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Servet: A Benchmark Suite for Autotuning on Multicore Clusters
(Institute of Electrical and Electronics Engineers, 2010-05-24)
[Abstract] MapReduce is a powerful tool for processing large data sets used by many applications running in distributed environments. However, despite the increasing number of computationally intensive problems that require ...
Toxo: A Library for Calculating Penetrance Tables of High-Order Epistasis Models
(BioMed Central Ltd., 2020-04-09)
[Abstract]
Background
Epistasis is defined as the interaction between different genes when expressing a specific phenotype. The most common way to characterize an epistatic relationship is using a penetrance table, which ...
BetaGPU: Harnessing GPU power for parallelized beta distribution functions
(Elsevier, 2025-02)
[Abstract]: The efficient computation of Beta distribution functions, particularly the Probability Density Function (PDF) and Cumulative Distribution Function (CDF), is critical in various scientific fields, including ...
A SIMD Algorithm for the Detection of Epistatic Interactions of Any Order
(Elsevier, 2022)
[Abstract] Epistasis is a phenomenon in which a phenotype outcome is determined by the interaction of genetic variation at two or more loci and it cannot be attributed to the additive combination of effects corresponding ...
PyToxo: a Python tool for calculating penetrance tables of high-order epistasis models
(BMC, 2022)
[Abstract] Background
Epistasis is the interaction between different genes when expressing a certain phenotype. If epistasis involves more than two loci it is called high-order epistasis. High-order epistasis is an area ...
Parallelization of ARACNe, an Algorithm for the Reconstruction of Gene Regulatory Networks
(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 ...
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 ...
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 ...
