Now showing items 1-17 of 17

  • Accelerating K-mer Frequency Counting with GPU and Non-Volatile Memory 

    Cadenelli, Nicola; Polo, Jordà; Carrera, David (IEEE, 2018-02-15)
    Conference lecture
    Open Access
    The emergence of Next Generation Sequencing (NGS) platforms has increased the throughput of genomic sequencing and in turn the amount of data that needs to be processed, requiring highly efficient computation for its ...
  • Automatic identification of informative regions with epigenomic changes associated to hematopoiesis 

    Carrillo-de-Santa-Pau, Enrique; Juan, David; Pancaldi, Vera; Were, Felipe; Martin-Subero, Ignacio; Rico, Daniel; Valencia, Alfonso (Oxford University Press, 2017-09-19)
    Article
    Open Access
    Hematopoiesis is one of the best characterized biological systems but the connection between chromatin changes and lineage differentiation is not yet well understood. We have developed a bioinformatic workflow to generate ...
  • Big data analytics for obesity prediction 

    Bilal, Hasan; Vellido Alcacena, Alfredo; Ribas Ripoll, Vicent (IOS Press, 2018)
    Part of book or chapter of book
    Open Access
    Feature selection (FS) is essential for the analysis of genomic datasets with millions of features. In such context, Big Data tools are paramount, but the use of standard machine learning models is limited for data with ...
  • Evolving protein interaction networks through gene duplication 

    Pastor Satorras, Romualdo; Smith, E; Solé, Ricard Vicenç (2003-05-21)
    Article
    Open Access
    The topology of the proteome map revealed by recent large-scale hybridization methods has shown that the distribution of protein–protein interactions is highly heterogeneous, with many proteins having few edges while a few ...
  • Gelada vocal sequences follow Menzerath's linguistic law 

    Gustison, Morgan; Semple, Stuart; Ferrer Cancho, Ramon; Bergman, Thore (2016-03-04)
    Article
    Open Access
    Identifying universal principles underpinning diverse natural systems is a key goal of the life sciences. A powerful approach in addressing this goal has been to test whether patterns consistent with linguistic laws are ...
  • High evolutionary turnover of satellite families in Caenorhabditis 

    Subirana Torrent, Juan A.; Albà, M. Mar; Messeguer Peypoch, Xavier (2015-10-05)
    Article
    Open Access
    Background: The high density of tandem repeat sequences (satellites) in nematode genomes and the availability of genome sequences from several species in the group offer a unique opportunity to better understand the ...
  • Histogram based Hierarchical Data Representation for Microarray Classification 

    Kottath, Sandeep (Universitat Politècnica de Catalunya, 2012-09-03)
    Master thesis
    Open Access
    [ANGLÈS] A general framework for microarray classification relying on histogram based hierarchical clustering is proposed in this work. It produces precise and reliable classifiers based on a two-step approach. In the first ...
  • How long are long tandem repeats? A challenge for current methods of whole-genome sequence assembly: The case of satellites in caenorhabditis elegans 

    Subirana Torrent, Juan A.; Messeguer Peypoch, Xavier (2018-10-16)
    Article
    Open Access
    Repetitive genome regions have been difficult to sequence, mainly because of the comparatively small size of the fragments used in assembly. Satellites or tandem repeats are very abundant in nematodes and offer an excellent ...
  • Metadata to Describe Genomic Information 

    Delgado, Jaime; Naro, Daniel; Llorente, Silvia; Gelpí, Josep Ll.; Royo, Romina (IOS Press, 2018)
    Part of book or chapter of book
    Open Access
    Interoperable metadata is key for the management of genomic information. We propose a flexible approach that we contribute to the standardization by ISO/IEC of a new format for efficient and secure compressed storage and ...
  • 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 ...
  • Next generation sequencing to dissect the genetic architecture of KNG1 and F11 loci using factor XI levels as an intermediate phenotype of thrombosis 

    Martin-Fernandez, Laura; Gavidia Bovadilla, Giovana Elizabeth; Corrales, Irene; Brunel, Helena; Ramirez, Lorena; Lopez Esteban, Sonia; Carlos Souto, Juan; Vidal, Francisco; Soria, José Manuel (2017-04-26)
    Article
    Open Access
    Venous thromboembolism is a complex disease with a high heritability. There are significant associations among Factor XI (FXI) levels and SNPs in the KNG1 and F11 loci. Our aim was to identify the genetic variation of KNG1 ...
  • Un prototipo de codificador MPEG-G 

    Iqbal, Omair (Universitat Politécnica de Catalunya / Universitat Politècnica de Catalunya, 2018-06)
    Bachelor thesis
    Open Access
    El objetivo de este proyecto es implementar una primera versión de estándar de datos MPEG-G para uso interno de la Universidad Universidad Politécnica de Cataluña (UPC) y proponer mejoras para el desarrollo futuro.
  • Random models of Menzerath-Altmann law in genomes 

    Baixeries i Juvillà, Jaume; Hernández Fernández, Antonio; Ferrer Cancho, Ramon (2011-12-16)
    Article
    Open Access
    Recently, a random breakage model has been proposed to explain the negative correlation between mean chromosome length and chromosome number that is found in many groups of species and is consistent with Menzerath–Altmann ...
  • Study of digital signal processing tools to infer gene regulatory networks from microarrays 

    Bellot Pujalte, Pau (Universitat Politècnica de Catalunya, 2012-09-07)
    Master thesis
    Open Access
    [ANGLÈS] Since the mid-1990's, the field of genomic signal processing has exploded due to the development of DNA microarray technology, which made possible the measurement of mRNA expression of thousands of genes in parallel. ...
  • System for turnkey analysis of semi-automated genome annotations 

    Asenjo Ponce de León, Marc (Universitat Politècnica de Catalunya, 2018-07-03)
    Bachelor thesis
    Open Access
    Covenantee:  Princess Margaret Cancer Centre
    Un software ha sigut desenvolupat per ajudar en l'anàlisi de segmentacions del genoma, descarregant dades, executant anàlisis i resumint els resultats en una sola visualització que és fàcil d'interpretar i de la qual els ...
  • Ten steps to get started in Genome Assembly and Annotation 

    Dominguez del Angel, Victoria; Hjerde, Erik; Sterck, Lieven; Capella-Gutierrez, Salvador; Notredame, Cederic; Vinnere Pettersson, Olga; Amselem, Joelle; Bouri, Laurent; Bocs, Stephanie; Klopp, Christophe; Gibrat, Jean-Francois; Vlasova, Anna; Leskosek, Brane L.; Soler, Lucile; Binzer-Panchal, Mahesh; Lantz, Henrik (F1000Research, 2018-02-05)
    Article
    Open Access
    As a part of the ELIXIR-EXCELERATE efforts in capacity building, we present here 10 steps to facilitate researchers getting started in genome assembly and genome annotation. The guidelines given are broadly applicable, ...
  • When is Menzerath-Altmann law mathematically trivial? A new approach 

    Ferrer Cancho, Ramon; Hernández Fernández, Antonio; Baixeries i Juvillà, Jaume; Debowski, Lukasz; Macutek, Jan (2014-12-12)
    Article
    Open Access
    Menzerath’s law, the tendency of Z (the mean size of the parts) to decrease as X (the number of parts) increases, is found in language, music and genomes. Recently, it has been argued that the presence of the law in genomes ...