Browsing by Author "González-Domínguez, Jorge"

Now showing items 21-40 of 51

    • 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 ...

    • Multithreaded and Spark parallelization of feature selection filters 

      Eiras-Franco, Carlos; Bolón-Canedo, Verónica; Ramos Garea, Sabela; González-Domínguez, Jorge; Alonso-Betanzos, Amparo; Touriño, Juan (2016)
      [Abstract]: Vast amounts of data are generated every day, constituting a volume that is challenging to analyze. Techniques such as feature selection are advisable when tackling large datasets. Among the tools that provide ...

    • 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, 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 feature selection for distributed-memory clusters 

      González-Domínguez, Jorge; Bolón-Canedo, Verónica; Freire, Borja; Touriño, Juan (2019)
      [Abstract]: Feature selection is nowadays an extremely important data mining stage in the field of machine learning due to the appearance of problems of high dimensionality. In the literature there are numerous feature ...

    • 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 ...

    • Parallel-FST: A feature selection library for multicore clusters 

      Beceiro, Bieito; González-Domínguez, Jorge; Touriño, Juan (Elsevier, 2022-11)
      [Abstract]: Feature selection is a subfield of machine learning focused on reducing the dimensionality of datasets by performing a computationally intensive process. This work presents Parallel-FST, a publicly available ...

    • 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 ...

    • PARamrfinder: detecting allele-specific DNA methylation on multicore clusters 

      Fernández Fraga, Alejandro; González-Domínguez, Jorge; Martín, María J. (Springer, 2024-01)
      [Abstract]: The discovery of Allele-Specific Methylation (ASM) is an important research field in biology as it regulates genomic imprinting, which has been identified as the cause of some genetic diseases. Nevertheless, ...

    • ParBiBit: Parallel tool for binary biclustering on modern distributed-memory systems 

      González-Domínguez, Jorge; Expósito, Roberto R. (PLoS, 2018)
      [Abstract]: Biclustering techniques are gaining attention in the analysis of large-scale datasets as they identify two-dimensional submatrices where both rows and columns are correlated. In this work we present ParBiBit, ...

    • 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 ...

    • ParRADMeth: Identification of Differentially Methylated Regions on Multicore Clusters 

      Fernández Fraga, Alejandro; González-Domínguez, Jorge; Touriño, Juan (IEEE, 2023)
      [Abstract]: The discovery of Differentially Methylated (DM) regions is an important research field in biology, as it can help to anticipate the risk of suffering from specific diseases. Nevertheless, the high computational ...

    • parSRA: A framework for the parallel execution of short read aligners on compute clusters 

      González-Domínguez, Jorge; Hundt, Christian; Schmidt, Bertil (2018)
      [Abstract]: The growth of next generation sequencing datasets poses as a challenge to the alignment of reads to reference genomes in terms of both accuracy and speed. In this work we present parSRA, a parallel framework ...

    • PATO: genome-wide prediction of lncRNA-DNA triple helices 

      Amatria Barral, Iñaki; González-Domínguez, Jorge; Touriño, Juan (Oxford University Press, 2023-03)
      [Abstract]: Motivation: Long non-coding RNA (lncRNA) plays a key role in many biological processes. For instance, lncRNA regulates chromatin using different molecular mechanisms, including direct RNA-DNA hybridization via ...

    • Performance Evaluation of Sparse Matrix Products in UPC 

      González-Domínguez, Jorge; García-López, Óscar; Taboada, Guillermo L.; Martín, María J.; 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 ...

    • pRIblast: A highly efficient parallel application for comprehensive lncRNA–RNA interaction prediction 

      Amatria Barral, Iñaki; González-Domínguez, Jorge; Touriño, Juan (Elsevier, 2023-01)
      [Abstract]: Long non-coding RNAs (lncRNAs) play a key role in several biological processes and scientists are constantly trying to come up with new strategies to elucidate their functions. One common approach to characterize ...