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2019
1 Acencio, Marcio Luis; Touré, Vasundra; Kuiper, Martin.
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
NTNU Untitled
 
2 Efstathiou, Sophia; Nydal, Rune; Lægreid, Astrid; Kuiper, Martin.
Scientific knowledge in the age of computation: Explicated, computable and manageable?. Theoria. An international Journal of Theory, History and Foundations of Science 2019
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3 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.
CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination. Bioinformatics 2019
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4 The Gene Ontology, Consortium; that, includes; Acencio, Marcio Luis; Lægreid, Astrid; Kuiper, Martin; among, others.
The Gene Ontology Resource: 20 years and still GOing strong.. Nucleic Acids Research 2019 (gky1055)
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5 Vercruysse, Steven; Zobolas, John; Touré, Vasundra; Kuiper, Martin.
VSM-box: the general-purpose curation interface as an open-source web-component. Biocuration 2019; 2019-04-08 - 2019-04-11
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6 Vercruysse, Steven; Zobolas, John; Touré, Vasundra; Kuiper, Martin.
VSM-box: the general-purpose curation interface as an open-source web-component [version 1; not peer reviewed].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
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7 Zobolas, John; Vázquez, Miguel; Kuiper, Martin; Flobak, Åsmund.
DrugLogics: An ensemble model analysis related to drug prediction performance [version 1; not peer reviewed]. F1000Research 2019, 8:113 (poster). NBS 2019; 2019-01-24 - 2019-01-27
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2018
8 Acencio, Marcio Luis; Krallinger, Martin; Kuiper, Martin; Lægreid, Astrid.
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
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9 Kuiper, Martin.
In Silico Clinical Trials. Invited seminar at the ERACoSysMed meeting in Paris, June 2018; 2018-06-15 - 2018-06-15
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10 Kuiper, Martin; Holmås, Stian.
Network building in Cytoscape using the BioGateway App: benefits of hiding the SPARQL from your eyes. Invited seminar at the European Bioinformatics Institute (EBI); 2018-11-20 - 2018-11-20
NTNU Untitled
 
11 Niederdorfer, Barbara; Vázquez, Miguel; Thommesen, Liv; Kuiper, Martin; Lægreid, Astrid; Flobak, Åsmund.
Logical model simulations predict drug synergies across different cancer cell lines. ISMB 2018; 2018-07-06 - 2018-07-10
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12 Nydal, Rune; Lægreid, Astrid; Kuiper, Martin; Gabrielsen, Ane Møller.
Introduction. Visions for Life Science Knowledge Commons. Visions for Life Science Knowledge Commons; 2018-05-23 - 2018-05-24
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13 Touré, Vasundra; Flobak, Åsmund; Lægreid, Astrid; Kuiper, Martin.
Knowledge management and standard representation of causal statements for systems modeling.. JOBIM 2018; 2018-07-03 - 2018-07-06
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14 Vercruysse, Steven; Kuiper, Martin.
The VSM-pages: How to Easily Plant Complex Ideas into Computers.
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2017
15 Acencio, Marcio Luis; Lægreid, Astrid; Kuiper, Martin; Thommesen, Liv; Leitner, Florian; Krallinger, Martin; Lourenço, Analia; Vázquez, Miguel; Valencia, Alfonso.
NTNU DbTF Curation: current status and Mining Transcription Regulation Information from Literature. Short Research Stay at the European Bioinformatics Institute (EBI); 2017-05-08 - 2017-05-10
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16 Acencio, Marcio Luis; Vázquez, Miguel; Kuiper, Martin; Lægreid, Astrid.
DbTF-TG interactions and regulatory relationships: a survey. Curation workshop on molecular and causal interactions; 2017-12-05 - 2017-12-07
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17 Chawla, Konika.
Discovering, analysing and taking care of knowledge. Trondheim, Norway: Norwegian University of Science and Technology 2017 (ISBN 978-82-326-2316-7) 182 s.
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18 Kuiper, Martin.
