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2019
1 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
 
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 ;Volum 34.(2) s. 213-236
NTNU Untitled
 
3 Flobak, Åsmund; Niederdorfer, Barbara; To, Vu; Thommesen, Liv; Klinkenberg, Geir; Lægreid, Astrid.
A high-throughput drug combination screen of targeted small molecule inhibitors in cancer cell lines. Scientific Data 2019 ;Volum 6. s. 1-10
NTNU SINTEF STO Untitled
 
4 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)
NTNU Untitled
 
5 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
NTNU Untitled
 
6 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.
NTNU Untitled
 
2018
7 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
NTNU Untitled
 
8 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
NTNU Untitled
 
9 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
NTNU Untitled
 
10 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
NTNU Untitled
 
2017
11 Acencio, Marcio Luis; Lægreid, Astrid.
Representation of sequence-specific DNA binding transcription factors (DbTFs) complexes. Curation workshop on molecular and causal interactions; 2017-12-05 - 2017-12-07
NTNU Untitled
 
12 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
 
13 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
NTNU Untitled
 
14 Flobak, Åsmund; Garcia, Miguel Vazquez; Lægreid, Astrid; Valencia, Alfonso.
CImbinator: a web-based tool for drug synergy analysis in small- and large-scale datasets. Bioinformatics 2017 ;Volum 33.(15) s. 2410-2412
NTNU Untitled
 
15 Touré, Vasundra; Flobak, Åsmund; Lægreid, Astrid; Kuiper, Martin Tremen R..
Extraction and representation of causal statements: Creating a model building resource for Systems Biology. COMBINE 2017; 2017-10-09 - 2017-10-13
NTNU Untitled
 
2016
16 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
 
17 Acencio, Marcio Luis; Lægreid, Astrid; Kuiper, Martin.
Knowledge Commons digitalization - curation. Crossover Seminar; 2016-04-14 - 2016-04-15
NTNU Untitled
 
18 Flobak, Åsmund; Steigedal, Tonje S.; Thommesen, Liv; Kuiper, Martin Tremen R.; Lægreid, Astrid.
Logical models for drug screen prioritization. European Conference on Computational Biology; 2016-09-03 - 2016-09-07
NTNU UiO Untitled
 
19 Lægreid, Astrid.
Why we need the Knowledge Commons. Today's biology is not possible without. Science for the common good – visions of technological opportunities; 2016-06-13 - 2016-06-14
NTNU Untitled
 
20 Nydal, Rune; Lægreid, Astrid; Kuiper, Martin.
Curation strategeis of NTNU project. Workshop upstart crossover at EBI; 2016-04-22 - 2016-04-23
NTNU Untitled
 
21 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
22 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
 
23 Lægreid, Astrid; Kuiper, Martin.
Health and the information commons.
NTNU Untitled
 
24 Tripathi, Sushil; Flobak, Åsmund; Chawla, Konika; Baudot, Anaïs; Bruland, Torunn; Thommesen, Liv; Kuiper, Martin Tremen R.; Lægreid, Astrid.
The gastrin and cholecystokinin receptors mediated signaling network: a scaffold for data analysis and new hypotheses on regulatory mechanisms. BMC Systems Biology 2015 ;Volum 9.(40) s. -
NTNU Untitled
 
2014
25 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
 
26 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
 
27 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
 
28 Lægreid, Astrid; Kuiper, Martin.
Å ta seg av kunnskap.
NTNU Untitled
 
29 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
 
30 Orchard, Sandra; Ammari, M; Aranda, B; Breuza, L; Briganti, L; Broackes-Carter, F; Campbell, NH; Chavali, G; Chen, C; Del-Toro, N; Duesbury, M; Dumousseau, M; Galeota, E; Hinz, U; Iannuccelli, M; Jagannathan, S; Jimenez, R.; Khadake, J; Lægreid, Astrid; Licata, L; Lovering, RC; Meldal, B; Melidoni, AN; Milagros, M; Peluso, D; Perfetto, Livia; Porras, P; Raghunath, A; Ricard-Blum, S; Roechert, B; Stutz, A; Tognolli, M; Van Roey, K; Cesareni, G; Hermjakob, H.
The MIntAct project - IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Research 2014 ;Volum 42.(1) s. D358-D363
NTNU Untitled
 
31 Selvik, Linn-Karina M.; Rao, Shalini; Steigedal, Tonje; Haltbakk, Ildri; Misund, Kristine; Bruland, Torunn; Prestvik, Wenche S; Lægreid, Astrid; Thommesen, Liv.
Salt-inducible kinase 1 (SIK1) is induced by gastrin and inhibits migration of gastric adenocarcinoma cells. PLOS ONE 2014 ;Volum 9.(11) s. -
NTNU Untitled
 
32 Vange, Pål; Beisvag, Vidar; Flatberg, Arnar; Afroz, Wahida; Nordrum, Ivar Skjåk; Sørdal, Øystein Finset; Qvigstad, Gunnar; Thommesen, Liv; Lægreid, Astrid; Sandvik, Arne Kristian; Bruland, Torunn; Bakke, Ingunn.
Molecular mechanisms of cellular stress responses in gastric cancer. Digestive Disease Week 2014; 2014-05-03 - 2014-05-06
NTNU STO Untitled
 
33 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
34 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
 
