Evaluating the role of the nuclear microenvironment in gene function by population-based modeling
The nuclear folding of chromosomes relative to nuclear bodies is an integral part of gene
function. Here, we demonstrate that population-based modeling—from ensemble Hi-C data …
function. Here, we demonstrate that population-based modeling—from ensemble Hi-C data …
Chromosomal dynamics predicted by an elastic network model explains genome-wide accessibility and long-range couplings
Understanding the three-dimensional (3D) architecture of chromatin and its relation to gene
expression and regulation is fundamental to understanding how the genome functions …
expression and regulation is fundamental to understanding how the genome functions …
Integrative genome modeling platform reveals essentiality of rare contact events in 3D genome organizations
A multitude of sequencing-based and microscopy technologies provide the means to
unravel the relationship between the three-dimensional organization of genomes and key …
unravel the relationship between the three-dimensional organization of genomes and key …
Reconstructing spatial organizations of chromosomes through manifold learning
Decoding the spatial organizations of chromosomes has crucial implications for studying
eukaryotic gene regulation. Recently, chromosomal conformation capture based …
eukaryotic gene regulation. Recently, chromosomal conformation capture based …
Predicting three-dimensional genome organization with chromatin states
Y Qi, B Zhang - PLoS computational biology, 2019 - journals.plos.org
We introduce a computational model to simulate chromatin structure and dynamics. Starting
from one-dimensional genomics and epigenomics data that are available for hundreds of …
from one-dimensional genomics and epigenomics data that are available for hundreds of …
Integrative modeling reveals the principles of multi-scale chromatin boundary formation in human nuclear organization
Background Interphase chromosomes adopt a hierarchical structure, and recent data have
characterized their chromatin organization at very different scales, from sub-genic regions …
characterized their chromatin organization at very different scales, from sub-genic regions …
A unified framework for inferring the multi-scale organization of chromatin domains from Hi-C
Chromosomes are giant chain molecules organized into an ensemble of three-dimensional
structures characterized with its genomic state and the corresponding biological functions …
structures characterized with its genomic state and the corresponding biological functions …
Perspectives: using polymer modeling to understand the formation and function of nuclear compartments
N Haddad, D Jost, C Vaillant - Chromosome Research, 2017 - Springer
Compartmentalization is a ubiquitous feature of cellular function. In the nucleus, early
observations revealed a non-random spatial organization of the genome with a large-scale …
observations revealed a non-random spatial organization of the genome with a large-scale …
Mesoscale modeling reveals formation of an epigenetically driven HOXC gene hub
Gene expression is orchestrated at the structural level by nucleosome positioning, histone
tail acetylation, and linker histone (LH) binding. Here, we integrate available data on …
tail acetylation, and linker histone (LH) binding. Here, we integrate available data on …
Hi-C-constrained physical models of human chromosomes recover functionally-related properties of genome organization
Combining genome-wide structural models with phenomenological data is at the forefront of
efforts to understand the organizational principles regulating the human genome. Here, we …
efforts to understand the organizational principles regulating the human genome. Here, we …