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2024
1 Niarakis, Anna; Ostaszewski, Marek; Mazein, Alexander; Kuperstein, Inna; Kutmon, Martina; Gillespie, Marc E.; Funahashi, Akira; Acencio, Marcio Luis; Hemedan, Ahmed; Aichem, Michael; Klein, Karsten; Czauderna, Tobias; Burtscher, Felicia; Yamada, Takahiro G.; Hiki, Yusuke; Hiroi, Noriko F.; Hu, Finterly; Pham, Nhung; Ehrhart, Friederike; Willighagen, Egon L.; Valdeolivas, Alberto; Dugourd, Aurelien; Messina, Francesco; Esteban-Medina, Marina; Peña-Chilet, Maria; Rian, Kinza; Soliman, Sylvain; Aghamiri, Sara Sadat; Puniya, Bhanwar Lal; Naldi, Aurélien; Helikar, Tomáš; Singh, Vidisha; Farinas Fernandez, Marco; Bermudez Paiva, Viviam Solangeli; Tsirvouli, Eirini; Montagud, Arnau; Noël, Vincent; Ponce-de-Leon, Miguel; Maier, Dieter; Bauch, Angela; Gyori, Benjamin M.; Bachman, John A.; Luna, Augustin; Piñero, Janet; Furlong, Laura I.; Balaur, Irina; Rougny, Adrien; Jarosz, Yohan; Overall, Rupert W.; Phair, Robert; Perfetto, Livia; Matthews, Lisa; Rex, Devasahayam Arokia Balaya; Orlic-Milacic, Marija; Gomez, Luis Cristobal Monraz; De Meulder, Bertrand; Ravel, Jean Marie; Jassal, Bijay; Satagopam, Venkata; Wu, Guanming; Golebiewski, Martin; Gawron, Piotr; Calzone, Laurence; Beckmann, Jacques S.; Evelo, Chris T.; D’Eustachio, Peter; Schreiber, Falk; Saez-Rodriguez, Julio; Dopazo, Joaquin; Kuiper, Martin; Valencia, Alfonso; Wolkenhauer, Olaf; Kitano, Hiroaki; Barillot, Emmanuel; Auffray, Charles; Balling, Rudi; Schneider, Reinhard.
Drug-target identification in COVID-19 disease mechanisms using computational systems biology approaches. Frontiers in Immunology 2024 ;Volume 14. p. -
NTNU Untitled
 
2 Tsirvouli, Eirini; Noël, Vincent; Flobak, Åsmund; Calzone, Laurence; Kuiper, Martin.
Dynamic Boolean modeling of molecular and cellular interactions in psoriasis predicts drug target candidates. iScience 2024 ;Volume 27.(2) p. -
NTNU STO SINTEF Untitled
 
2023
3 Acencio, Marcio Luis; Vázquez, Miguel; Chawla, Konika; Lægreid, Astrid Renner; Kuiper, Martin.
TFCheckpoint database update, a cross-referencing system for transcription factors from human, mouse and rat. Nucleic Acids Research (NAR) 2023 ;Volume 52.(1) p. 1-11
NTNU Untitled
 
4 Flobak, Åsmund; Zobolas, John; Vázquez, Miguel; Steigedal, Tonje S.; Thommesen, Liv; Grislingås, Asle Andreas; Niederdorfer, Barbara; Folkesson, Emma Evelina; Kuiper, Martin.
Fine tuning a logical model of cancer cells to predict drug synergies: combining manual curation and automated parameterization. Frontiers in Systems Biology 2023 ;Volume 3.
NTNU UiO Untitled
 
5 Heck, Kathleen; Lindholm, Håvard Takle; Niederdorfer, Barbara; Tsirvouli, Eirini; Kuiper, Martin; Flobak, Åsmund; Lægreid, Astrid Renner; Thommesen, Liv.
Characterisation of Colorectal Cancer Cell Lines through Proteomic Profiling of Their Extracellular Vesicles. Proteomes 2023 ;Volume 11.(1) p. -
NTNU STO Untitled
 
2022
6 Chatterjee, Anamika; Swierstra, Tsjalling; Kuiper, Martin.
Dealing with different conceptions of pollution in the Gene Regulation Knowledge Commons. Biochimica et Biophysica Acta. Gene Regulatory Mechanisms 2022 ;Volume 1865.(1)
NTNU Untitled
 
7 Hadzic, Maida; Sun, Yitong; Tomic, Nikolina; Tsirvouli, Eirini; Kuiper, Martin; Pojskic, Lejla.
Halogenated boroxine increases propensity to apoptosis in leukemia (UT-7) but not non-tumor cells in vitro. FEBS Open Bio 2022 ;Volume 13.(1) p. 143-153
NTNU Untitled
 
8 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.
The gene regulation knowledge commons: the action area of GREEKC. Biochimica et Biophysica Acta. Gene Regulatory Mechanisms 2022 ;Volume 1865.(1)
NTNU Untitled
 
9 Vazquez Garcia, Miguel; Krallinger, Martin; Leitner, Florian; Kuiper, Martin; Valencia, Alfonso; Lægreid, Astrid.
ExTRI: Extraction of transcription regulation interactions from literature. Biochimica et Biophysica Acta. Gene Regulatory Mechanisms 2022 ;Volume 1865.(1)
NTNU Untitled
 