The logical way to tackle cancer. Systems Medicine Conference in Slovenia; 2017-06-08 - 2017-06-09
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2016
19 Acencio, Marcio Luis; Lægreid, Astrid; Kuiper, Martin.
Causal statements for Gene Regulation & Signal Transduction: what can be done in PSI-MI. HUPO-PSI meeting 2016; 2016-04-18 - 2016-04-20
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20 Acencio, Marcio Luis; Lægreid, Astrid; Kuiper, Martin.
Knowledge Commons digitalization - curation. Crossover Seminar; 2016-04-14 - 2016-04-15
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21 Chawla, Konika; Kuiper, Martin.
Genes2GO: A web application for querying gene sets for specific GO terms. Bioinformation 2016 ;Volum 12.(3) s. 231-232
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22 Nydal, Rune; Lægreid, Astrid; Kuiper, Martin.
Curation strategeis of NTNU project. Workshop upstart crossover at EBI; 2016-04-22 - 2016-04-23
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23 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.
Gene regulation knowledge commons: community action takes care of DNA binding transcription factors. Database: The Journal of Biological Databases and Curation 2016 s. -
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2015
24 Flobak, Åsmund; Baudot, Anaïs; Remy, Elisabeth; Thommesen, Liv; Thieffry, Denis; Kuiper, Martin; Lægreid, Astrid.
Discovery of Drug Synergies in Gastric Cancer Cells Predicted by Logical Modeling. PLoS Computational Biology 2015 ;Volum 11.(8)
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25 Kuiper, Martin.
Keynote lecture: Taking care of knowledge to enable systems analysis. X-Meeting 2015 - 11th International Conference of th AB3C + Brazilian Symposium of Bioinformatics; 2015-11-03 - 2015-11-06
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26 Lægreid, Astrid; Kuiper, Martin.
Health and the information commons.
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27 Skancke, Jørgen; Bar, Nadav; Kuiper, Martin; Hsu, Lilian M.
Sequence-Dependent Promoter Escape Efficiency Is Strongly Influenced by Bias for the Pretranslocated State during Initial Transcription. Biochemistry 2015 ;Volum 54.(28) s. 4267-4275
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2014
28 Blondé, Ward; Antezana, Erick; Mironov, Vladimir; Schulz, Stefan; Kuiper, Martin; De baets, Bernard.
Using the relation ontology Metarel for modelling Linked Data as multi-digraphs. Semantic Web Journal 2014 ;Volum 5.(2) s. 115-126
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29 De Mulder, Wim; Zavareh, Zahra; Chawla, Konika; Kuiper, Martin.
Experimental Verification of the Quality of Clusterings Produced by Hard Clustering Algorithms After the Removal of Unstable Data Elements. BIOTECHNO 2014, DBKDA 2014; 2014-04-20 - 2014-04-24
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30 Flobak, Åsmund; Baudot, Anaïs; Remy, Elisabeth; Thommesen, Liv; Thieffry, Denis; Kuiper, Martin; Lægreid, Astrid.
Drug synergies in a gastric cancer cell line discovered by signal transduction modeling. Virtual Physiological Human Conference 2014; 2014-09-09 - 2014-09-12
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31 Gautam, Vinay Kumar; Czeizler, Eugen; Haddow, Pauline; Kuiper, Martin.
Design of a Minimal System for Self-replication of Rectangular Patterns of DNA Tiles. Lecture Notes in Computer Science 2014 ;Volum 8890. s. 119-133
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32 Kuiper, Martin.
Augmenting the human brain. Knowledge management and the futures of our society, a Virtual Physiological Human 2014 Satellite Workshop; 2014-09-08 - 2014-09-09
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33 Kuiper, Martin.
Keynote lecture: Networks for Knowledge. IEEE International Conference Bioinformatics and Biomedicine 2014; 2014-11-02 - 2014-11-05
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34 Kuiper, Martin; Lægreid, Astrid.
The GRECO initiative: taking care of Gene Regulation knowledge. Virtual Physiological Human Conference 2014; 2014-09-09 - 2014-09-12
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35 Kuiper, Martin; Mironov, Vladimir; Venkatesan, Aravind; Tripathi, Sushil; Blondé, Ward; Sanz de Galdeano, Alejandro; Lægreid, Astrid.
