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Scalable PGAS collective operations in NUMA clusters
(Springer New York LLC, 2014-12)
[Abstract] The increasing number of cores per processor is turning manycore-based systems in pervasive. This involves dealing with multiple levels of memory in non uniform memory access (NUMA) systems and processor cores ...
GPU-accelerated exhaustive search for third-order epistatic interactions in case–control studies
(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 ...
Parallel definition of tear film maps on distributed-memory clusters for the support of dry eye diagnosis
(Elsevier Ireland Ltd., 2017)
[Abstract] Background and objectives
The analysis of the interference patterns on the tear film lipid layer is a useful clinical test to diagnose dry eye syndrome. This task can be automated with a high degree of accuracy ...
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 ...
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 ...
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 ...
Parallel feature selection for distributed-memory clusters
(2019)
[Abstract]: Feature selection is nowadays an extremely important data mining stage in the field of machine learning due to the appearance of problems of high dimensionality. In the literature there are numerous feature ...
BigDEC: A multi-algorithm Big Data tool based on the k-mer spectrum method for scalable short-read error correction
(Elsevier, 2024-05)
[Abstract]: Despite the significant improvements in both throughput and cost provided by modern Next-Generation Sequencing (NGS) platforms, sequencing errors in NGS datasets can still degrade the quality of downstream ...
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, ...
SMusket: Spark-based DNA error correction on distributed-memory systems
(Elsevier B.V., 2020)
[Abstract]: Next-Generation Sequencing (NGS) technologies have revolutionized genomics research over the last decade, bringing new opportunities for scientists to perform groundbreaking biological studies. Error correction ...
