Paper Info
Title
Parallel Exploration of the Nuclear Chromosome Conformation with NuChart-II
Abstract
High-throughput molecular biology techniques are widely used to identify physical interactions between genetic elements located throughout the human genome. Chromosome Conformation Capture (3C) and other related techniques allow to investigate the spatial organisation of chromosomes in the cell's natural state. Recent results have shown that there is a large correlation between co-localization and co-regulation of genes, but these important information are hampered by the lack of biologists-friendly analysis and visualisation software. In this work we introduce NuChart-II, a tool for Hi-C data analysis that provides a gene-centric view of the chromosomal neighbourhood in a graph-based manner. NuChart-II is an efficient and highly optimized C++ re-implementation of a previous prototype package developed in R. Representing Hi-C data using a graph-based approach overcomes the common view relying on genomic coordinates and permits the use of graph analysis techniques to explore the spatial conformation of a gene neighbourhood.
Year
DOI
Venue
2015
10.1109/PDP.2015.104
PDP
Keywords
Field
DocType
genomics,data visualization,computational modeling,systems biology,parallel processing,graph theory,prototypes,parallel computing,chromosome conformation capture,bioinformatics,data analysis
Gene,Chromosome,Visualization,Computer science,Systems biology,Theoretical computer science,Power graph analysis,Software,Human genome,Chromosome conformation capture
Conference
ISSN
Citations 
PageRank 
1066-6192
1
0.43
References 
Authors
9
7
Name
Order
Citations
PageRank
Fabio Tordini143.28
Maurizio Drocco28812.09
Claudia Misale3235.44
Luciano Milanesi482387.40
Pietro Liò555099.98
Ivan Merelli629435.36
Marco Aldinucci763859.87