10 Zobolas, John; Monteiro, Pedro T.; Kuiper, Martin; Flobak, Åsmund.
Boolean function metrics can assist modelers to check and choose logical rules. Journal of Theoretical Biology 2022 ;Volume 538. p. 111025-
NTNU STO Untitled
 
2021
11 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.
The Gene Ontology resource: enriching a GOld mine. Nucleic Acids Research (NAR) 2021
NTNU Untitled
 
12 Gaudet, Pascale; Logie, Colin; Lovering, Ruth C.; Kuiper, Martin; Lægreid, Astrid; Thomas, Paul D..
Gene Ontology representation for transcription factor functions. Biochimica et Biophysica Acta. Gene Regulatory Mechanisms 2021 ;Volume 1864.(11-12) p. -
NTNU Untitled
 
13 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.
Formalization of gene regulation knowledge using ontologies and gene ontology causal activity models. Biochimica et Biophysica Acta. Gene Regulatory Mechanisms 2021 ;Volume 1864.(11-12)
NTNU Untitled
 
14 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.
A GO catalogue of human DNA-binding transcription factors. Biochimica et Biophysica Acta. Gene Regulatory Mechanisms 2021 ;Volume 1864.(11-12)
NTNU Untitled
 
15 Touré, Vasundra; Flobak, Asmund; Niarakis, Anna; Vercruysse, Steven; Kuiper, Martin.
The status of causality in biological databases: data resources and data retrieval possibilities to support logical modeling. Briefings in Bioinformatics 2021 ;Volume 22.(4) p. -
NTNU Untitled
 
16 Touré, Vasundra; Zobolas, John; Kuiper, Martin; Vercruysse, Steven.
CausalBuilder: bringing the MI2CAST causal interaction annotation standard to the curator. Database: The Journal of Biological Databases and Curation 2021 p. -
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17 Tsirvouli, Eirini; Ashcroft, Felicity; Johansen, Berit; Kuiper, Martin.
Logical and experimental modeling of cytokine and eicosanoid signaling in psoriatic keratinocytes. iScience 2021 ;Volume 24. p. -
NTNU Untitled
 
2020
18 Bermúdez, Viviam; Fariñas, Marco; Tsirvouli, Eirini; Kuiper, Martin.
From COVID-19 Disease Map molecular mechanisms to executable cell-specific logical models. 2020 Disease Maps Community Meeting; 2020-11-12 - 2020-11-14
NTNU Untitled
 
19 Bermúdez, Viviam; Tsirvouli, Eirini; Fariñas, Marco; Sridhar, Arun; Johansen, Berit; Pestana, Carolina; Kuiper, Martin.
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; 2020-10-21 - 2020-10-23
NTNU Untitled
 
20 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
STO NTNU Untitled
 
21 De Mulder, Wim; Kuiper, Martin.
A foundation for reference models for drug combinations with an application to Loewe’s reference model. BMC Bioinformatics 2020 ;Volume 21.(460) p. 1-11
NTNU Untitled
 
22 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.
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 p. -
NTNU Untitled
 
23 Nydal, Rune; Bennett, Gaymon; Kuiper, Martin; Lægreid, Astrid.
Silencing trust: confidence and familiarity in re-engineering knowledge infrastructures. Medicine, Health care and Philosophy 2020 p. -
NTNU Untitled
 
24 Puig, Rafael Riudavets; Holmås, Stian; Mironov, Vladimir; Kuiper, Martin.
Network Building with the Cytoscape BioGateway App Explained in Five Use Cases. Current Protocols in Bioinformatics 2020 ;Volume 72.(1)
NTNU Untitled
 
25 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 p. -
STO NTNU Untitled
 
26 Tsirvouli, Eirini; Touré, Vasundra; Niederdorfer, Barbara; Vazquez Garcia, Miguel; 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 Molecular Biosciences 2020 ;Volume 7:502573. p. 1-19
STO NTNU Untitled
 
27 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 p. -
STO NTNU Untitled
 
28 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 ;Volume 5.(53)
NTNU Untitled
 
29 Zobolas, John; Touré, Vasundra; Kuiper, Martin; Vercruysse, Steven.
UniBioDicts: Unified access to biological dictionaries. Bioinformatics 2020 ;Volume 37.(1) p. 143-144
NTNU Untitled
 
2019
30 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
 
31 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 (NAR) 2019 ;Volume 47.(gky1055) Suppl. D1 p. D330-D338
NTNU Untitled
 
32 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 ;Volume 34.(2) p. 213-236
NTNU Untitled
 
33 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
 
34 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 p. -
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35 Kuiper, Martin.
Towards a curation platform for causal interaction statements.. Basel Life 2019 Workshop; 2019-09-09 - 2019-09-09
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36 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 ;Volume 10.(2674)
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37 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 ;Volume 35.(19) p. 3779-3785
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38 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 ;Volume 2518.
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39 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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40 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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41 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
42 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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43 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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44 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
 
45 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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46 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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47 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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48 Vercruysse, Steven; Kuiper, Martin.
The VSM-pages: How to Easily Plant Complex Ideas into Computers.
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2017
49 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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50 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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