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 …
Computational methods for analysing multiscale 3D genome organization
Recent progress in whole-genome mapping 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 structure determination via 3C-based data integration by the Integrative Modeling Platform
D Bau, MA Marti-Renom - Methods, 2012 - Elsevier
The three-dimensional (3D) architecture of a genome determines the spatial localization of
regulatory elements and the genes they regulate. Thus, elucidating the 3D structure of a …
regulatory elements and the genes they regulate. Thus, elucidating the 3D structure of a …
Reconstruct high-resolution 3D genome structures for diverse cell-types using FLAMINGO
High-resolution reconstruction of spatial chromosome organizations from chromatin contact
maps is highly demanded, but is hindered by extensive pairwise constraints, substantial …
maps is highly demanded, but is hindered by extensive pairwise constraints, substantial …
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 …
Structure determination of genomic domains by satisfaction of spatial restraints
D Baù, MA Marti-Renom - Chromosome research, 2011 - Springer
Abstract The three-dimensional (3D) architecture of a genome is non-random and known to
facilitate the spatial colocalization of regulatory elements with the genes they regulate …
facilitate the spatial colocalization of regulatory elements with the genes they regulate …
4D nucleomes in single cells: what can computational modeling reveal about spatial chromatin conformation?
Genome-wide sequencing technologies enable investigations of the structural properties of
the genome in various spatial dimensions. Here, we review computational techniques …
the genome in various spatial dimensions. Here, we review computational techniques …
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 …
[HTML][HTML] Machine learning methods for exploring sequence determinants of 3D genome organization
In higher eukaryotic cells, chromosomes are folded inside the nucleus. Recent advances in
whole-genome mapping technologies have revealed the multiscale features of 3D genome …
whole-genome mapping technologies have revealed the multiscale features of 3D genome …
Population-based 3D genome structure analysis reveals driving forces in spatial genome organization
Conformation capture technologies (eg, Hi-C) chart physical interactions between chromatin
regions on a genome-wide scale. However, the structural variability of the genome between …
regions on a genome-wide scale. However, the structural variability of the genome between …