• 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 ...
    • An ensemble framework for identifying essential proteins 

      Zhang, Xue; Xiao, W; Acencio, Marcio Luis; Lemke, Ney; Wang, X (Peer reviewed; Journal article, 2016)
      Many centrality measures have been proposed to mine and characterize the correlations between network topological properties and protein essentiality. However, most of them show limited prediction accuracy,and the number ...
    • 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 ...
    • Genome-wide microRNA screening in Nile tilapia reveals pervasive isomiRs’ transcription, sex-biased arm switching and increasing complexity of expression throughout development 

      Pinhal, Danillo; Bovolenta, Luiz Augusto; Moxon, Simon; Oliveira, Arthur; Nachtigall, Pedro; Acencio, Marcio Luis; Patton, James; Hilsdorf, Alexandre; Lemke, Ney; Martins, Cesar (Journal article; Peer reviewed, 2018)
      MicroRNAs (miRNAs) are key regulators of gene expression in multicellular organisms. The elucidation of miRNA function and evolution depends on the identification and characterization of miRNA repertoire of strategic ...
    • 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 ...
    • TFCheckpoint database update, a cross-referencing system for transcription factors from human, mouse and rat 

      Acencio, Marcio Luis; Vázquez, Miguel; Chawla, Konika; Lægreid, Astrid Renner; Kuiper, Martin (Journal article; Peer reviewed, 2023)
      Prior knowledge about DNA-binding transcription factors (dbTFs), transcription co-regulators (coTFs) and general transcriptional factors (GTFs) is crucial for the study and understanding of the regulation of transcription. ...
    • 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 ...
    • The Gene Ontology Resource: 20 years and still GOing strong. 

      The Gene Ontology, Consortium; that, includes; Acencio, Marcio Luis; Lægreid, Astrid; Kuiper, Martin; among, others (Journal article; Peer reviewed, 2019)
      The Gene Ontology resource (GO; http://geneontology.org) provides structured, computable knowledge regarding the functions of genes and gene products. Founded in 1998, GO has become widely adopted in the life sciences, and ...