• BioGateway: A Semantic Systems Biology Tool for the Life Sciences 

      Antezana, Erick; Blondé, Ward; Egaña, Mikel; Rutherford, Alistair; Stevens, Robert; De baets, Bernard; Mironov, Vladimir; Kuiper, Martin (Journal article; Peer reviewed, 2009)
      Background: Life scientists need help in coping with the plethora of fast growing and scattered knowledge resources. Ideally, this knowledge should be integrated in a form that allows them to pose complex questions that ...
    • CausalBuilder: bringing the MI2CAST causal interaction annotation standard to the curator 

      Touré, Vasundra; Zobolas, John; Kuiper, Martin; Vercruysse, Steven (Journal article; Peer reviewed, 2021)
      Molecular causal interactions are defined as regulatory connections between biological components. They are commonly retrieved from biological experiments and can be used for connecting biological molecules together to ...
    • CausalTAB: the PSI-MITAB 2.8 updated format for signalling data representation and dissemination 

      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 (Peer reviewed; Journal article, 2019)
      Motivation Combining multiple layers of information underlying biological complexity into a structured framework represent a challenge in systems biology. A key task is the formalization of such information in models ...
    • Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen 

      Kuiper, Martin; Lægreid, Astrid; Flobak, Åsmund; Thommesen, Liv; Team, Dream (Journal article; Peer reviewed, 2019)
      The effectiveness of most cancer targeted therapies is short-lived. Tumors often developresistance that might be overcome with drug combinations. However, the number of possiblecombinations is vast, necessitating data-driven ...
    • Contributions of the EMERALD project to assessing and improving microarray data quality 

      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 (Journal article; Peer reviewed, 2011)
      While minimum information about a microarray experiment (MIAME) standards have helped to increase the value of the microarray data deposited into public databases like ArrayExpress and Gene Expression Omnibus (GEO), limited ...
    • Determination of quality metabolites in different brands of salmon fillets 

      Sokolová, Tatiana (Master thesis, 2017)
      Fish offer a multitude of nutritional benefits and its world´s food supply has grown rapidly in the last years. The quality of fish is an important factor for the fish industry and consumers, this field is required to be ...
    • Discovery of Drug Synergies in Gastric Cancer Cells Predicted by Logical Modeling 

      Flobak, Åsmund; Baudot, Anaïs; Remy, Elisabeth; Thommesen, Liv; Thieffry, Denis; Kuiper, Martin; Lægreid, Astrid (Peer reviewed; Journal article, 2015)
      Discovery of efficient anti-cancer drug combinations is a major challenge, since experimental testing of all possible combinations is clearly impossible. Recent efforts to computationally predict drug combination responses ...
    • Dynamically Controlled DNA Tiles: Looking Beyond the Self-assembly of Static Two-dimensional DNA-based Computational Structures 

      Gautam, Vinay Kumar (Doctoral theses at NTNU;2017:58, Doctoral thesis, 2017)
      Algorithmic self-assembly of DNA tiles enables computation and construction of DNA structures at the nanoscale, where the assembly process is guided by specific DNA interactions between complementary sticky-ends of tiles. ...
    • emba: R package for analysis and visualization of biomarkers in boolean model ensembles 

      Zobolas, John; Kuiper, Martin; Flobak, Åsmund (Journal article; Peer reviewed, 2020)
    • Experimental-Computational Approaches to Identify Synergistic Effects of Anti-Cancer Drugs 

      Niederdorfer, Barbara (Doctoral theses at NTNU;2019:384, Doctoral thesis, 2019)
      Drug combinations are hoped to improve treatment response to anti-cancer drugs by targeting the cancers vulnerabilities at diverse trajectories. With a large number of approved agents of chemotherapeutic and targeted ...
    • Finding gene regulatory network candidates using the gene expression knowledge base 

      Venkatesan, Aravind; Tripathi, Sushil; Sanz de Galdeano, Alejandro; Blondé, Ward; Lægreid, Astrid; Mironov, Vladimir; Kuiper, Martin (Journal article; Peer reviewed, 2014)
      Background: Network-based approaches for the analysis of large-scale genomics data have become well established. Biological networks provide a knowledge scaffold against which the patterns and dynamics of ?omics? data can ...
    • Flexible network reconstruction from relational databases with Cytoscape and CytoSQL 

      Laukens, K; Hollunder, J; Thanh, HD; De Jaeger, G; Kuiper, Martin; Witters, E; Verschoren, A; Van Leemput, K (Journal article; Peer reviewed, 2010)
      Background: Molecular interaction networks can be efficiently studied using network visualization software such as Cytoscape. The relevant nodes, edges and their attributes can be imported in Cytoscape in various file ...
    • A foundation for reference models for drug combinations with an application to Loewe’s reference model 

      De Mulder, Wim; Kuiper, Martin (Peer reviewed; Journal article, 2020)
      Background Treating patients with combinations of drugs that have synergistic effects has become widespread practice in the clinic. Drugs work synergistically when the observed effect of a drug combination is larger ...
    • 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 ...
    • 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 ...
    • 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 ...