - 25.10.2012
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Academic lectureKuiper, Martin. (2012) The Emergence of Semantic Systems Biology. The Ethos of Integrative Research:The case of systems biology , Trondheim 26.11.2012 - 27.11.2012
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PosterVenkatesan, 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 , Trondheim 18.10.2012 - 19.10.2012
2011
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PosterTripathi, 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. Bio-Ontologies 2011 , Vienna 15.07.2011 - 16.07.2011
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Academic lectureVercruysse, 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 29.08.2011 - 31.08.2011
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Academic lectureMironov, Vladimir; Venkatesan, Aravind; Kuiper, Martin. (2011) RDF Foundry - a call for a community effort to harmonize triple store practices. BioHackathon 2011 , Kyoto University 20.08.2011 - 26.08.2011
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Academic lectureAntezana, Erick; Blondé, Ward; Venkatesan, Aravind; baets, Bernard De; Mironov, Vladimir; Kuiper, Martin. (2011) Semantic SB: enablng integrative biology via SW technologies. WIMS: International Conferences on Web Intelligence, Mining and Semantics. , Sogndal 25.05.2011 - 27.05.2011
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Academic lectureVenkatesan, Aravind; Blondé, Ward; Antezana, Erick; Skillingstad, Mats Gløer Løkås; Marshall, Scott M; baets, Bernard De. (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 25.05.2011 - 27.05.2011
2010
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Academic lectureMironov, 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 , Berlin 10.12.2010 - 10.12.2010
2009
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Academic lectureBlondé, Ward; Antezana, Erick; baets, Bernard De; 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 20.07.2009 - 23.07.2009
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PosterBeisvag, Vidar; Sandvik, Arne Kristian; Kuiper, Martin. (2009) EMERALD – Enhancing Microarray Data Quality. Norsk Biokjemisk Selskap Kontaktmøte 2009 , Røros 29.01.2009 - 31.01.2009
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PosterBeisvag, Vidar; Sandvik, Arne Kristian; Kuiper, Martin. (2009) EMERALD – Enhancing Microarray Data Quality. The 5th Advinces in Microarray Technology 2009 , Stockholm 18.05.2009 - 20.05.2009
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PosterBeisvag, Vidar; Sandvik, Arne Kristian; Kuiper, Martin. (2009) EMERALD – Enhancing Microarray Data Quality. MGED12 , Phoenix, Arizona 05.10.2009 - 08.10.2009
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Academic lectureKuiper, Martin. (2009) BioGateway: an overture to Semantic Systems Biology. NBS Contact meeting – 2009 , Roros 29.01.2009 - 01.02.2009
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Academic lectureKuiper, 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 , Washington DC 25.10.2009 - 25.10.2009
2008
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PosterBeisvåg, 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) , Vien 04.12.2008 - 06.12.2008
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PosterBeisvåg, Vidar; Sandvik, Arne Kristian; Kuiper, Marius Tremen Roelof. (2008) EMERALD – Enhancing Microarray Data Quality. 4th EMBO Conference: From Functional Genomics to Systems Biology , EMBL, Heidelberg 15.11.2008 - 18.11.2008
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PosterBeisvåg, Vidar; Sandvik, Arne Kristian; Kuiper, Marius Tremen Roelof. (2008) EMERALD – Enhancing Microarray Data Quality. 11th International Meeting of MGED , Riva Del Garda 01.09.2008 - 06.09.2008
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PosterBeisvåg, Vidar; Kuiper, Marius Tremen Roelof; Sandvik, Arne Kristian. (2008) EMERALD – Enhancing Microarray Data Quality. 3rd ESF Conference on Functional Genomics and Disease , Innsbruck 01.10.2008 - 04.10.2008
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PosterBeisvåg, Vidar; Sandvik, Andreas; Kuiper, Marius Tremen Roelof. (2008) EMERALD – Enhancing Microarray Data Quality. Genes at work on time , Torina 15.10.2008 - 18.10.2008
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Academic lectureKuiper, Martin. (2008) The Cell Cycle Ontology: an overture to Semantic Systems Biology. Systems Biology Approaches to Study the Cell Cycle , Malaga 20.10.2008 - 21.10.2008