Recent Submissions

  • Polymorphic Inversions Underlie the Shared Genetic Susceptibility of Obesity-Related Diseases 

    González, Juan R.; Ruiz Arenas, Carlos; Cáceres, Alejandro; Morán, Ignasi; López Sánchez, Marcos; Alonso, Lorena; Tolosona, Ignacio; Guindo Martínez, Marta; Mercader, Josep M.; Esko, Tonu; Torrents, David; González, Josefa; Pérez Jurado, Luis A. (Elsevier, 2020)
    Contribution to periodical
    Restricted access - publisher's policy
    The burden of several common diseases including obesity, diabetes, hypertension, asthma, and depression is increasing in most world populations. However, the mechanisms underlying the numerous epidemiological and genetic ...
  • Time to kick-start text mining for biomaterials 

    Hakimi, Osnat; Krallinger, Martin; Ginebra Molins, Maria Pau (Springer Nature, 2020)
    Article
    Restricted access - publisher's policy
    Covenantee:  Barcelona Supercomputing Center
    The rapidly expanding biomaterials data are challenging to organize. Text mining systems are powerful tools that automatically extract and integrate information in large textual collections. As text mining leaps forward ...
  • Multi-year prediction of European summer drought conditions for the agricultural sector 

    Solaraju Murali, Balakrishnan; Caron, Louis-Philippe; Gonzalez-Reviriego, Nube; Doblas-Reyes, Francisco J (2019-11-27)
    Article
    Open Access
    Decadal climate prediction, where climate models are initialized with the contemporaneous state of the Earth system and run for a decade into the future, represents a new source of near-term climate information to better ...
  • Fungal evolution: diversity, taxonomy and phylogeny of the Fungi 

    Naranjo Ortíz, Miguel A; Gabaldon, Toni (Wiley, 2019)
    Article
    Open Access
    The fungal kingdom comprises a hyperdiverse clade of heterotrophic eukaryotes characterized by the presence of a chitinous cell wall, the loss of phagotrophic capabilities and cell organizations that range from completely ...
  • Genome Assemblies of Two Rare Opportunistic Yeast Pathogens: Diutina rugosa (syn. Candida rugosa) and Trichomonascus ciferrii (syn. Candida ciferrii) 

    Mixão, Verónica; Saus, Ester; Perez Hansen, Antonio; Lass Florl, Cornelia; Gabaldon, Toni (Genetics Society of America (GSA), 2019)
    Article
    Open Access
    Infections caused by opportunistic yeast pathogens have increased over the last years. These infections can be originated by a large number of diverse yeast species of varying incidence, and with distinct clinically relevant ...
  • Nucleosome Dynamics: a new tool for the dynamic analysis of nucleosome positioning 

    Diana, Buitrago; Codó, Laia; Illa, Ricard; Jorge, Pau de; Battistini, Federica; Flores, Oscar; Bayarri, Genis; Royo, Romina; Pino, Marc del; Heath, Simon; Hospital, Adam; Gelpí, Josep Lluís; Heath, Isabelle Brun; Orozco, Modesto (Oxford University Press (OUP), 2019-10-10)
    Article
    Open Access
    We present Nucleosome Dynamics, a suite of programs integrated into a virtual research environment and created to define nucleosome architecture and dynamics from noisy experimental data. The package allows both the ...
  • Next generation community assessment of biomedical entity recognition web servers: metrics, performance, interoperability aspects of BeCalm 

    Pérez Pérez, Martín; Pérez Rodríguez, Gael; Blanco Míguez, Aitor; Fernández Riverola, Florentino; Valencia, Alfonso; Krallinger, Martin; Lourenço, Anália (BMC, 2019)
    Article
    Open Access
    Background Shared tasks and community challenges represent key instruments to promote research, collaboration and determine the state of the art of biomedical and chemical text mining technologies. Traditionally, such ...
  • Interpreting molecular similarity between patients as a determinant of disease comorbidity relationships 

    Sánchez, Jon; Tejero, Héctor; Fernández, José María; Juan, David; Urda García, Beatriz; Capella Gutiérrez, Salvador; Al-Shahrour, Fátima; Tabarés Seisdedos, Rafael; Baudot, Anais; Pancaldi, Vera; Valencia, Alfonso (Springer Nature, 2020)
    Article
    Open Access
    Comorbidity is a medical condition attracting increasing attention in healthcare and biomedical research. Little is known about the involvement of potential molecular factors leading to the emergence of a specific disease ...
  • PharmacoNER Tagger: a deep learning-based tool for automatically finding chemicals and drugs in Spanish medical texts 

    Armengol Estapé, Jordi; Soares, Felipe; Marimon, Montserrat; Krallinger, Martin (Korea Genome Organization, 2019-06-19)
    Article
    Open Access
    Automatically detecting mentions of pharmaceutical drugs and chemical substances is key for the subsequent extraction of relations of chemicals with other biomedical entities such as genes, proteins, diseases, adverse ...
  • Sex and gender differences and biases in artificial intelligence for biomedicine and healthcare 

    Cirillo, Davide; Catuara Solarz, Silvina; Morey, Czuee; Guney, Emre; Subirats, Laia; Mellino, Simona; Gigante, Annalisa; Valencia, Alfonso; Rementeria, María José; Santuccione Chadha, Antonella; Mavridis, Nikolaos (Springer Nature, 2020)
    Article
    Open Access
    Precision Medicine implies a deep understanding of inter-individual differences in health and disease that are due to genetic and environmental factors. To acquire such understanding there is a need for the implementation ...
  • Minimal spatial heterogeneity in chronic lymphocytic leukemia at diagnosis 

    Nadeu, Ferran; Royo, Romina; Maura, Francesco; Dawson, Kevin J; Dueso Barroso, Ana; Aymerich, Marta; Pinyol, Magda; Beà, Sílvia; López Guillermo, Armando; Delgado, Julio; Puente, Xosé S.; Campo, Elías (Springer Nature, 2020)
    Article
    Restricted access - publisher's policy
  • Using GARDEN-NET and ChAseR to explore human haematopoietic 3D chromatin interaction networks 

    Madrid, Miguel; Raineri, Emanuele; Cao, Tran Bich Ngoc; Pancaldi, Vera (Oxford University Press (OUP), 2020-05-07)
    Article
    Open Access
    We introduce an R package and a web-based visualization tool for the representation, analysis and integration of epigenomic data in the context of 3D chromatin interaction networks. GARDEN-NET allows for the projection of ...

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