ListarGrupo de Arquitectura de Computadores (GAC) por tema "Bioinformatics"
Mostrando ítems 1-13 de 13
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bioScience: A new python science library for high-performance computing bioinformatics analytics
(Elsevier Ltd, 2024)[Abstract]: BioScience is an advanced Python library designed to satisfy the growing data analysis needs in the field of bioinformatics by leveraging High-Performance Computing (HPC). This library encompasses a vast multitude ... -
Fast search of third-order epistatic interactions on CPU and GPU clusters
(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 ... -
High-speed exhaustive 3-locus interaction epistasis analysis on FPGAs
(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
(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
(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, ... -
MPI-dot2dot: A Parallel Tool to Find DNA Tandem Repeats on Multicore Clusters
(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 ... -
Multimethod Optimization for Reverse Engineering of Complex Biological Networks
(Association for Computing Machinery, 2018-09)[Abstract] Optimization problems appears in different areas of science and engineering. This paper considers the general problem of reverse engineering in computational biology by means of mixed-integer nonlinear dynamic ... -
Parallel and Scalable Short-Read Alignment on Multi-Core Clusters Using UPC++
(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 ... -
Parallelizing Epistasis Detection in GWAS on FPGA and GPU-Accelerated Computing Systems
(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 ... -
parSRA: A framework for the parallel execution of short read aligners on compute clusters
(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 ... -
Performance Optimization of a Parallel Error Correction Tool
(MDPI, 2021)[Abstract] Due to the continuous development in the field of Next Generation Sequencing (NGS) technologies that have allowed researchers to take advantage of greater genetic samples in less time, it is a matter of relevance ... -
pRIblast: A highly efficient parallel application for comprehensive lncRNA–RNA interaction prediction
(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 ... -
SeQual: Big Data Tool to Perform Quality Control and Data Preprocessing of Large NGS Datasets
(Institute of Electrical and Electronics Engineers, 2020-08-07)[Abstract] This paper presents SeQual, a scalable tool to efficiently perform quality control of large genomic datasets. Our tool currently supports more than 30 different operations (e.g., filtering, trimming, formatting) ...