The gene expression knowledge base. Virtual Physiological Human Conference 2014; 2014-09-09 - 2014-09-12
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36 Lægreid, Astrid; Kuiper, Martin.
Å ta seg av kunnskap.
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37 Mironov, Vladimir; Kuiper, Martin; Ekseth, Ole Kristian.
OrthAgogue: An agile tool for the rapid prediction of orthology relations. Bioinformatics 2014 ;Volum 30.(5) s. 734-736
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38 Nydal, Rune; Efstathiou, Sophia; Lægreid, Astrid; Kuiper, Martin.
Setting the stage: Tragedy of the knowledge commons. Knowledge management and the futures of our society, a Virtual Physiological Human 2014 Satellite Workshop; 2014-09-08 - 2014-09-09
NTNU Untitled
 
39 Venkatesan, Aravind; Tripathi, Sushil; Sanz de Galdeano, Alejandro; Blondé, Ward; Lægreid, Astrid; Mironov, Vladimir; Kuiper, Martin.
Finding gene regulatory network candidates using the gene expression knowledge base. BMC Bioinformatics 2014 ;Volum 15.(1)
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2013
40 Antezana, Erick; Mironov, Vladimir; Kuiper, Martin.
The emergence of Semantic Systems Biology. New Biotechnology 2013 ;Volum 30.(3) s. 286-290
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41 Chawla, Konika; Tripathi, Sushil; Thommesen, Liv; Lægreid, Astrid; Kuiper, Martin.
TFcheckpoint: a curated compendium of specific DNA-binding RNA polymerase II transcription factors. Bioinformatics 2013 ;Volum 29.(19) s. 2519-2520
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42 Gautam, Vinay Kumar; Haddow, Pauline; Kuiper, Martin.
Reliable Self-assembly by Self-triggered Activation of Enveloped DNA Tiles. 2nd International Conference on the Theory and Practice of Natural Computing; 2013-12-03 - 2013-12-05
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43 Kuiper, Martin.
It's all semantics for the user. LBM 2013 – International Symposium on Languages in Biology and Medicine; 2013-12-12 - 2013-12-13
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44 Kuiper, Martin; Antezana, Erick; Mironov, Vladimir.
Cell Cycle Ontology (CCO).
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45 Niehl, A; Zhang, Z.J.; Kuiper, Martin; Peck, SC; Heinlein, M.
Label-Free Quantitative Proteomic Analysis of Systemic Responses to Local Wounding and Virus Infection in Arabidopsis thaliana. Journal of Proteome Research 2013 ;Volum 12.(6) s. 2491-2503
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46 Tripathi, Sushil; Christie, KR; Balakrishnan, Ravin; Huntley, R; Hill, DP; Thommesen, Liv; Blake, JA; Kuiper, Martin; Lægreid, Astrid.
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 2013 s. -
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47 Vercruysse, Steven; Kuiper, Martin.
WordVis: JavaScript and Animation to Visualize the WordNet Relational Dictionary. Advances in Intelligent Systems and Computing 2013 ;Volum 179. s. 137-145
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2012
48 Efstathiou, Sophia; Carusi, Annamaria; Kuiper, Martin; Lægreid, Astrid; Nydal, Rune.
Research Systems for Systems Biology. European Meetings on Cybernetics and Systems Research; 2012-04-10 - 2012-04-13
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49 Efstathiou, Sophia; Nydal, Rune; Carusi, Annamaria; Kuiper, Martin; Lægreid, Astrid.
Well-constructed systems biology: Integrating socio-humanist research. European Meetings on Cybernetics and Systems Research; 2012-04-12 - 2012-04-14
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50 Efstathiou, Sophia; Nydal, Rune; Kuiper, Martin; Lægreid, Astrid; Carusi, Annamaria.
When ‘Knowledge’ Becomes Something to Manage. Society for the Study of Nanoscience and Emerging Technologies; 2012-10-23 - 2012-10-25
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