Browsing by Author "Capella Gutiérrez, Salvador"Més informació

Now showing items 1-19 of 19

    • A catalogue of 863 Rett-syndrome-causing MECP2 mutations and lessons learned from data integration 

      Ehrhart, Friederike; Jacobsen, Annika; Rigau, Maria; Bosio, Mattia; Kaliyaperumal, Rajaram; Laros, Jeroen F. J.; Willighagen, Egon L.; Valencia, Alfonso; Roos, Marco; Capella Gutiérrez, Salvador; Curfs, Leopold M. G.; Evelo, Chris T. (Springer Nature, 2021)
      Article
      Open Access
      Rett syndrome (RTT) is a rare neurological disorder mostly caused by a genetic variation in MECP2. Making new MECP2 variants and the related phenotypes available provides data for better understanding of disease mechanisms ...

    • Automatic, efficient and scalable provenance registration for FAIR HPC workflows 

      Sirvent Pardell, Raül; Conejero Bañón, Francisco Javier; Lordan Gomis, Francesc; Ejarque Artigas, Jorge; Rodríguez Navas, Laura; Fernández González, José María; Capella Gutiérrez, Salvador; Badia Sala, Rosa Maria (Institute of Electrical and Electronics Engineers (IEEE), 2022)
      Conference report
      Open Access
      Provenance registration is becoming more and more important, as we increase the size and number of experiments performed using computers. In particular, when provenance is recorded in HPC environments, it must be efficient ...

    • COVID-19 Flow-Maps an open geographic information system on COVID-19 and human mobility for Spain 

      Ponce De Leon, Miguel; Valle, Javier del; Fernández González, Jose María; Bernardo, Marc; Cirillo, Davide; Sanchez Valle, Jon; Smith, Matthew; Capella Gutiérrez, Salvador; Gullón, Tania; Valencia, Alfonso (Nature Research, 2021)
      Article
      Open Access
      COVID-19 is an infectious disease caused by the SARS-CoV-2 virus, which has spread all over the world leading to a global pandemic. The fast progression of COVID-19 has been mainly related to the high contagion rate of the ...

    • DEBBIE: the open access database of experimental scaffolds and biomaterials built using an automated text mining pipeline 

      Corvi, Javier Omar; McKitrick, Austin; Fernández González, José María; Fuenteslópez, Carla V.; Gelpí Buchaca, Josep Lluís; Ginebra Molins, Maria Pau; Capella Gutiérrez, Salvador; Hakimi, Osnat (John Wiley & sons, 2023-10-06)
      Article
      Restricted access - publisher's policy
      Covenantee:   Barcelona Supercomputing Center / University of Oxford / Universitat de Barcelona / Universitat Internacional de Catalunya
      Biomaterials research output has experienced an exponential increase over the last three decades. The majority of research is published in the form of scientific articles and is therefore available as unstructured text, ...

    • Detection of early seeding of Richter transformation in chronic lymphocytic leukemia 

      Nadeu, Ferran; Royo, Romina; Massoni Badosa, Ramon; Playa Albinyana, Heribert; Garcia Torre, Beatriz; Dueso Barroso, Ana; Capella Gutiérrez, Salvador; Gelpi, Josep; Torrents, David (Nature Research, 2022)
      Article
      Open Access
      Richter transformation (RT) is a paradigmatic evolution of chronic lymphocytic leukemia (CLL) into a very aggressive large B cell lymphoma conferring a dismal prognosis. The mechanisms driving RT remain largely unknown. ...

    • FAIRification of genomic track metadata [version 1; peer review: 2 approved] 

      Gundersen, Sveinung; Boddu, Sanjay; Capella Gutiérrez, Salvador; Drabløs, Finn; Fernández González, Jose María; Kompova, Radmila; Taylor, Kieron; Titov, Dmytro; Zerbino, Daniel; Hovig, Eivind (F1000 Research, 2021)
      Article
      Open Access
      Background: Many types of data from genomic analyses can be represented as genomic tracks, i.e. features linked to the genomic coordinates of a reference genome. Examples of such data are epigenetic DNA methylation data, ...

    • FAIRsoft - A practical implementation of FAIR principles for research software 

      Martín del Pico, Eva; Capella Gutiérrez, Salvador; Gelpi, Josep (Barcelona Supercomputing Center, 2022-05)
      Conference report
      Open Access
      Computational tools are increasingly becoming constitutive parts of scientific research, from experimentation and data collection to the dissemination and storage of results. Unfortunately, however, research software is ...

    • FAIRsoft—a practical implementation of FAIR principles for research software 

      Martin del Pico, Eva; Gelpi, Josep; Capella Gutiérrez, Salvador (Oxford University Press, 2024)
      Article
      Open Access
      Abstract Motivation: Software plays a crucial and growing role in research. Unfortunately, the computational component in Life Sciences research is often challenging to reproduce and verify. It could be undocumented, opaque, ...

    • 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 ...

    • Open Sciences principles for Life Sciences: is it everything about data? 

      Capella Gutiérrez, Salvador (Universitat Politècnica de Catalunya, 2023-10-25)
      Conference lecture
      Open Access

    • Perspectives on automated composition of workflows in the life sciences [version 1; peer review: 2 approved] 

      Lamprecht, Anna-Lena; Palmblad, Magnus; Ison, Jon; Schwämmle, Veit; Al Manir, Mohammad Sadnan; Capella Gutiérrez, Salvador (F1000Research, 2021)
      Article
      Open Access
      Scientific data analyses often combine several computational tools in automated pipelines, or workflows. Thousands of such workflows have been used in the life sciences, though their composition has remained a cumbersome ...

    • PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies 

      Fuentes, Diego; Molina, Manuel; Chorostecki, Uciel; Capella Gutiérrez, Salvador; Marcet Houben, Marina; Gabaldón, Toni (Oxford University Press, 2021)
      Article
      Open Access
      PhylomeDB is a unique knowledge base providing public access to minable and browsable catalogues of pre-computed genome-wide collections of annotated sequences, alignments and phylogenies (i.e. phylomes) of homologous ...

    • Rare disease research workflow using multilayer networks elucidates the molecular determinants of severity in Congenital Myasthenic Syndromes 

      Nuñez Carpintero, Iker; Rigau, Maria; Bosio, Mattia; O’Connor, Emily; Spendiff, Sally; Capella Gutiérrez, Salvador; Cirillo, Davide; Valencia, Alfonso (Nature Research, 2024)
      Article
      Open Access
      Exploring the molecular basis of disease severity in rare disease scenarios is a challenging task provided the limitations on data availability. Causative genes have been described for Congenital Myasthenic Syndromes (CMS), ...

    • Reaching a modular, domain-agnostic and containerized development in biomedical Natural Language Processing systems. 

      Corvi, Javier; Gelpi, Josep; Capella Gutiérrez, Salvador (Barcelona Supercomputing Center, 2022-05)
      Conference report
      Open Access
      The last century saw an exponential increase in scientific publications in the biomedical domain. Despite the potential value of this knowledge; most of this data is only available as unstructured textual literature, which ...

    • RegulonDB v12.0: a comprehensive resource of transcriptional regulation in E. coli K-12 

      Salgado, Heladia; Gama Castro, Socorro; Lara, Paloma; Mejia Almonte, Citlalli; Alarcón Carranza, Gabriel; Capella Gutiérrez, Salvador; Gelpi, Josep (Oxford University Press, 2023)
      Article
      Open Access
      RegulonDB is a database that contains the most comprehensive corpus of knowledge of the regulation of transcription initiation of Escherichia coli K-12, including data from both classical molecular biology and high-throughput ...

    • Systematic assessment of long-read RNA-seq methods for transcript identification and quantification 

      Pardo Palacios, Francisco J.; Wang, Dingjie; Reese, Fairlie; Diekhans, Mark; Carbonell Sala, Sílvia; Capella Gutiérrez, Salvador (Nature Research, 2024)
      Article
      Open Access
      The Long-read RNA-Seq Genome Annotation Assessment Project Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. Using different protocols and sequencing platforms, the ...

    • The eTRANSAFE project on translational safety assessment through integrative knowledge management: achievements and perspectives 

      Pognan, François; Steger-Hartmann, Thomas; Díaz, Carlos; Blomberg, Niklas; Bringezu, Frank; Briggs, Katharine; Callegaro, Giulia; Capella Gutiérrez, Salvador; Centeno, Emilio; Corvi, Javier; Drew, Philip; Drewe, William C.; Fernández González, Jose María; Furlong, Laura I.; Guney, Emre; Kors, Jan A.; Mayer, Miguel Angel; Pastor, Manuel; Piñero, Janet; Ramírez-Anguita, Juan Manuel; Ronzano, Francesco; Rowell, Philip; Saüch-Pitarch, Josep; Valencia, Alfonso; Water, Bob van de; Lei, Johan van der; Mulligen, Erik van; Sanz, Ferran (MDPI, 2021)
      Article
      Open Access
      eTRANSAFE is a research project funded within the Innovative Medicines Initiative (IMI), which aims at developing integrated databases and computational tools (the eTRANSAFE ToxHub) that support the translational safety ...

    • The landscape of expression and alternative splicing variation across human traits 

      García Pérez, Raquel; Ramírez Cardeñosa, José Miguel; Ripoll Cladellas, Aida; Chazarra Gil, Rubén; Oliveros Díez, Winona; Soldatkina, Oleksandra; Bosio, Mattia; Rognon, Paul Joris Denis; Capella Gutiérrez, Salvador; Calvo Llorca, Miguel; Reverter Comes, Ferran; Guigo Serra, Roderic; Aguet, François; Ferreira, Pedro G.; Ardlie, Kristin G.; Mele Messeguer, Marta (Elsevier, 2023-01-11)
      Article
      Open Access
      Understanding the consequences of individual transcriptome variation is fundamental to deciphering human biology and disease. We implement a statistical framework to quantify the contributions of 21 individual traits as ...

    • The quest for orthologs benchmark service and consensus calls in 2020 

      Altenhoff, Adrian M; Garrayo Ventas, Javier; Consentino, Salvatore; Emms, David; Glover, Natasha M; Hernández Plaza, Ana; Nevers, Yannis; Szklarczyk, Damian; Fernández González, Jose María; Codó, Laia; Gelpi, Josep; Huertas Cepas, Jaime; Iwasaki, Wataru; Kelly, Steven; Lecompte, Odile; Muffato, Matthieu; Martín, María Jesús; Capella Gutiérrez, Salvador; Thomas, Paul D.; Sonnhammer, Erik; Dessimoz, Christophe; the Quest for Orthologs Consortium (Oxford University Press (OUP), 2020-05-06)
      Article
      Open Access
      The identification of orthologs—genes in different species which descended from the same gene in their last common ancestor—is a prerequisite for many analyses in comparative genomics and molecular evolution. Numerous ...