Browsing by Author "Rambla de Argila, Jordi"

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  • A quality control portal for sequencing data deposited at the European genome-phenome archive
    Fernández-Orth, Dietmar; Rueda, Manuel; Singh, Babita, 1986-; Moldes, Mauricio; Jene, Aina; Ferri, Marta; Vasallo, Claudia; Fromont, Lauren A.; Navarro i Cuartiellas, Arcadi, 1969-; Rambla de Argila, Jordi (Oxford University Press, 2022)
    Since its launch in 2008, the European Genome-Phenome Archive (EGA) has been leading the archiving and distribution of human identifiable genomic data. In this regard, one of the community concerns is the potential usability ...
  • Analysis of five gene sets in chimpanzees suggests decoupling between the action of selection on protein-coding and on noncoding elements
    Santpere Baró, Gabriel, 1981-; Carnero-Montoro, Elena, 1985-; Petit, Natalia; Serra, François; Hvilsom, Christina; Rambla de Argila, Jordi; Heredia Genestar, José María, 1985-; Halligan, Daniel L.; Dopazo, Hernán; Navarro i Cuartiellas, Arcadi, 1969-; Bosch Fusté, Elena (Oxford University Press, 2015)
    We set out to investigate potential differences and similarities between the selective forces acting upon the coding and noncoding regions of five different sets of genes defined according to functional and evolutionary ...
  • Beacon v2 and Beacon networks: A "lingua franca" for federated data discovery in biomedical genomics, and beyond
    Rambla de Argila, Jordi; Baudis, Michael; Ariosa, Roberto; Beck, Timothy; Fromont, Lauren A.; Navarro i Cuartiellas, Arcadi, 1969-; Paloots, Rahel; Rueda, Manuel; Saunders, Gary; Singh, Babita, 1986-; Spalding, J. Dylan; Törnoos, Juha; Vasallo, Claudia; Veal, Colin D.; Brookes, Anthony J. (Wiley, 2022)
    Beacon is a basic data discovery protocol issued by the Global Alliance for Genomics and Health (GA4GH). The main goal addressed by version 1 of the Beacon protocol was to test the feasibility of broadly sharing human ...
  • Consent codes: Maintaining consent in an ever-expanding open science ecosystem
    Dyke, Stephanie O. M.; Connor, Kathleen; Nembaware, Victoria; Munung, Nchangwi S.; Reinold, Kathy; Kerry, Giselle; Mbiyavanga, Mamana; Zass, Lyndon; Moldes, Mauricio; Das, Samir; Davis, John M.; Rambla de Argila, Jordi; Spalding, J. Dylan; Evans, Alan C.; Mulder, Nicola; Karamchandani, Jason (Springer, 2023)
    We previously proposed a structure for recording consent-based data use 'categories' and 'requirements' - Consent Codes - with a view to supporting maximum use and integration of genomic research datasets, and reducing ...
  • Consent codes: upholding standard data use conditions
    Dyke, Stephanie O. M.; Philippakis, Anthony A.; Rambla de Argila, Jordi; Paltoo, Dina N.; Luetkemeier, Erin S.; Knoppers, Bartha M.; Brookes, Anthony J.; Spalding, J. Dylan; Thompson, Mark; Roos, Marco; Boycott, Kym M.; Brudno, Michael; Hurles, Matthew; Rehm, Heidi L.; Matern, Andreas; Fiume, Marc; Sherry, Stephen T. (Public Library of Science (PLoS), 2016)
    A systematic way of recording data use conditions that are based on consent permissions as found in the datasets of the main public genome archives (NCBI dbGaP and EMBL-EBI/CRG EGA).
  • Federated discovery and sharing of genomic data using Beacons
    Fiume, Marc; Rambla de Argila, Jordi; Torre, Sabela de la; Scollen, Serena (Nature Research, 2019)
  • International federation of genomic medicine databases using GA4GH standards
    Thorogood, Adrian; Rehm, Heidi L.; Goodhand, Peter; Page, Angela J. H.; Joly, Yann; Baudis, Michael; Rambla de Argila, Jordi; Navarro i Cuartiellas, Arcadi, 1969-; Nyronen, Tommi H.; Linden, Mikael; Dove, Edward S.; Fiume, Marc; Brudno, Michael; Cline, Melissa S.; Bimey, Ewan (Elsevier, 2021)
    We promote a shared vision and guide for how and when to federate genomic and health-related data sharing, enabling connections and insights across independent, secure databases. The GA4GH encourages a federated approach ...
