Now showing items 1-10 of 10

    • 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 ...
    • High-speed exhaustive 3-locus interaction epistasis analysis on FPGAs 

      Kässens, Jan Christian; Wienbrandt, Lars; González-Domínguez, Jorge; Schmidt, Bertil; Schimmler, Manfred (Elsevier B.V., 2015-07)
      [Abstract]: Epistasis, the interaction between genes, has become a major topic in molecular and quantitative genetics. It is believed that these interactions play a significant role in genetic variations causing complex ...
    • 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, ...
    • 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 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 ...
    • 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 ...
    • Speed and accuracy improvement of higher-order epistasis detection on CUDA-enabled GPUs 

      Jünger, Daniel; Hundt, Christian; González-Domínguez, Jorge; Schmidt, Bertil (Springer, 2017)
      [Abstract]: The discovery of higher-order epistatic interactions is an important task in the field of genome wide association studies which allows for the identification of complex interaction patterns between multiple ...