Listar GI-GAC - Artigos por título
Mostrando ítems 131-150 de 181
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Parallel Pairwise Epistasis Detection on Heterogeneous Computing Architectures
(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 ... -
Parallel simulation of Brownian dynamics on shared memory systems with OpenMP and Unified Parallel C
(Springer New York LLC, 2013-09)[Abstract] The simulation of particle dynamics is an essential method to analyze and predict the behavior of molecules in a given medium. This work presents the design and implementation of a parallel simulation of Brownian ... -
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 ... -
Parallelization of shallow water simulations on current multi-threaded systems
(SAGE Journals, 2013-11)[Abstract]: In this work, several parallel implementations of a numerical model of pollutant transport on a shallow water system are presented. These parallel implementations are developed in two phases. First, the sequential ... -
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 ... -
Parameter estimation in large-scale systems biology models: a parallel and self-adaptive cooperative strategy
(BioMed Central Ltd., 2017)[Abstract] Background The development of large-scale kinetic models is one of the current key issues in computational systems biology and bioinformatics. Here we consider the problem of parameter estimation in nonlinear ... -
PARamrfinder: detecting allele-specific DNA methylation on multicore clusters
(Springer, 2024-01)[Abstract]: The discovery of Allele-Specific Methylation (ASM) is an important research field in biology as it regulates genomic imprinting, which has been identified as the cause of some genetic diseases. Nevertheless, ... -
ParBiBit: Parallel tool for binary biclustering on modern distributed-memory systems
(PLoS, 2018)[Abstract]: Biclustering techniques are gaining attention in the analysis of large-scale datasets as they identify two-dimensional submatrices where both rows and columns are correlated. In this work we present ParBiBit, ... -
ParDRe: faster parallel duplicated reads removal tool for sequencing studies
(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 ... -
ParRADMeth: Identification of Differentially Methylated Regions on Multicore Clusters
(IEEE, 2023)[Abstract]: The discovery of Differentially Methylated (DM) regions is an important research field in biology, as it can help to anticipate the risk of suffering from specific diseases. Nevertheless, the high computational ... -
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 ... -
PATO: genome-wide prediction of lncRNA-DNA triple helices
(Oxford University Press, 2023-03)[Abstract]: Motivation: Long non-coding RNA (lncRNA) plays a key role in many biological processes. For instance, lncRNA regulates chromatin using different molecular mechanisms, including direct RNA-DNA hybridization via ... -
Performance analysis of HPC applications in the cloud
(Elsevier BV * North-Holland, 2013-01)[Abstract] The scalability of High Performance Computing (HPC) applications depends heavily on the efficient support of network communications in virtualized environments. However, Infrastructure as a Service (IaaS) providers ... -
Performance Evaluation of Data-Intensive Computing Applications on a Public IaaS Cloud
(Oxford University Press, 2016)[Abstract] The advent of cloud computing technologies, which dynamically provide on-demand access to computational resources over the Internet, is offering new possibilities to many scientists and researchers. Nowadays, ... -
Performance Evaluation of Sparse Matrix Products in UPC
(Springer New York LLC, 2013-04)[Abstract] Unified Parallel C (UPC) is a Partitioned Global Address Space (PGAS) language whose popularity has increased during the last years owing to its high programmability and reasonable performance through an efficient ... -
Population based metaheuristics in Spark: Towards a general framework using PSO as a case study
(Elsevier, 2024-03)[Abstract]: Over the years metaheuristics have been successfully applied to optimization problems in many real-world applications. The increasing complexity and scale of the problems addressed has posed new challenges to ... -
Portable and efficient FFT and DCT algorithms with the Heterogeneous Butterfly Processing Library
(Elsevier, 2019-03)[Abstract]: The existence of a wide variety of computing devices with very different properties makes essential the development of software that is not only portable among them, but which also adapts to the properties of ... -
Prediction of missing sequences and branch lengths in phylogenomic data
(Oxford University Press, 2016-01-05)[Abstract] Motivation: The presence of missing data in large-scale phylogenomic datasets has negative effects on the phylogenetic inference process. One effect that is caused by alignments with missing per-gene or per-partition ... -
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 ... -
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 ...
