Computational methods for analysing multiscale 3D genome organization
Recent progress in whole-genome map** and imaging technologies has enabled the
characterization of the spatial organization and folding of the genome in the nucleus. In …
characterization of the spatial organization and folding of the genome in the nucleus. In …
Genome-wide map** and analysis of chromosome architecture
Chromosomes of eukaryotes adopt highly dynamic and complex hierarchical structures in
the nucleus. The three-dimensional (3D) organization of chromosomes profoundly affects …
the nucleus. The three-dimensional (3D) organization of chromosomes profoundly affects …
[HTML][HTML] A 3D map of the human genome at kilobase resolution reveals principles of chromatin loo**
We use in situ Hi-C to probe the 3D architecture of genomes, constructing haploid and
diploid maps of nine cell types. The densest, in human lymphoblastoid cells, contains 4.9 …
diploid maps of nine cell types. The densest, in human lymphoblastoid cells, contains 4.9 …
HiC-Pro: an optimized and flexible pipeline for Hi-C data processing
HiC-Pro is an optimized and flexible pipeline for processing Hi-C data from raw reads to
normalized contact maps. HiC-Pro maps reads, detects valid ligation products, performs …
normalized contact maps. HiC-Pro maps reads, detects valid ligation products, performs …
A chromosome conformation capture ordered sequence of the barley genome
Cereal grasses of the Triticeae tribe have been the major food source in temperate regions
since the dawn of agriculture. Their large genomes are characterized by a high content of …
since the dawn of agriculture. Their large genomes are characterized by a high content of …
Chromatin architecture reorganization during stem cell differentiation
Higher-order chromatin structure is emerging as an important regulator of gene expression.
Although dynamic chromatin structures have been identified in the genome, the full scope of …
Although dynamic chromatin structures have been identified in the genome, the full scope of …
[HTML][HTML] A compendium of chromatin contact maps reveals spatially active regions in the human genome
The three-dimensional configuration of DNA is integral to all nuclear processes in
eukaryotes, yet our knowledge of the chromosome architecture is still limited. Genome-wide …
eukaryotes, yet our knowledge of the chromosome architecture is still limited. Genome-wide …
Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation
N Kubo, H Ishii, X **
The organization of the genome in the nucleus and the interactions of genes with their
regulatory elements are key features of transcriptional control and their disruption can cause …
regulatory elements are key features of transcriptional control and their disruption can cause …
HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient
Hi-C is a powerful technology for studying genome-wide chromatin interactions. However,
current methods for assessing Hi-C data reproducibility can produce misleading results …
current methods for assessing Hi-C data reproducibility can produce misleading results …