Exploració per tema "Genòmica -- Informàtica"

Ara es mostren els items 1-12 de 12

    • A multi-objective genetic algorithm to find active modules in multiplex biological networks 

      Novoa del Toro, Elva María; Mezura Montes, Efrén; Vignes, Matthieu; Térézol, Morgane; Magdinier, Frédérique; Tichit, Laurent; Baudot, Anais (Public Library of Science (PLoS), 2021)
      Article
      Accés obert
      The identification of subnetworks of interest—or active modules—by integrating biological networks with molecular profiles is a key resource to inform on the processes perturbed in different cellular conditions. We here ...

    • Assessing the accuracy of contact and distance predictions in CASP14 

      Ruiz Serra, Victoria; Pontes, Camila; Milanetti, Edoardo; Kryshtafovych, Andriy; Lepore, Rosalba; Valencia, Alfonso (Wiley, 2021)
      Article
      Accés obert
      We present the results of the assessment of the intramolecular residue–residue contact and distance predictions from groups participating in the 14th round of the CASP experiment. The performance of contact prediction ...

    • Bioinformatics methods for the genomics and metabolomics analysis of immune-mediated inflammatory diseases 

      Alonso, Arnald (Universitat Politècnica de Catalunya, 2015-09-28)
      Tesi
      Accés obert
      During the last decade, genomics have been widely used to the characterization of the molecular basis of common diseases. Genome-wide association studies (GWAS) have been highly successful in characterizing the genetic ...

    • CROSSMAPPER: estimating cross-mapping rates and optimizing experimental design in multi-species sequencing studies 

      Hovhannisyan, Hrant; Hafez, Ahmed; Llorens, Carlos; Gabaldon, Toni (Oxford University Press, 2020)
      Article
      Accés obert
      Motivation Numerous sequencing studies, including transcriptomics of host-pathogen systems, sequencing of hybrid genomes, xenografts, mixed species systems, metagenomics and meta-transcriptomics, involve samples containing ...

    • Dissemination and visualisation of biological data 

      Gel Moreno, Bernat (Universitat Politècnica de Catalunya, 2014-07-29)
      Tesi
      Accés obert
      With the recent advent of various waves of technological advances, the amount of biological data being generated has exploded. As a consequence of this data deluge, new challenges have emerged in the field of biological ...

    • GStream: improving SNP and CNV coverage on genome-wide association studies 

      Alonso Pastor, Arnald; Marsal Barril, Sara; Tortosa Mendez, Raul; Canela Xandri, Oriol; Julià Cano, Antonio (2013-07-03)
      Article
      Accés obert
      We present GStream, a method that combines genome-wide SNP and CNV genotyping in the Illumina microarray platform with unprecedented accuracy. This new method outperforms previous well-established SNP genotyping software. ...

    • IgCaller for reconstructing immunoglobulin gene rearrangements and oncogenic translocations from whole-genome sequencing in lymphoid neoplasms 

      Nadeu, Ferran; Mas-de-les-Valls, Rut; Navarro, Alba; Royo, Romina; Martín, Silvia; Villamor, Neus; Suárez-Cisneros, Helena; Mares, Rosó; Lu, Junyan; Enjuanes, Anna; Rivas-Delgado, Alfredo; Aymerich, Marta; Baumann, Tycho; Colomer, Dolors; Delgado, Julio; Morin, Ryan D.; Zenz, Thorsten; Puente, Xose S.; Campbell, Peter J.; Beà, Sílvia; Maura, Francesco; Campo, Elías (Springer Nature, 2020-07)
      Article
      Accés obert
      Immunoglobulin (Ig) gene rearrangements and oncogenic translocations are routinely assessed during the characterization of B cell neoplasms and stratification of patients with distinct clinical and biological features, ...

    • MetaPhOrs 2.0: integrative, phylogeny-based inference of orthology and paralogy across the tree of life 

      Chorostecki, Uciel; Molina, Manuel; Pryszcz, Leszek P.; Gabaldon, Toni (Oxford University Press (OUP), 2020-04-28)
      Article
      Accés obert
      Inferring homology relationships across genes in different species is a central task in comparative genomics. Therefore, a large number of resources and methods have been developed over the years. Some public databases ...

    • 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
      Accés obert
      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 ...

    • 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
      Accés obert
      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 ...

    • The transcriptional aftermath in two independently formed hybrids of the opportunistic pathogen candida orthopsilosis 

      Hovhannisyan, Hrant; Saus, Ester; Ksiezopolska, Ewa; Gabaldón, Toni (American Society for Microbiology, 2020)
      Article
      Accés obert
      Interspecific hybridization can drive evolutionary adaptation to novel environments. The Saccharomycotina clade of budding yeasts includes many hybrid lineages, and hybridization has been proposed as a source for new ...

    • TIGER: The gene expression regulatory variation landscape of human pancreatic islets 

      Alonso, Lorena; Piron, Anthony; Morán, Ignasi; Guindo Martínez, Marta; Bonàs Guarch, Sílvia; Royo, Romina; Puiggròs, Montserrat; Amela, Ramon; Mercader, Josep M.; Torrents, David (Cell Press, 2021)
      Article
      Accés obert
      Genome-wide association studies (GWASs) identified hundreds of signals associated with type 2 diabetes (T2D). To gain insight into their underlying molecular mechanisms, we have created the translational human pancreatic ...