Now showing items 1-20 of 73

    • A FM-index transformation to enable large k-steps 

      Langarita, Rubén; Armejach Sanosa, Adrià; Moreto Planas, Miquel (Barcelona Supercomputing Center, 2019-05-07)
      Conference report
      Open Access
    • A hardware/software co-design of K-mer counting using a CAPI-enabled FPGA 

      Haghi, Abbas; Álvarez Martí, Lluc; Polo Bardés, Jorda; Diamantopoulos, Dionysios; Hagleitner, Christoph; Moreto Planas, Miquel (Institute of Electrical and Electronics Engineers (IEEE), 2020)
      Conference report
      Open Access
      Advances in Next Generation Sequencing (NGS) technologies have caused the proliferation of genomic applications to detect DNA mutations and guide personalized medicine. These applications have an enormous computational ...
    • A model of large-scale proteome evolution 

      Vicente Solé, Ricardo; Pastor Satorras, Romualdo; Smith, E; Kepler, T .B. (2002-03)
      Article
      Open Access
      The next step in the understanding of the genome organization, after the determination of complete sequences, involves proteomics. The proteome includes the whole set of protein-protein interactions, and two recent independent ...
    • A multilayer network approach to elucidate severity in Congenital Myasthenic Syndromes 

      Núñez-Carpintero, Iker; Cirillo, Davide; Valencia, Alfonso (Barcelona Supercomputing Center, 2019-05-07)
      Conference report
      Open Access
    • A novel MMR pathway in prokaryotes 

      Rojas, Ana (Barcelona Supercomputing Center, 2019)
      Other
      Open Access
    • A user guide for the online exploration and visualization of PCAWG data 

      Goldman, Mary J.; Zhang, Junjun; Fonseca, Nuno A.; Cortés-Ciriano, Isidro; Xiang, Qian; Craft, Brian; Piñeiro-Yáñez, Elena; O'connor, Brian D.; Bazant, Wojciech; Barrera, Elisabet; Muñoz-Pomer, Alfonso; Petryszak, Robert; Füllgrabe, Anja; Al-Shahrour, Fatima; Keays, Maria; Haussler, David; Weinstein, John N; Huber, Wolfgang; Park, Peter J.; Papatheodorou, Elena; Valencia, Alfonso; Zhu, Jingchun; Ferretti, Vincent; Vazquez, Miguel (Springer Nature, 2020)
      Article
      Open Access
      The Pan-Cancer Analysis of Whole Genomes (PCAWG) project generated a vast amount of whole-genome cancer sequencing resource data. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which ...
    • Accelerating K-mer Frequency Counting with GPU and Non-Volatile Memory 

      Cadenelli, Nicola; Polo Cantero, José; Carrera Pérez, David (2018)
      Conference report
      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 ...
    • Accelerating K-mer Frequency Counting with GPU and Non-Volatile Memory 

      Cadenelli, Nicola; Polo Bardés, 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 ...
    • Adding security and privacy to genomic information representation 

      Delgado Mercè, Jaime; Llorente Viejo, Silvia; Naro, Daniel (2019)
      Article
      Open Access
      Provision of security and privacy to genomic data is a key issue in current genomic information representation. Existing formats do not give a solution to these issues (or they provide a partial one), so new solutions are ...
    • Adding security and privacy to genomic information representation 

      Delgado Mercè, Jaime; Llorente Viejo, Silvia; Naro, Daniel (IOS Press, 2019)
      Conference lecture
      Open Access
      Provision of security and privacy to genomic data is a key issue in current genomic information representation. Existing formats do not give a solution to these issues (or they provide a partial one), so new solutions are ...
    • Assessment of kinship detection using RNA-seq data 

      Blay Magriñá, Natàlia; Casas, Eduard; Galván Femenía, Iván; Graffelman, Jan; de Cid, Rafael; Vavouri, Tanya (2019-12-02)
      Article
      Open Access
      Analysis of RNA sequencing (RNA-seq) data from related individuals is widely used in clinical and molecular genetics studies. Prediction of kinship from RNA-seq data would be useful for confirming the expected relationships ...
    • Big data analytics for obesity prediction 

      Bilal, Ahsan (Universitat Politècnica de Catalunya, 2018-04-26)
      Master thesis
      Open Access
      Covenantee:   Fundació Eurecat
      Feature selection is an important technique to find the most relevant features. Apache Spark is a big data processing framework but unable to cope with approx. 0.74 million features in our Obesity dataset. However, we ...
    • BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data 

      Hospital, Adam; Andrio, Pau; Cugnasco, Cesare; Codo, Laia; Becerra Fontal, Yolanda; Dans, Pablo D.; Battistini, Federica; Torres Viñals, Jordi; Goñi, Ramon; Orozco, Modesto; Gelpí, Josep Lluís (2016-01-04)
      Article
      Open Access
      Molecular dynamics simulation (MD) is, just behind genomics, the bioinformatics tool that generates the largest amounts of data, and that is using the largest amount of CPU time in supercomputing centres. MD trajectories ...
    • Building from scratch: de novo gene birth 

      Albà, M. Mar (Barcelona Supercomputing Center, 2019)
      Other
      Open Access
    • Chromatin 3D organization revealed by chromatin networks: gene-regulation, replication, and beyond 

      Pancaldi, Vera (Barcelona Supercomputing Center, 2019)
      Other
      Open Access
    • Class c gpcr metabotropic glutamate receptors subtype discrimination using computation intelligence methods 

      Halka, Christiana (Universitat Politècnica de Catalunya, 2014-11-16)
      Master thesis
      Open Access
    • Complex networks in genomics and proteomics 

      Vicente Solé, Ricardo; Pastor Satorras, Romualdo (Wiley-VCH, 2003)
      Part of book or chapter of book
      Restricted access - publisher's policy
      Complex interacting networks are observed in systems from such diverse areas as physics, biology, economics, ecology, and computer science. For example, economic or social interactions often organize themselves in complex ...
    • Compressed sparse FM-index: Fast sequence alignment using large K-steps 

      Langarita Benítez, Rubén; Armejach Sanosa, Adrià; Setoain, Javier; Ibáñez Marín, Pablo Enrique; Alastruey Benedé, Jesús; Moreto Planas, Miquel (2020-06-05)
      Article
      Open Access
      The FM-index is a data structure used in genomics for exact search of input sequences over large reference genomes. Algorithms based on the FM-index show an irregular memory access pattern, resulting in a memory bound ...
    • Compression-based classification of biological sequences and structures via the Universal Similarity Metric: experimental assessment 

      Ferragina, Paolo; Giancarlo, Raffaele; Greco, Valentina; Manzini, Giovanni; Valiente Feruglio, Gabriel Alejandro (2007-07)
      Article
      Open Access
      Similarity of sequences is a key mathematical notion for Classification and Phylogenetic studies in Biology. It is currently primarily handled using alignments. However, the alignment methods seem inadequate for post-genomic ...
    • Computational approaches for personalised medicine: from crowdsourced machine learning to dynamic mechanistic models 

      Sáez-Rodríguez, Julio (Barcelona Supercomputing Center, 2019)
      Other
      Open Access