Browsing by Author "Torrents, David"

Now showing items 1-20 of 21

    • Adaptation to environmental factors shapes the organization of regulatory regions in microbial communities 

      Fernandez, Leyden; Mercader, Josep M.; Planas-Fèlix, Mercè; Torrents, David (BioMed Central, 2014-10-08)
      Article
      Open Access
      Background: It has been shown in a number of metagenomic studies that the addition and removal of specific genes have allowed microbiomes to adapt to specific environmental conditions by losing and gaining specific functions. ...

    • Adherence to a supplemented Mediterranean diet drives changes in the gut microbiota of HIV-1-infected individuals 

      Pastor Ibáñez, Roque; Blanco Heredia, Juan; Etcheverry, Florencia; Sánchez Palomino, Sonsoles; Torrents, David (MDPI, 2021)
      Article
      Open Access
      Objective: The health effects of a supplemented Mediterranean diet (SMD) with extra-virgin olive oil (EVOO) and nuts are well documented in non-HIV-infected individuals. We hypothesised that the benefits of an SMD could ...

    • Classification of retrotransposition during somatic variant calling in cancer genomes 

      Valls Margarit, Jordi; Torrents, David (Barcelona Supercomputing Center, 2017-05-04)
      Other
      Open Access

    • 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. ...

    • Enhancer hijacking determines extrachromosomal circular MYCN amplicon architecture in neuroblastoma 

      Helmsauer, Konstantin; Valieva, Maria E.; Ali, Salaheddine; Chamorro González, Rocío; Rodriguez-Fos, Elias; Puiggròs, Montserrat; Torrents, David (Springer Nature, 2020)
      Article
      Open Access
      MYCN amplification drives one in six cases of neuroblastoma. The supernumerary gene copies are commonly found on highly rearranged, extrachromosomal circular DNA (ecDNA). The exact amplicon structure has not been described ...

    • Epigenomic analysis detects aberrant super-enhancer DNA methylation in human cancer 

      Heyn, Holger; Vidal, Enrique; Ferreira, Humberto J.; Vizoso, Miguel; Sayols, Sergi; Gomez, Antonio; Moran, Sebastian; Boque-Sastre, Raquel; Guil, Sonia; Martinez-Cardus, Anna; Lin, Charles Y.; Romina, Royo; Sanchez-Mut, Jose V.; Martinez, Ramon; Gut, Marta; Torrents, David; Orozco, Modesto; Gut, Ivo; Young, Richard A.; Esteller, Manel (BioMed Central, 2016-01-26)
      Article
      Open Access
      Background One of the hallmarks of cancer is the disruption of gene expression patterns. Many molecular lesions contribute to this phenotype, and the importance of aberrant DNA methylation profiles is increasingly recognized. ...

    • Functional implications of the structural genomic rearrangements in cancer 

      Delgado-Serrano, Luisa; Torrents, David (Barcelona Supercomputing Center, 2017-05-04)
      Other
      Open Access

    • GCAT|Panel, a comprehensive structural variant haplotype map of the Iberian population from high-coverage whole-genome sequencing 

      Valls Margarit, Jordi; Galván Femenía, Iván; Matías Sánchez, Daniel; Blay, Natalia; Puiggròs, Montserrat; Salvoro, Cecilia; Amela, Ramon; Torrents, David (Oxford University Press, 2022-02)
      Article
      Open Access
      The combined analysis of haplotype panels with phenotype clinical cohorts is a common approach to explore the genetic architecture of human diseases. However, genetic studies are mainly based on single nucleotide variants ...

    • Genomic instability promoted by expression of human transposase-derived gene 

      Rodríguez-Fos, Elias; González, Santi; Puiggros, Montserrat; Henssen, Anton G.; Kentsis, Alex; Torrents, David (Barcelona Supercomputing Center, 2015-05-05)
      Conference report
      Open Access
      DNA Transposases are enzymes that recognize and catalyze the movement of mobile elements in the human genome known as transposons. There are abundant transposase-derived genes in the human genome that have been conserved ...

    • Germline NPAT inactivating variants as cause of hereditary colorectal cancer 

      Terradas, Mariona; Schubert, Stephanie A.; Viana Errasti, Julen; Ruano, Dina; Aiza, Gemma; Torrents, David (Springer Nature, 2024)
      Article
      Open Access
      Two independent exome sequencing initiatives aimed to identify new genes involved in the predisposition to nonpolyposis colorectal cancer led to the identification of heterozygous loss-of-function variants in NPAT, a gene ...

