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2017
1 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
NTNU Untitled
 
2 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.
NTNU Untitled
 
3 Kuiper, Martin.
The logical way to tackle cancer. Systems Medicine Conference in Slovenia; 2017-06-08 - 2017-06-09
NTNU Untitled
 
2016
4 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
NTNU Untitled
 
5 Acencio, Marcio Luis; Lægreid, Astrid; Kuiper, Martin.
Knowledge Commons digitalization - curation. Crossover Seminar; 2016-04-14 - 2016-04-15
NTNU Untitled
 
6 Chawla, Konika; Kuiper, Martin.
Genes2GO: A web application for querying gene sets for specific GO terms. Bioinformation 2016 ;Volum 12.(3) s. 231-232
NTNU Untitled
 
7 Nydal, Rune; Lægreid, Astrid; Kuiper, Martin.
Curation strategeis of NTNU project. Workshop upstart crossover at EBI; 2016-04-22 - 2016-04-23
NTNU Untitled
 
8 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. -
NTNU Untitled
 
2015
9 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)
NTNU Untitled
 
10 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
NTNU Untitled
 
11 Lægreid, Astrid; Kuiper, Martin.
Health and the information commons.
NTNU Untitled
 
12 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
NTNU Untitled
 
2014
13 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 2014 ;Volum 5.(2) s. 115-126
NTNU Untitled
 
14 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
NTNU Untitled
 
15 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
NTNU Untitled
 
16 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
NTNU Untitled
 
17 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
NTNU Untitled
 
18 Kuiper, Martin.
Keynote lecture: Networks for Knowledge. IEEE International Conference Bioinformatics and Biomedicine 2014; 2014-11-02 - 2014-11-05
NTNU Untitled
 
19 Kuiper, Martin; Lægreid, Astrid.
The GRECO initiative: taking care of Gene Regulation knowledge. Virtual Physiological Human Conference 2014; 2014-09-09 - 2014-09-12
NTNU Untitled
 
20 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
NTNU Untitled
 
21 Lægreid, Astrid; Kuiper, Martin.
Å ta seg av kunnskap.
NTNU Untitled
 
22 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
NTNU Untitled
 
23 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
 
24 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)
NTNU Untitled
 
2013
25 Antezana, Erick; Mironov, Vladimir; Kuiper, Martin.
The emergence of Semantic Systems Biology. New Biotechnology 2013 ;Volum 30.(3) s. 286-290
NTNU Untitled
 
26 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
NTNU Untitled
 
27 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
NTNU Untitled
 
28 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
NTNU Untitled
 
29 Kuiper, Martin; Antezana, Erick; Mironov, Vladimir.
Cell Cycle Ontology (CCO).
NTNU Untitled
 
30 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
NTNU Untitled
 
31 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. -
NTNU Untitled
 
32 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
NTNU Untitled
 
2012
33 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
NTNU Untitled
 
34 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
NTNU Untitled
 
35 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
NTNU Untitled
 
36 Hollunder, Jens; Mironov, Vladimir; Antezana, Erick; Hoehndorf, Robert; Kuiper, Martin.
Profiling of Semantically Annotated Proteins. Semantic Web Applications and Tools for Life Sciences 2012; 2012-11-28 - 2012-11-30
NTNU Untitled
 
37 Kuiper, Martin.
The Emergence of Semantic Systems Biology. The Ethos of Integrative Research:The case of systems biology; 2012-11-26 - 2012-11-27
NTNU Untitled
 
38 Kuiper, Martin; Venkatesan, Aravind; Antezana, Erick; Vercruysse, Steven; Mironov, Vladimir; Blondé, Ward.
Putting Semantics in Systems Biology. META 2012 ;Volum 2012.(3) s. 22-30
NTNU Untitled
 
39 Mironov, Vladimir; Seethappan, Nirmala; Blondé, Ward; Antezana, Erick; Splendiani, Andrea; Kuiper, Martin.
Gauging triple stores with actual biological data. BMC Bioinformatics 2012 ;Volum 13. s. -
NTNU Untitled
 
40 Venkatesan, Aravind; Antezana, Erick; Blondé, Ward; Vercruysse, Steven; Mironov, Vladimir; Kuiper, Martin.
Putting Semantics in Systems Biology. NTNU Bioinformatics Network Seminar 2012 Norwegian Bioinformatics Forum 2012; 2012-10-18 - 2012-10-19
NTNU Untitled
 
41 Venkatesan, Aravind; Mironov, Vladimir; Kuiper, Martin.
Towards an integrated knowledge system for capturing gene expression events. 3rd International Conference on Biomedical Ontology (ICBO 2012); 2012-07-21 - 2012-07-25
NTNU Untitled
 
42 Vercruysse, Steven; Kuiper, Martin.
Jointly creating digital abstracts: dealing with synonymy and polysemy. BMC Research Notes 2012 ;Volum 5.(601) s. -
NTNU Untitled
 
43 Vercruysse, Steven; Venkatesan, Aravind; Kuiper, Martin.
OLSVis: an animated, interactive visual browser for bio-ontologies. BMC Bioinformatics 2012 ;Volum 13. s. -
NTNU Untitled
 
2011
44 Antezana, Erick; Blondé, Ward; Venkatesan, Aravind; De baets, Bernard; Mironov, Vladimir; Kuiper, Martin.
Semantic SB: enablng integrative biology via SW technologies. WIMS: International Conferences on Web Intelligence, Mining and Semantics.; 2011-05-25 - 2011-05-27
NTNU Untitled
 
45 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.
Contributions of the EMERALD project to assessing and improving microarray data quality. BioTechniques 2011 ;Volum 50.(1) s. 27-31
NTNU STO Untitled
 
46 Blondé, Ward; Mironov, Vladimir; Venkatesan, Aravind; Antezana, Erick; De baets, Bernard; Kuiper, Martin.
Reasoning with bio-ontologies: using relational closure rules to enable practical querying. Bioinformatics 2011 ;Volum 27.(11) s. 1562-1568
NTNU Untitled
 
47 Chawla, Konika; Barah, Pankaj; Kuiper, Martin; Bones, Atle M..
Systems Biology: a Promising Tool to Study Abiotic Stress Responses. I: Omics and Plant Abiotic Stress Tolerance. Bentham eBooks 2011 ISBN 978-1-60805-058-1. s. -
NTNU Untitled
 
48 Hu, QA; Hollunder, Jens; Niehl, A; Körner, Camilla J; Gereige, Dalya; Windels, David; Arnold, Andreas; Kuiper, Martin; Vazquez, Frank; Pooggin, M; Heinlein, M.
Specific Impact of Tobamovirus Infection on the Arabidopsis Small RNA Profile. PLoS ONE 2011 ;Volum 6.(5) s. -
NTNU Untitled
 
49 Mironov, Vladimir; Antezana, Erick; Egaña, Mikel; Blondé, Ward; De baets, Bernard; Kuiper, Martin; Stevens, Robert.
Flexibility and utility of the cell cycle ontology. Applied Ontology 2011 ;Volum 6.(3) s. 247-261
NTNU Untitled
 
50 Mironov, Vladimir; Venkatesan, Aravind; Kuiper, Martin.
RDF Foundry - a call for a community effort to harmonize triple store practices. BioHackathon 2011; 2011-08-20 - 2011-08-26
NTNU Untitled
 
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