35 Feuerherm, Astrid Jullumstrø; Jørgensen, Katarina Mariann; Sommerfelt, Randi Magnus; Eidem, Live Egeland; Lægreid, Astrid; Johansen, Berit.
Platelet-activating factor induces proliferation in differentiated keratinocytes. Molecular and Cellular Biochemistry 2013 ;Volum 384.(1-2) s. 83-94
NTNU Untitled
 
36 Misund, Kristine; Selvik, Linn-Karina M.; Rao, Shalini; Nørsett, Kristin Gabestad; Bakke, Ingunn; Sandvik, Arne; Lægreid, Astrid; Bruland, Torunn; Prestvik, Wenche S; Thommesen, Liv.
NR4A2 is regulated by Gastrin and involved in gastrin-induced migration and invasion of gastric adenocarcinoma cells. PLOS ONE 2013 ;Volum 8.(9) Suppl. e76234 s. -
NTNU STO Untitled
 
37 Rao, Shalini; Selvik, Linn-Karina M.; Nørsett, Kristin Gabestad; Bakke, Ingunn; Misund, Kristine; Bruland, Torunn; Wenche S, Prestvik; Lægreid, Astrid; Thommesen, Liv.
NR4A2 is regulated by gastrin and influences cellular responses in gastric adenocarcinoma cells. Nuclear receptors: Linking molecules, genomes & physiology; 2013-09-06 - 2013-09-10
NTNU Untitled
 
38 Rao, Shalini; Thommesen, Liv; Nørsett, Kristin; Bakke, Ingunn; Misund, Kristine; Bruland, Torunn; Prestvik, Wenche S; Lægreid, Astrid.
Nr4A2 is regulated by gastrin and influences cellular responses in gastric adenocarcinoma cells. Kontaktmøte Norsk Biokjemisk Selskap; 2013-01-17 - 2013-01-20
NTNU Untitled
 
39 Selvik, Linn-Karina M.; Fjeldbo, Christina Sæten; Flatberg, Arnar; Steigedal, Tonje; Misund, Kristine; Anderssen, Endre; Doseth, Berit; Langaas, Mette; Tripathi, Sushil; Beisvag, Vidar; Lægreid, Astrid; Thommesen, Liv; Bruland, Torunn.
The duration of gastrin treatment affects global gene expression and molecular responses involved in ER stress and anti-apoptosis. BMC Genomics 2013 ;Volum 14. s. -
NTNU Untitled
 
40 Steigedal, Tonje; Prestvik, Wenche S; Selvik, Linn-Karina M.; Fjeldbo, Christina Sæten; Bruland, Torunn; Lægreid, Astrid; Thommesen, Liv.
Gastrin-induced proliferation involves MEK partner 1 (MP1). In vitro Cellular & Developmental Biology-Animal 2013 ;Volum 49.(3) s. 162-169
NTNU Untitled
 
41 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
 
2012
42 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
 
43 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
 
44 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
 
45 Fjeldbo, Christina Sæten; Bakke, Ingunn; Erlandsen, Sten Even; Holmseth, Jannicke; Lægreid, Astrid; Sandvik, Arne Kristian; Thommesen, Liv; Bruland, Torunn.
Gastrin upregulates the pro-survival factor secretory clusterin (sCLU) in adenocarcinoma cells and in oxyntic mucosa of hypergastrinemic rats. American Journal of Physiology - Gastrointestinal and Liver Physiology 2012 ;Volum 302.(1) s. G21-G33
NTNU STO Untitled
 
46 Nydal, Rune; Efstathiou, Sophia; Lægreid, Astrid.
Crossover Research: Exploring a Collaborative Mode of Integration. I: Little by Little. Expansions of Nanoscience and Emerging Technologies. IOS Press 2012 ISBN 978-1-61499-148-9. s. 181-194
NTNU Untitled
 
47 Nydal, Rune; Efstathiou, Sophia; Lægreid, Astrid.
Widening the circles of collaboration - Integrating philosophy in systems biology. Fourth Annual converence of the society for the study of nanoscience and emerging technologies; 2012-10-22 - 2012-10-25
NTNU Untitled
 
2011
48 Nydal, Rune; Efstathiou, Sophia; Lægreid, Astrid.
Well-constructed systems biology. Integrating Socio-humanist Research. S-Net, Third annual meeting; 2011-11-07 - 2011-11-10
NTNU Untitled
 
49 Tripathi, Sushil; Venkatesan, Aravind; Egaña, Mikel; Zavareh, Zahra; Chawla, Konika; Mironov, Vladimir; Thommesen, Liv; Bruland, Torunn; Kuiper, Martin; Lægreid, Astrid.
Automated Assessment of High Throughput Hypotheses on Gene Regulatory Mechanisms Involved in the Gastrin Response. Bio-Ontologies 2011; 2011-07-15 - 2011-07-16
NTNU Untitled
 
2010
50 Bruland, Torunn; Anderssen, Endre; Misund, Kristine; Fjeldbo, Christina Sæten; Flatberg, Arnar; Selvik, Linn-Karina M.; Beisvag, Vidar; Sandvik, Arne Kristian; Lægreid, Astrid; Thommesen, Liv.
Exploring signal-induced cellular regulatory subnetworks by use of partial least square regression (PLSR) multidimensional analysis of gene expression time series data. 13th Annual MGED meeting , Boston, Massachusetts, USA; 2010-07-13 - 2010-07-15
NTNU Untitled
 
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