    • GUIDANCE: an integrated framework for large-scale genome and phenome-wide association studies on parallel computing platforms 

      Guindo-Martínez, Marta; Sánchez, Friman; Bonàs-Guarch, Silvia; Puiggròs, Montserrat; Ejarque, Jorge; Díaz, Carlos; Tejedor, Enric; Badia Sala, Rosa Maria; Mercader, Josep M.; Torrents, David (Barcelona Supercomputing Center, 2017-05-04)
      Other
      Open Access

    • Identification and characterization of recurrent deletions in the human genome promoted by expression of transposase-derived gene across different tumor types 

      Rodriguez-Fos, Elías; González, Santi; Puiggròs, Montserrat; Henssen, Anton G.; Kentsis, Alex; Torrents, David (Barcelona Supercomputing Center, 2017-05-04)
      Other
      Open Access

    • Impact of transcriptome and gut microbiome on the response of HIV-1 infected individuals to a dendritic cell-based HIV therapeutic vaccine 

      Pastor Ibáñez, Roque; Díez Fuertes, Francisco; Sánchez Palomino, Sonsoles; Alcamí, Jose; Plana, Montserrat; Torrents, David; Leal, Lorna; García, Felipe (MDPI, 2021)
      Article
      Open Access
      Therapeutic vaccines based on dendritic cells offer a good approach to HIV-specific T-cell responses and partial control of the viral load after antiretroviral therapy interruption. The aim of the present study was to ...

    • In search of complex disease risk through genome wide association studies 

      Alonso, Lorena; Morán, Ignasi; Salvoro, Cecilia; Torrents, David (MDPI, 2021)
      Article
      Open Access
      The identification and characterisation of genomic changes (variants) that can lead to human diseases is one of the central aims of biomedical research. The generation of catalogues of genetic variants that have an impact ...

    • Multitrait genome association analysis identifies new susceptibility genes for human anthropometric variation in the GCAT cohort 

      Galván Femenía, Iván; Obón-Santacana, Mireia; Piñeyro, David; Guindo-Martinez, Marta; Duran, Xavier; Carreras, Anna; Pluvinet, Raquel; Velasco, Juan; Ramos, Laia; Aussó, Susanna; Puig, Lluis; Perucho, Manuel; Torrents, David; Moreno, Victor; Sumoy, Lauro; de Cid, Rafael (BMJ Publishing Group, 2018-08-30)
      Article
      Open Access
      Background Heritability estimates have revealed an important contribution of SNP variants for most common traits; however, SNP analysis by single-trait genome-wide association studies (GWAS) has failed to uncover their ...

    • ONCOLINER: A new solution for monitoring, improving, and harmonizing somatic variant calling across genomic oncology centers 

      Martin, Rodrigo; Gaitán, Nicolas; Jarlier, Frédéric; Feuerbach, Lars; Soyres, Henri de; Arbones, Marc; Puiggròs, Montserrat; Ferriz, Alvaro; Gonzalez, Asier; Capella Gutiérrez, Salvador; Royo, Romina; Torrents, David (Elsevier, 2024-09-11)
      Article
      Open Access
      The characterization of somatic genomic variation associated with the biology of tumors is fundamental for cancer research and personalized medicine, as it guides the reliability and impact of cancer studies and genomic-based ...

    • Pan-cancer analysis of whole genomes 

      The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium; Royo, Romina; Vazquez, Miguel; Bosio, Mattia; Valencia, Alfonso; Torrents, David; Gelpi, Josep; Milovanovic, Ana; Puiggròs, Montserrat; Bartolome, Javier; Vicente, David; Fink, J. Lynn; Dueso Barroso, Ana; Villasante, Izar; Bartolomé Rodriguez, Javier (Nature Research, 2020)
      Article
      Open Access
      Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale1,2,3. Here we report the integrative analysis of 2,658 ...

    • 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
      Open Access
      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 ...

    • Re-analysis of public genetic data reveals a rare X-chromosomal variant associated with type 2 diabetes 

      Bonàs-Guarch, Sílvia; Guindo-Martínez, Marta; Miguel-Escalada, Irene; Grarup, Niels; Sebastian, David; Rodriguez-Fos, Elias; Sánchez, Friman; Planas-Fèlix, Mercè; Cortes-Sánchez, Paula; González, Santi; Timshel, Pascal; Pers, Tune H.; Morgan, Claire C.; Moran, Ignasi; Atla, Goutham; González, Juan R.; Puiggros, Montserrat; Martí, Jonathan; Andersson, Ehm A.; Díaz, Carlos; Badia Sala, Rosa Maria; Udler, Miriam; Leong, Aaron; Kaur, Varindepal; Flannick, Jason; Jorgensen, Torben; Linneberg, Allan; Jorgensen, Marit E.; Witte, Daniel R.; Christensen, Cramer; Brandslund, Ivan; Appel, Emil V.; Scott, Robert A.; Luan, Jian' an; Langenberg, Claudia; Wareham, Nicholas J.; Pedersen, Oluf; Zorzano, Antonio; Florez, Jose C.; Hansen, Torben; Ferrer, Jorge; Mercader, Josep M.; Torrents, David (Nature Publishing Group, 2018-01-22)
      Article
      Open Access
      The reanalysis of existing GWAS data represents a powerful and cost-effective opportunity to gain insights into the genetics of complex diseases. By reanalyzing publicly available type 2 diabetes (T2D) genome-wide association ...

    • SMuFin2: generating and implementing new and more efficient search engines integrated in particular hardware architectures 

      Planas-Felix, Mercè; Polo Bardés, Jordà; Barberá-Mourelle, Alejandro; Cadenelli, Nicola; Carrera, David; Torrents, David (Barcelona Supercomputing Center, 2017-05-04)
      Other
      Open Access