Browsing by Author "Schmidt, Bertil"
Now showing items 1-11 of 11
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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 ... -
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, ... -
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 ...