ArticleNucleic acids research2013
A complex network framework for unbiased statistical analyses of DNA-DNA contact maps.
Article in Nucleic acids research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Extrachromosomal DNA associates with nuclear condensates and reorganizes chromatin structures to enhance oncogenic transcription.Cancer cell · 2025Article
- Comparative 3D genome architecture in vertebrates.BMC biology · 2022Article
- Oncogenic extrachromosomal DNA functions as mobile enhancers to globally amplify chromosomal transcription.Cancer cell · 2021Article
- RNA Biogenesis Instructs Functional Inter-Chromosomal Genome Architecture.Frontiers in genetics · 2021Article
- Network-based method for regions with statistically frequent interchromosomal interactions at single-cell resolution.BMC bioinformatics · 2020Article
- The corrected gene proximity map for analyzing the 3D genome organization using Hi-C data.BMC bioinformatics · 2020Article
- A subset of topologically associating domains fold into mesoscale core-periphery networks.Scientific reports · 2019Article
- BASiNET-BiologicAl Sequences NETwork: a case study on coding and non-coding RNAs identification.Nucleic acids research · 2018Article
- Computational Methods for Assessing Chromatin Hierarchy.Computational and structural biotechnology journal · 2018Review
- Connected Gene Communities Underlie Transcriptional Changes in Cornelia de Lange Syndrome.Genetics · 2017Article
- MrTADFinder: A network modularity based approach to identify topologically associating domains in multiple resolutions.PLoS computational biology · 2017Article
- Tracking the evolution of 3D gene organization demonstrates its connection to phenotypic divergence.Nucleic acids research · 2017Article
- Article
- Structure of the human chromosome interaction network.PloS one · 2017Article
- Integrating epigenomic data and 3D genomic structure with a new measure of chromatin assortativity.Genome biology · 2016Article
- Quantification of DNA cleavage specificity in Hi-C experiments.Nucleic acids research · 2016Article
- Improving 3D Genome Reconstructions Using Orthologous and Functional Constraints.PLoS computational biology · 2015Article
- Inter-chromosomal contact networks provide insights into Mammalian chromatin organization.PloS one · 2015Article
- Distance-based assessment of the localization of functional annotations in 3D genome reconstructions.BMC genomics · 2014Article
- HiBrowse: multi-purpose statistical analysis of genome-wide chromatin 3D organization.Bioinformatics (Oxford, England) · 2014Article
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3 authors.
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Abstract
Experimental techniques for the investigation of three-dimensional (3D) genome organization are being developed at a fast pace. Currently, the associated computational methods are mostly specific to the individual experimental approach. Here we present a general statistical framework that is widely applicable to the analysis of genomic contact maps, irrespective of the data acquisition and normalization processes. Within this framework DNA-DNA contact data are represented as a complex network, for which a broad number of directly applicable methods already exist. In such a network representation, DNA segments and contacts between them are denoted as nodes and edges, respectively. Furthermore, we present a robust method for generating randomized contact networks that explicitly take into account the inherent 3D nature of the genome and serve as realistic null-models for unbiased statistical analyses. By integrating a variety of large-scale genome-wide datasets we demonstrate that meiotic crossover sites display enriched genomic contacts and that cohesin-bound genes are significantly colocalized in the yeast nucleus. We anticipate that the complex network framework in conjunction with the randomization of DNA-DNA contact networks will become a widely used tool in the study of nuclear architecture.
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