  • Inversions and genomic differentiation after secondary contact: when drift contributes to maintenance, not loss, of differentiation
    Rafajlović, Marina; Rambla de Argila, Jordi; Feder, Jeffrey L.; Navarro i Cuartiellas, Arcadi, 1969-; Faria, Rui (Wiley, 2021)
    Due to their effects on reducing recombination, chromosomal inversions may play an important role in speciation by establishing and/or maintaining linked blocks of genes causing reproductive isolation (RI) between populations. ...
  • Machine learning methods applied to genotyping data capture interactions between single nucleotide variants in late onset Alzheimer's disease
    Arnal, Magdalena; Bini, Giorgio; Fernández Orth, Dietmar; Samaras, Eleftherios; Kassis, Maya; Aisopos, Fotis; Rambla de Argila, Jordi; Paliouras, George; Garrard, Peter; Giambartolomei, Claudia; Tartaglia, Gian Gaetano (Wiley Open Access, 2022)
    Introduction: Genome-wide association studies (GWAS) in late onset Alzheimer's disease (LOAD) provide lists of individual genetic determinants. However, GWAS do not capture the synergistic effects among multiple genetic ...
  • The data use ontology to streamline responsible access to human biomedical datasets
    Lawson, Jonathan; Jene, Aina; Rambla de Argila, Jordi; Courtot, Mélanie (Elsevier, 2021)
    Human biomedical datasets that are critical for research and clinical studies to benefit human health also often contain sensitive or potentially identifying information of individual participants. Thus, care must be taken ...
  • The European Genome-phenome Archive in 2021
    Freeberg, Mallory Ann; Fromont, Lauren A.; D'Altri, Teresa, 1984-; Jene, Aina; Moldes, Mauricio; Ariosa, Roberto; Fernández-Orth, Dietmar; Haziza, Frédéric; Martinez Llobet, Oscar; Milla, Gemma; Rueda, Manuel; Singh, Babita, 1986-; Torre, Sabela de la; Uyan, Umuthan; Vasallo, Claudia; Guigó Serra, Roderic; Navarro i Cuartiellas, Arcadi, 1969-; Rambla de Argila, Jordi (Oxford University Press, 2022)
    The European Genome-phenome Archive (EGA - https://ega-archive.org/) is a resource for long term secure archiving of all types of potentially identifiable genetic, phenotypic, and clinical data resulting from biomedical ...
  • The European Genome-phenome Archive of human data consented for biomedical research
    Lappalainen, Ilkka; Carreño Torres, Angel; Rambla de Argila, Jordi; Martinez Llobet, Oscar; Sitges Puy, Marc; Alberich, Mario; Torre, Sabela de la; Navarro i Cuartiellas, Arcadi, 1969-; Flicek, Paul (Nature Publishing Group, 2015)
    The European Genome-phenome Archive (EGA) is a permanent archive that promotes the distribution and sharing of genetic and phenotypic data consented for specific approved uses but not fully open, public distribution. The ...
  • The RD-Connect Genome-Phenome Analysis Platform: Accelerating diagnosis, research, and gene discovery for rare diseases
    Laurie, Steven, 1973-; Piscia, Davide; Matalonga, Leslie; Corvò, Alberto; Fernández Callejo, Marcos; Garcia-Linares, Carles; Hernandez-Ferrer, Carles, 1987-; Luengo, Cristina; Martínez, Inés; Papakonstantinou Ntalis, Anastasios; Picó-Amador, Daniel; Protasio, Joan; Tonda, Raúl; Bayés, Mònica; Bullich, Gemma; Camps-Puchadas, Jordi; Paramonov, Ida; Trotta, Jean-Remi; Pérez Jurado, Luis Alberto; Rambla de Argila, Jordi; Gut, Ivo Glynne; Lochmüller, Hanns; Beltran, Sergi (Wiley, 2022)
    Rare disease patients are more likely to receive a rapid molecular diagnosis nowadays thanks to the wide adoption of next-generation sequencing. However, many cases remain undiagnosed even after exome or genome analysis, ...