Now showing items 1-20 of 31

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

      González-Domínguez, Jorge; Marques, Osni A.; Martín, María J.; 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. ...
    • A SIMD Algorithm for the Detection of Epistatic Interactions of Any Order 

      Ponte-Fernández, Christian; González-Domínguez, Jorge; Martín, María J. (Elsevier, 2022)
      [Abstract] Epistasis is a phenomenon in which a phenotype outcome is determined by the interaction of genetic variation at two or more loci and it cannot be attributed to the additive combination of effects corresponding ...
    • Acceleration of a Feature Selection Algorithm Using High Performance Computing 

      Beceiro, Bieito; González-Domínguez, Jorge; Touriño, Juan (MDPI AG, 2020-09-01)
      [Abstract] Feature selection is a subfield of data analysis that is on reducing the dimensionality of datasets, so that subsequent analyses over them can be performed in affordable execution times while keeping the same ...
    • Analysis of I/O Performance on an Amazon EC2 Cluster Compute and High I/O Platform 

      Expósito, Roberto R.; López Taboada, Guillermo; Ramos Garea, Sabela; González-Domínguez, Jorge; Touriño, Juan; Doallo, Ramón (Springer Netherlands, 2013-12)
      [Abstract] Cloud computing is currently being explored by the scientific community to assess its suitability for High Performance Computing (HPC) environments. In this novel paradigm, compute and storage resources, as well ...
    • Automatic mapping of parallel applications on multicore architectures using the Servet benchmark suite 

      González-Domínguez, Jorge; López Taboada, Guillermo; Fraguela, Basilio B.; Martín, María J.; 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 ...
    • Communication avoiding and overlapping for numerical linear algebra 

      Georganas, Evangelos; González-Domínguez, Jorge; Solomonik, Edgar; Zheng, Yili; Touriño, Juan; Yelick, Katherine (IEEE Computer Society, 2013-02-25)
      [Abstract] To efficiently scale dense linear algebra problems to future exascale systems, communication cost must be avoided or overlapped. Communication-avoiding 2.5D algorithms improve scalability by reducing inter-processor ...
    • Evaluation of Existing Methods for High-Order Epistasis Detection 

      Ponte-Fernández, Christian; González-Domínguez, Jorge; Carvajal-Rodriguez, Antonio; Martín, María J. (Institute of Electrical and Electronics Engineers, 2020-10-15)
      [Abstract] Finding epistatic interactions among loci when expressing a phenotype is a widely employed strategy to understand the genetic architecture of complex traits in GWAS. The abundance of methods dedicated to the ...
    • Fast search of third-order epistatic interactions on CPU and GPU clusters 

      Ponte-Fernández, Christian; González-Domínguez, Jorge; María José, Martín Santamaría (Sage Publications Ltd., 2019-05-27)
      [Abstract] Genome-Wide Association Studies (GWASs), analyses that try to find a link between a given phenotype (such as a disease) and genetic markers, have been growing in popularity in the recent years. Relations between ...
    • 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 ...
    • Hybrid CPU/GPU Acceleration of Detection of 2-SNP Epistatic Interactions in GWAS 

      González-Domínguez, Jorge; Schmidt, Bertil; Kässens, Jan Christian; Wienbrandt, Lars (Springer, 2014-08)
      [Abstract] High-throughput genotyping technologies allow the collection of up to a few million genetic markers (such as SNPs) of an individual within a few minutes of time. Detecting epistasis, such as 2-SNP interactions, ...
    • 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 ...
    • MPI-dot2dot: A Parallel Tool to Find DNA Tandem Repeats on Multicore Clusters 

      González-Domínguez, Jorge; Martín Martínez, José Manuel; Expósito, Roberto R. (Springer, 2022)
      [Abstract] Tandem Repeats (TRs) are segments that occur several times in a DNA sequence, and each copy is adjacent to other. In the last few years, TRs have gained significant attention as they are thought to be related ...
    • 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, María J. (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 ...
    • Parallelization of ARACNe, an Algorithm for the Reconstruction of Gene Regulatory Networks 

      Casal, Uxía; González-Domínguez, Jorge; Martín, María J. (M D P I AG, 2019-07-31)
      [Abstract] Gene regulatory networks are graphical representations of molecular regulators that interact with each other and with other substances in the cell to govern the gene expression. There are different computational ...
    • 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 ...