Blar i NTNU Open på forfatter "Kuiper, Martin"
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Gauging triple stores with actual biological data
Mironov, Vladimir; Seethappan, Nirmala; Blondé, Ward; Antezana, Erick; Splendiani, Andrea; Kuiper, Martin (Journal article; Peer reviewed, 2012)Background: Semantic Web technologies have been developed to overcome the limitations of the current Web and conventional data integration solutions. The Semantic Web is expected to link all the data present on the Internet ... -
Gene Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a large-scale curation effort
Tripathi, Sushil; Christie, K R; Balakrishnan, Ravin; Huntley, R; Hill, D P; Thommesen, Liv; Blake, J A; Kuiper, Martin; Lægreid, Astrid (Journal article; Peer reviewed, 2013)Transcription factors control which information in a genome becomes transcribed to produce RNAs that function in the biological systems of cells and organisms. Reliable and comprehensive information about transcription ... -
Gene Ontology annotation of sequence-specific DNA binding transcription factors: setting the stage for a large-scale curation effort
Tripathi, Sushil; Christie, KR; Balakrishnan, Ravin; Huntley, R; Hill, DP; Thommesen, Liv; Blake, JA; Kuiper, Martin; Lægreid, Astrid (Journal article; Peer reviewed, 2013)Transcription factors control which information in a genome becomes transcribed to produce RNAs that function in the biological systems of cells and organisms. Reliable and comprehensive information about transcription ... -
The Gene Ontology resource: enriching a GOld mine
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 (Peer reviewed; Journal article, 2021)The Gene Ontology Consortium (GOC) provides the most comprehensive resource currently available for computable knowledge regarding the functions of genes and gene products. Here, we report the advances of the consortium ... -
Gene regulation knowledge commons: community action takes care of DNA binding transcription factors
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 (Journal article; Peer reviewed, 2016)A large gap remains between the amount of knowledge in scientific literature and the fraction that gets curated into standardized databases, despite many curation initiatives. Yet the availability of comprehensive knowledge ... -
Gene regulation knowledge commons: community action takes care of DNA binding transcription factors
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 (Journal article; Peer reviewed, 2016)A large gap remains between the amount of knowledge in scientific literature and the fraction that gets curated into standardized databases, despite many curation initiatives. Yet the availability of comprehensive knowledge ... -
The gene regulation knowledge commons: the action area of GREEKC
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 (Peer reviewed; Journal article, 2022)As computational modeling becomes more essential to analyze and understand biological regulatory mechanisms, governance of the many databases and knowledge bases that support this domain is crucial to guarantee reliability ... -
Halogenated boroxine increases propensity to apoptosis in leukemia (UT‐7) but not non‐tumor cells in vitro
Hadzic, Maida; Sun, Yitong; Tomic, Nikolina; Tsirvouli, Eirini; Kuiper, Martin; Pojskic, Lejla (Peer reviewed; Journal article, 2022)A hallmark of the development of solid and hematological malignancies is the dysregulation of apoptosis, which leads to an imbalance between cell proliferation, cell survival and death. Halogenated boroxine [K2(B3O3F4OH)] ... -
Improving the FAIRness of causal interactions in systems biology
Touré, Vasundra (Doctoral theses at NTNU;2020:293, Doctoral thesis, 2020)In molecular systems biology, regulatory process models are built and computationally simulated to represent and analyse the behaviour of cellular systems and how they respond to perturbations. A considerable amount of ... -
Integrative systems approaches to study plant stress responses
