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Applying dynamic balancing to improve the performance of MPI parallel genomics applications
(Association for Computing Machinery (ACM), 2024-05-21)
[Absctract]: Genomics applications are becoming more and more important in the field of bioinformatics, as they allow researchers to extract meaningful information from the huge amount of data generated by the new sequencing ...
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 ...
Parallel-FST: A feature selection library for multicore clusters
(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 ...
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 ...
MSAProbs-MPI: parallel multiple sequence aligner for distributed-memory systems
(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 ...
HSRA: Hadoop-based spliced read aligner for RNA sequencing data
(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 ...
UPCBLAS: a library for parallel matrix computations in Unified Parallel C
(John Wiley & Sons Ltd., 2012-09-25)
[Abstract] The popularity of Partitioned Global Address Space (PGAS) languages has increased during the last years thanks to their high programmability and performance through an efficient exploitation of data locality, ...
Evaluation of Existing Methods for High-Order Epistasis Detection
(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 ...
ScalaParBiBit: Scaling the Binary Biclustering in Distributed-Memory Systems
(SpringerLink, 2021-03-19)
[Abstract] Biclustering is a data mining technique that allows us to find groups of rows and columns that are highly correlated in a 2D dataset. Although there exist several software applications to perform biclustering, ...
A 2D algorithm with asymmetric workload for the UPC conjugate gradient method
(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. ...
