2016
DOI: 10.1177/1094342016668567
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Abstract: Availability: This is the author's manuscriptAbstract Recent advances in molecular biology and bioinformatics techniques brought to an explosion of the information about the spatial organisation of the DNA in the nucleus of a cell. High-throughput molecular biology techniques provide a genome-wide capture of the spatial organization of chromosomes at unprecedented scales, which permit to identify physical interactions between genetic elements located throughout a genome. This important information is however h… Show more

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Cited by 4 publications
(5 citation statements)
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References 21 publications
(26 reference statements)
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“…A possible improvement is the implementation of a parallel version of the algorithms used in HiCeekR or the split-up of the computations on multiple cores/CPUs. In this regards, a good example is given by the NuChart-II R packages, where particular attention is reserved for the implementation of parallel routines for Hi-C data analysis (Merelli et al, 2013; Tordini et al, 2017).…”
Section: Discussionmentioning
confidence: 99%
“…A possible improvement is the implementation of a parallel version of the algorithms used in HiCeekR or the split-up of the computations on multiple cores/CPUs. In this regards, a good example is given by the NuChart-II R packages, where particular attention is reserved for the implementation of parallel routines for Hi-C data analysis (Merelli et al, 2013; Tordini et al, 2017).…”
Section: Discussionmentioning
confidence: 99%
“…In order to overcome this problem, we advocate a parallelization schema that supports the concurrent processing of different genomic regions, exploiting the computational power of modern multi-core architectures for improving the overall application performance. We deploy our solution using the FastFlow framework [13], [14], that natively supports highlevel parallel programming patterns for working both on data streams and static datasets, and exhibits an efficient lock-free run-time support.…”
Section: Refactoring Freebayes After Profiling the Application We Realized That Most Of The Execution Time Is Devoted To The Search Of Almentioning
confidence: 99%
“…High-throughput sequencing Chromosome Conformation Capture (Hi-C) technique allows the study of chromatin interactions and 3D chromosome folding on a larger scale [ 7 , 8 ]. The graph-based representation of Hi-C data produced, for example, by NuChart [ 9 , 10 ] or CytoHic [ 11 ], which are software for representing the spatial position of genes in the nucleus, are essential for creating maps where further omics data can be mapped, in order to characterise different spatially associated domains. This represents an effective complement of the traditional matrix-based representation, as for example produced by Juicer [ 12 ] or TADbit [ 13 ].…”
Section: Introductionmentioning
confidence: 99%
“…All the authors equally contributed in the design of the NeoHiC architecture and paper writing. DD developed NeoHiC service, IM performed the experiments, MA provided NeoHiC with a parallel graph building stage (NuChart-II [ 10 ]), PL validated the results. All authors read and approved the final manuscript.…”
mentioning
confidence: 99%