• A comprehensive analysis of the structure-function relationship in proteins based on local structure similarity 

      Hvidsten, Torgeir; Lægreid, Astrid; Kryshtafovych, Andriy; Andersson, Gunnar; Fidelis, Krzysztof; Komorowski, J (Peer reviewed, 2009)
      Background:Sequence similarity to characterized proteins provides testable functional hypotheses for less than 50% of the proteins identified by genome sequencing projects. With structural genomics it is believed that ...
    • A high-throughput drug combination screen of targeted small molecule inhibitors in cancer cell lines 

      Flobak, Åsmund; Niederdorfer, Barbara; To, Vu; Thommesen, Liv; Klinkenberg, Geir; Lægreid, Astrid (Journal article; Peer reviewed, 2019)
      While there is a high interest in drug combinations in cancer therapy, openly accessible datasets for drug combination responses are sparse. Here we present a dataset comprising 171 pairwise combinations of 19 individual ...
    • Augmenting Bioinformatics Research with Biomedical Ontologies 

      Kusnierczyk, Waclaw (Doktoravhandlinger ved NTNU, 1503-8181; 2008:78, Doctoral thesis, 2008)
      The main objective of the reported study was to investigate how biomedical ontologies, logically structured representations of various aspects of the biomedical reality, can help researchers in analyzing experimental data. ...
    • 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 ...
    • CImbinator: a web-based tool for drug synergy analysis in small- and large-scale datasets 

      Flobak, Åsmund; Vázquez, Miguel; Lægreid, Astrid; Valencia, Alfonso (Journal article; Peer reviewed, 2017)
      Motivation: Drug synergies are sought to identify combinations of drugs particularly beneficial. User-friendly software solutions that can assist analysis of large-scale datasets are required. Results: CImbinator is a ...
    • 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 ...
    • 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 ...
    • 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 ...
    • 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 ...
    • High-throughput screening reveals higher synergistic effect of MEK inhibitor combinations in colon cancer spheroids 

      Folkesson, Evelina; Niederdorfer, Barbara; To, Vu; Thommesen, Liv; Klinkenberg, Geir; Lægreid, Astrid; Flobak, Åsmund (Peer reviewed; Journal article, 2020)
      Drug combinations have been proposed to combat drug resistance, but putative treatments are challenged by low bench-to-bed translational efficiency. To explore the effect of cell culture format and readout methods on ...
    • 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 ...
    • Investigation of Transfection Using Silica-coated Cupric Oxide Nanowires 

      Flobak, Åsmund (Master thesis, 2013)
      One-dimensional high aspect ratio nanostructures grown from a copper foil are considered for intracellular delivery of bioactive molecules, such as drugs and genetic material. The cupric oxide (CuO) nanowires are coated ...
    • 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 ...
    • NR4A2 Is Regulated by Gastrin and Influences Cellular Responses of Gastric Adenocarcinoma Cells 

      Misund, Kristine; Selvik, Linn-Karina M.; Rao, Shalini; Nørsett, Kristin Gabestad; Bakke, Ingunn; Sandvik, Arne; Lægreid, Astrid; Bruland, Torunn; Prestvik, Wenche S; Thommesen, Liv (Journal article; Peer reviewed, 2013)
    • NR4A2 Is Regulated by Gastrin and Influences Cellular Responses of Gastric Adenocarcinoma Cells 

      Misund, Kristine; Selvik, Linn-Karina M.; Rao, Shalini; Nørsett, Kristin Gabestad; Bakke, Ingunn; Sandvik, Arne; Lægreid, Astrid; Bruland, Torunn; Prestvik, Wenche S; Thommesen, Liv (Journal article; Peer reviewed, 2013)
      The peptide hormone gastrin is known to play a role in differentiation, growth and apoptosis of cells in the gastric mucosa. In this study we demonstrate that gastrin induces Nuclear Receptor 4A2 (NR4A2) expression in ...
    • NR4A2 is regulated by Gastrin and involved in gastrin-induced migration and invasion of gastric adenocarcinoma cells 

      Misund, Kristine; Selvik, Linn-Karina M.; Rao, Shalini; Nørsett, Kristin Gabestad; Bakke, Ingunn; Sandvik, Arne; Lægreid, Astrid; Bruland, Torunn; Prestvik, Wenche S; Thommesen, Liv (Peer reviewed; Journal article, 2013)
      The peptide hormone gastrin is known to play a role in differentiation, growth and apoptosis of cells in the gastric mucosa. In this study we demonstrate that gastrin induces Nuclear Receptor 4A2 (NR4A2) expression in the ...