Blar i Institutt for klinisk og molekylær medisin på tidsskrift "Bioinformatics"

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    • 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 ...

    • Methplotlib: Analysis of modified nucleotides from nanopore sequencing 

      De Coster, Wouter; Stovner, Endre Bakken; Strazisar, Mojca (Journal article; Peer reviewed, 2020)
      Summary Modified nucleotides play a crucial role in gene expression regulation. Here, we describe methplotlib, a tool developed for the visualization of modified nucleotides detected from Oxford Nanopore Technologies ...

    • 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 ...

    • PyRanges: efficient comparison of genomic intervals in Python 

      Stovner, Endre Bakken; Sætrom, Pål (Journal article; Peer reviewed, 2019)
      Complex genomic analyses often use sequences of simple set operations like intersection, overlap and nearest on genomic intervals. These operations, coupled with some custom programming, allow a wide range of analyses to ...

    • The Cytoscape BioGateway App: explorative network building from an RDF store 

      Holmås, Stian; Riudavets Puig, Rafael; Acencio, Marcio Luis; Mironov, Vladimir; Kuiper, Martin (Journal article; Peer reviewed, 2019)
      The BioGateway App is a Cytoscape (version 3) plugin designed to provide easy query access to the BioGateway Resource Description Framework triple store, which contains functional and interaction information for proteins ...