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2020
1 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.
Network and Systems Medicine: Position Paper of the European Collaboration on Science and Technology Action on Open Multiscale Systems Medicine. Network and Systems Medicine 2020
NTNU Untitled
 
2 Niarakis, Anna; Kuiper, Martin; Ostaszewski, Marek; Sheriff, Rahuman Malik; Casals, Cristina; Thieffry, Denis; Freeman, Tom; Thomas, Paul; Touré, Vasundra; Noel, Vincent; Stoll, Gauthier; Saez-Rodriguez, Julio; Naldi, Aurélien; Oshurko, Eugenia; Xenarios, Ioannis; Soliman, Sylvain; Chaouiya, Claudine; Helikar, Tomas; Calzone, Laurence.
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 2020
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3 Nydal, Rune; Bennett, Gaymon; Kuiper, Martin; Lægreid, Astrid.
Silencing trust: confidence and familiarity in re-engineering knowledge infrastructures. Medicine, Health care and Philosophy 2020 s. -
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4 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.
The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST). Bioinformatics 2020
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5 Tsirvouli, Eirini; Touré, Vasundra; Niederdorfer, Barbara; Flobak, Åsmund; Kuiper, Martin.
A middle-out modeling strategy to extend a colon cancer logical model improves drug synergy predictions in epithelial-derived cancer cell lines. Frontiers in Physiology 2020
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6 Zobolas, John; Kuiper, Martin; Flobak, Åsmund.
emba: R package for analysis and visualization of biomarkers in boolean model ensembles. Journal of Open Source Software (JOSS) 2020
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2019
7 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
 
8 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.
The Gene Ontology Resource: 20 years and still GOing strong.. Nucleic Acids Research 2019 ;Volum 47.(gky1055) Suppl. D1 s. D330-D338
NTNU Untitled
 
9 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 ;Volum 34.(2) s. 213-236
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10 Holmås, Stian; Mironov, Vladimir; Kuiper, Martin.
Network building in Cytoscape using the BioGateway App. SWAT4(HC)LS 2019: Semantic Web Applications and Tools for Healthcare and Life Sciences; 2019-12-09 - 2019-12-12
NTNU Untitled
 
11 Holmås, Stian; Riudavets Puig, Rafael; Acencio, Marcio Luis; Mironov, Vladimir; Kuiper, Martin.
The Cytoscape BioGateway App: explorative network building from an RDF store. Bioinformatics 2019 s. -
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12 Kuiper, Martin.
Towards a curation platform for causal interaction statements.. Basel Life 2019 Workshop; 2019-09-09 - 2019-09-09
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13 Menden, Michael Patrick; Wang, Dennis; Mason, Mike J.; Szalai, Bence; Bulusu, Krishna C.; Guan, Yuanfang; Flobak, Åsmund; Kuiper, Martin; Lægreid, Astrid; Thommesen, Liv.
Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen. Nature Communications 2019 ;Volum 10.(2674)
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14 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 ;Volum 35.(19) s. 3779-3785
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15 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.
An example of multimodal biological knowledge representation. CEUR Workshop Proceedings 2019 ;Volum 2518.
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16 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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17 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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18 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
19 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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20 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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21 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
 
22 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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23 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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24 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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25 Vercruysse, Steven; Kuiper, Martin.
The VSM-pages: How to Easily Plant Complex Ideas into Computers.
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2017
26 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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27 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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28 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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29 Kuiper, Martin.
The logical way to tackle cancer. Systems Medicine Conference in Slovenia; 2017-06-08 - 2017-06-09
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2016
30 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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31 Acencio, Marcio Luis; Lægreid, Astrid; Kuiper, Martin.
Knowledge Commons digitalization - curation. Crossover Seminar; 2016-04-14 - 2016-04-15
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32 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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33 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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34 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
35 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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36 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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37 Lægreid, Astrid; Kuiper, Martin.
Health and the information commons.
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38 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
39 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 (LNCS) 2014 ;Volum 8890. s. 119-133
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40 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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41 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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42 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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43 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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44 Kuiper, Martin.
Keynote lecture: Networks for Knowledge. IEEE International Conference Bioinformatics and Biomedicine 2014; 2014-11-02 - 2014-11-05
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45 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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46 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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47 Lægreid, Astrid; Kuiper, Martin.
Å ta seg av kunnskap.
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48 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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49 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
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50 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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