Now showing items 1-20 of 100

    • 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 edit-distance sequence alignment on GPU using the wavefront algorithm 

      Aguado Puig, Quim; Marco-Sola, Santiago; Moure López, Juan Carlos; Castells Rufas, David; Álvarez Martí, Lluc; Espinosa Morales, Antonio; Moreto Planas, Miquel (Institute of Electrical and Electronics Engineers (IEEE), 2022-06-10)
      Article
      Open Access
      Sequence alignment remains a fundamental problem with practical applications ranging from pattern recognition to computational biology. Traditional algorithms based on dynamic programming are hard to parallelize, require ...
    • Accelerating pairwise sequence alignment on GPUs using the Wavefront Algorithm 

      Aguado Puig, Quim (Universitat Politècnica de Catalunya, 2022-10-19)
      Master thesis
      Open Access
      Advances in genomics and sequencing technologies demand faster and more scalable analysis methods that can process longer sequences with higher accuracy. However, classical pairwise alignment methods, based on dynamic ...
    • 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 ...
    • An FPGA accelerator of the wavefront algorithm for genomics pairwise alignment 

      Haghi, Abbas; Marco-Sola, Santiago; Álvarez Martí, Lluc; Diamantopoulos, Dionysios; Hagleitner, Christoph; Moreto Planas, Miquel (Institute of Electrical and Electronics Engineers (IEEE), 2021)
      Conference report
      Open Access
      In the last years, advances in next-generation sequencing technologies have enabled the proliferation of genomic applications that guide personalized medicine. These applications have an enormous computational cost due to ...
    • Analysis and improvement of security and privacy techniques for genomic information 

      García Perez, José Antonio (Universitat Politècnica de Catalunya, 2021-10-28)
      Master thesis
      Open Access
      The purpose of this thesis is to review the current literature of privacy preserving techniques for genomic information on the last years. Based on the analysis, we propose a long-term classification system for the reviewed ...
    • Analysis of transposon dynamics in Prunus species using a pangenome approach 

      Serrano Jorcano, Daniel (Universitat Politècnica de Catalunya, 2021-09-02)
      Bachelor thesis
      Open Access
      Covenantee:   Centre for Research in Agricultural Genomics
      Transposable elements (TEs) are repetitive DNA sequences found in all prokaryotic and eukaryotic organisms. They are able to move from one genome location to another and replicate in the genome, producing mutations and ...
    • AnchorWave: Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism, and whole-genome duplication 

      Song, Baoxing; Marco-Sola, Santiago; Moreto Planas, Miquel; Johnson, Lynn; Buckler, Edward S.; Stitzer, Michelle C. (2022-01-04)
      Article
      Open Access
      Millions of species are currently being sequenced, and their genomes are being compared. Many of them have more complex genomes than model systems and raise novel challenges for genome alignment. Widely used local alignment ...
    • 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 ...
    • ATM germline variants in a young adult with chronic lymphocytic leukemia: 8 years of genomic evolution 

      Royo, Romina; Magnano, Laura; Delgado, Julio; Ruiz Gil, Sara; Gelpí, Josep Ll.; Heyn, Holger; Taylor, Malcom A.; Stankovic, Tatjana; Puente, Xose S.; Nadeu, Ferran; Campo, Elías (Springer Nature, 2022-06)
      Article
      Open Access
    • 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