An overview of methods for reconstructing 3-D chromosome and genome structures from Hi-C data
O Oluwadare, M Highsmith, J Cheng - Biological procedures online, 2019 - Springer
Over the past decade, methods for predicting three-dimensional (3-D) chromosome and
genome structures have proliferated. This has been primarily due to the development of high …
genome structures have proliferated. This has been primarily due to the development of high …
Techniques for and challenges in reconstructing 3D genome structures from 2D chromosome conformation capture data
Chromosome conformation capture technologies that provide frequency information for
contacts between genomic regions have been crucial for increasing our understanding of …
contacts between genomic regions have been crucial for increasing our understanding of …
Exploring genomic data coupled with 3D chromatin structures using the WashU Epigenome Browser
To the Editor—Three-dimensional (3D) genomic structures are vital for gene regulation and
cell function1. High-throughput technologies based on chromosome conformation capture …
cell function1. High-throughput technologies based on chromosome conformation capture …
3D chromatin maps of a brown alga reveal U/V sex chromosome spatial organization
Nuclear three dimensional (3D) folding of chromatin structure has been linked to gene
expression regulation and correct developmental programs, but little is known about the 3D …
expression regulation and correct developmental programs, but little is known about the 3D …
INT-Hi-C reveals distinct chromatin architecture in endosperm and leaf tissues of Arabidopsis
VK Yadav, J Santos-González… - Nucleic Acids Research, 2021 - academic.oup.com
Higher-order chromatin structure undergoes striking changes in response to various
developmental and environmental signals, causing distinct cell types to adopt specific …
developmental and environmental signals, causing distinct cell types to adopt specific …
VEHiCLE: a variationally encoded Hi-C loss enhancement algorithm for improving and generating Hi-C data
M Highsmith, J Cheng - Scientific Reports, 2021 - nature.com
Chromatin conformation plays an important role in a variety of genomic processes. Hi-C is
one of the most popular assays for inspecting chromatin conformation. However, the utility of …
one of the most popular assays for inspecting chromatin conformation. However, the utility of …
Single-cell Hi-C data enhancement with deep residual and generative adversarial networks
Motivation The spatial genome organization of a eukaryotic cell is important for its function.
The development of single-cell technologies for probing the 3D genome conformation …
The development of single-cell technologies for probing the 3D genome conformation …
A maximum-entropy model to predict 3D structural ensembles of chromatin from pairwise distances with applications to interphase chromosomes and structural …
G Shi, D Thirumalai - Nature Communications, 2023 - nature.com
The principles that govern the organization of genomes, which are needed for an
understanding of how chromosomes are packaged and function in eukaryotic cells, could be …
understanding of how chromosomes are packaged and function in eukaryotic cells, could be …
GenomeFlow: a comprehensive graphical tool for modeling and analyzing 3D genome structure
Abstract Motivation Three-dimensional (3D) genome organization plays important functional
roles in cells. User-friendly tools for reconstructing 3D genome models from chromosomal …
roles in cells. User-friendly tools for reconstructing 3D genome models from chromosomal …
Hierarchical reconstruction of high-resolution 3D models of large chromosomes
Eukaryotic chromosomes are often composed of components organized into multiple scales,
such as nucleosomes, chromatin fibers, topologically associated domains (TAD) …
such as nucleosomes, chromatin fibers, topologically associated domains (TAD) …