Now showing items 1-17 of 17

    • A 2D algorithm with asymmetric workload for the UPC conjugate gradient method 

      González Domínguez, Jorge; Marques, Osni A.; Martín Santamaría, María José; Touriño, Juan (Springer New York LLC, 2014)
      [Abstract] This paper examines four different strategies, each one with its own data distribution, for implementing the parallel conjugate gradient (CG) method and how they impact communication and overall performance. ...
    • Automatic mapping of parallel applications on multicore architectures using the Servet benchmark suite 

      González Domínguez, Jorge; López Taboada, Guillermo; Fraguela, Basilio B.; Martín Santamaría, María José; Touriño, Juan (Pergamon Press, 2012-03)
      [Abstract] Servet is a suite of benchmarks focused on detecting a set of parameters with high influence on the overall performance of multicore systems. These parameters can be used for autotuning codes to increase their ...
    • GPU-accelerated exhaustive search for third-order epistatic interactions in case–control studies 

      González Domínguez, Jorge; Schmidt, Bertil (Elsevier Ltd, 2015)
      [Abstract] Interest in discovering combinations of genetic markers from case–control studies, such as Genome Wide Association Studies (GWAS), that are strongly associated to diseases has increased in recent years. Detecting ...
    • HSRA: Hadoop-based spliced read aligner for RNA sequencing data 

      Expósito, Roberto R.; González Domínguez, Jorge; Touriño, Juan (Public Library of Science, 2018-07-31)
      [Abstract] Nowadays, the analysis of transcriptome sequencing (RNA-seq) data has become the standard method for quantifying the levels of gene expression. In RNA-seq experiments, the mapping of short reads to a reference ...
    • Large-scale genome-wide association studies on a GPU cluster using a CUDA-accelerated PGAS programming model 

      González Domínguez, Jorge; Kässens, Jan Christian; Wienbrandt, Lars; Schmidt, Bertil (Sage Publications Ltd., 2015)
      [Abstract] Detecting epistasis, such as 2-SNP interactions, in genome-wide association studies (GWAS) is an important but time consuming operation. Consequently, GPUs have already been used to accelerate these studies, ...
    • MarDRe: efficient MapReduce-based removal of duplicate DNA reads in the cloud 

      Expósito, Roberto R.; Veiga, Jorge; González Domínguez, Jorge; Touriño, Juan (Oxford University Press, 2017)
      [Abstract] This article presents MarDRe, a de novo cloud-ready duplicate and near-duplicate removal tool that can process single- and paired-end reads from FASTQ/FASTA datasets. MarDRe takes advantage of the widely adopted ...
    • MSAProbs-MPI: parallel multiple sequence aligner for distributed-memory systems 

      González Domínguez, Jorge; Liu, Yongchao; Touriño, Juan; Schmidt, Bertil (Oxford University Press, 2016)
      [Abstracts] MSAProbs is a state-of-the-art protein multiple sequence alignment tool based on hidden Markov models. It can achieve high alignment accuracy at the expense of relatively long runtimes for large-scale input ...
    • Parallel and Scalable Short-Read Alignment on Multi-Core Clusters Using UPC++ 

      Liu, Yongchao; Schmidt, Bertil; González Domínguez, Jorge (Johannes Gutenberg University Mainz, 2016)
      [Abstract]: The growth of next-generation sequencing (NGS) datasets poses a challenge to the alignment of reads to reference genomes in terms of alignment quality and execution speed. Some available aligners have been shown ...
    • Parallel definition of tear film maps on distributed-memory clusters for the support of dry eye diagnosis 

      González Domínguez, Jorge; Remeseiro López, Beatriz; Martín Santamaría, María José (Elsevier Ireland Ltd., 2017)
      [Abstract] Background and objectives The analysis of the interference patterns on the tear film lipid layer is a useful clinical test to diagnose dry eye syndrome. This task can be automated with a high degree of accuracy ...
    • Parallel Pairwise Epistasis Detection on Heterogeneous Computing Architectures 

      González Domínguez, Jorge; Ramos Garea, Sabela; Touriño, Juan; Schmidt, Bertil (Institute of Electrical and Electronics Engineers, 2016-08)
      [Abstract] Development of new methods to detect pairwise epistasis, such as SNP-SNP interactions, in Genome-Wide Association Studies is an important task in bioinformatics as they can help to explain genetic influences on ...
    • Parallelizing Epistasis Detection in GWAS on FPGA and GPU-Accelerated Computing Systems 

      González Domínguez, Jorge; Wienbrandt, Lars; Kässens, Jan Christian; Ellinghaus, David; Schimmler, Manfred; Schmidt, Bertil (Institute of Electrical and Electronics Engineers, 2015)
      [Abstract] High-throughput genotyping technologies (such as SNP-arrays) allow the rapid collection of up to a few million genetic markers of an individual. Detecting epistasis (based on 2-SNP interactions) in Genome-Wide ...
    • ParDRe: faster parallel duplicated reads removal tool for sequencing studies 

      González Domínguez, Jorge; Schmidt, Bertil (Oxford University Press, 2016)
      [Abstract] Summary: Current next generation sequencing technologies often generate duplicated or near-duplicated reads that (depending on the application scenario) do not provide any interesting biological information but ...
    • Performance Evaluation of Sparse Matrix Products in UPC 

      González Domínguez, Jorge; García-López, Óscar; López Taboada, Guillermo; Martín Santamaría, María José; Touriño, Juan (Springer New York LLC, 2013-04)
      [Abstract] Unified Parallel C (UPC) is a Partitioned Global Address Space (PGAS) language whose popularity has increased during the last years owing to its high programmability and reasonable performance through an efficient ...
    • Performance evaluation of sparse matrix products in UPC 

      González Domínguez, Jorge; García-López, Óscar; López Taboada, Guillermo; Martín Santamaría, María José; Touriño, Juan (Springer New York LLC, 2013)
      [Abstract] Unified Parallel C (UPC) is a Partitioned Global Address Space (PGAS) language whose popularity has increased during the last years owing to its high programmability and reasonable performance through an efficient ...
    • Scalable PGAS collective operations in NUMA clusters 

      Mallón, Damián A.; Teijeiro, Carlos; González Domínguez, Jorge; López Taboada, Guillermo; Gómez, Andrés (Springer New York LLC, 2014-12)
      [Abstract] The increasing number of cores per processor is turning manycore-based systems in pervasive. This involves dealing with multiple levels of memory in non uniform memory access (NUMA) systems and processor cores ...
    • The Servet 3.0 benchmark suite: characterization of network performance degradation 

      González Domínguez, Jorge; Martín Santamaría, María José; López Taboada, Guillermo; Expósito, Roberto R.; Touriño, Juan (Pergamon Press, 2013-11)
      [Abstract] Servet is a suite of benchmarks focused on extracting a set of parameters with high influence on the overall performance of multicore clusters. These parameters can be used to optimize the performance of parallel ...
    • UPCBLAS: a library for parallel matrix computations in Unified Parallel C 

      González Domínguez, Jorge; Martín Santamaría, María José; López Taboada, Guillermo; Touriño, Juan; Doallo Biempica, Ramón; Mallón, Damián A.; Wibecan, Brian (John Wiley & Sons Ltd., 2012-09-25)
      [Abstract] The popularity of Partitioned Global Address Space (PGAS) languages has increased during the last years thanks to their high programmability and performance through an efficient exploitation of data locality, ...