Barah, Pankaj (Doktoravhandlinger ved NTNU, 1503-8181; 2013:93, Doctoral thesis, 2013)The world’s population is growing at an alarming rate. As of 2010, out of 7 billion people in the world, 925 million are hungry. It represents 13.1 percent of the total world population, or almost 1 in 7 people are hungry ... -
Jointly creating digital abstracts: dealing with synonymy and polysemy
Vercruysse, Steven; Kuiper, Martin (Journal article; Peer reviewed, 2012)Background Ideally each Life Science article should get a ‘structured digital abstract’. This is a structured summary of the paper’s findings that is both human-verified and machine-readable. But articles can contain a ... -
Logical and experimental modeling of cytokine and eicosanoid signaling in psoriatic keratinocytes
Tsirvouli, Eirini; Ashcroft, Felicity; Johansen, Berit; Kuiper, Martin (Peer reviewed; Journal article, 2021)Psoriasis is a chronic skin disease, in which immune cells and keratinocytes keep each other in a state of inflammation. It is believed that phospholipase A2 (PLA2)-dependent eicosanoid release plays a key role in this. ... -
Logical Modeling of Basal Cell Carcinoma Keratinocytes for Drug Target Prediction
Aker, Ingrid (Master thesis, 2022)Keratinocyttkarsinom, nemlig basalcellekreft og plateepitelkreft, er kreft som oppstår på huden hovedsakelig grunnet overdreven soleksponering. Disse hudkreftformene metastaserer sjeldent, men til tross for dette kan de ... -
Logical Modeling of High-Grade Serous Ovarian Cancer for in silico Prediction of Synergistic Drug Combinations
Sjurgard, Ingrid Vikan (Master thesis, 2022)Høygradig serøs eggstokkreft er den vanligste og dødeligste formen for eggstokkreft. Svake og uspesifikke symptomer kombinert med utilstrekkelige screeningmetoder gjør at sykdommen ofte har utviklet seg i lang tid allerede ... -
LOGICAL MODELING OF MACROPHAGE EICOSANOID METABOLISM AND CONTRIBUTION TO COVID-19
Fariñas Fernández, Marco (Master thesis, 2021)Macrophages are innate immune cells whose main role is the clearance and phagocytosis of microbes and damaged or stressed cells. Also, as antigen-presentingcells, macrophages constitute a bridge between the innate and the ... -
Logical Modelling of Triple Negative Breast Cancer and in silico DRug Synergy Predictions
Diatchenko, Alizée (Master thesis, 2022)Brystkreft er den hyppigst diagnostiserte kreften på verdensbasis med mer enn 2 millioner nye tilfeller hvert år, og dette tallet forventes bare å stige. Brystkreft som mangler ekspresjonen av østrogen- og progesteronreseptorene, ... -
A middle-out modeling strategy to extend a colon cancer logical model improves drug synergy predictions in epithelial-derived cancer cell lines
Tsirvouli, Eirini; Touré, Vasundra; Niederdorfer, Barbara; Vazquez Garcia, Miguel; Flobak, Åsmund; Kuiper, Martin (Peer reviewed; Journal article, 2020)Cancer is a heterogeneous and complex disease and one of the leading causes of death worldwide. The high tumor heterogeneity between individuals affected by the same cancer type is accompanied by distinct molecular and ... -
The Minimum Information about a Molecular Interaction Causal Statement (MI2CAST)
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 (Peer reviewed; Journal article, 2020)Motivation A large variety of molecular interactions occurs between biomolecular components in cells. When a molecular interaction results in a regulatory effect, exerted by one component onto a downstream component, a ... -
Network and Systems Medicine: Position Paper of the European Collaboration on Science and Technology Action on Open Multiscale Systems Medicine
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 (Journal article; Peer reviewed, 2020)Introduction: Network and systems medicine has rapidly evolved over the past decade, thanks to computational and integrative tools, which stem in part from systems biology. However, major challenges and hurdles are still ... -
OLSVis: an animated, interactive visual browser for bio-ontologies
Vercruysse, Steven; Venkatesan, Aravind; Kuiper, Martin (Journal article; Peer reviewed, 2012)Background: More than one million terms from biomedical ontologies and controlled vocabularies are available through the Ontology Lookup Service (OLS). Although OLS provides ample possibility for querying and browsing terms, ...