Blar i NTNU Open på tidsskrift "Bioinformatics"

Viser treff 1-9 av 9

    • 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 ...

    • ErrorTracer: an algorithm for identifying the origins of inconsistencies in genome-scale metabolic models 

      Martyushenko, Nikolay; Almaas, Eivind (Journal article; Peer reviewed, 2019)
      Motivation: The number and complexity of genome-scale metabolic models is steadily increasing, empowered by automated model-generation algorithms. The quality control of the models, however, has always remained a significant ...

    • 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 ...

    • Modeling dependency structures in 450k DNA methylation data 

      Nustad, Haakon Egdetveit; Steinsland, Ingelin; Ollikainen, Miina; Cazaly, Emma; Kaprio, Jaakko; Benjamini, Yuval; Gervin, Kristina; Lyle, Robert (Peer reviewed; Journal article, 2022)
      Motivation DNA methylation has been shown to be spatially dependent across chromosomes. Previous studies have focused on the influence of genomic context on the dependency structure, while not considering differences ...

    • 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 ...

    • UniBioDicts: Unified access to biological dictionaries 

      Zobolas, John; Touré, Vasundra; Kuiper, Martin; Vercruysse, Steven (Peer reviewed; Journal article, 2020)
      We present a set of software packages that provide uniform access to diverse biological vocabulary resources that are instrumental for current biocuration efforts and tools. The Unified Biological Dictionaries (UniBioDicts ...