[HTML][HTML] Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project
The four-dimensional nucleome (4DN) consortium studies the architecture of the genome
and the nucleus in space and time. We summarize progress by the consortium and highlight …
and the nucleus in space and time. We summarize progress by the consortium and highlight …
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 …
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 …
From Nucleosomes to Compartments: Physicochemical Interactions Underlying Chromatin Organization
Chromatin organization plays a critical role in cellular function by regulating access to
genetic information. However, understanding chromatin folding is challenging due to its …
genetic information. However, understanding chromatin folding is challenging due to its …
[HTML][HTML] High-resolution spatial multi-omics reveals cell-type specific nuclear compartments
The mammalian nucleus is compartmentalized by diverse subnuclear structures. These
subnuclear structures, marked by nuclear bodies and histone modifications, are often cell …
subnuclear structures, marked by nuclear bodies and histone modifications, are often cell …
Compartmentalization with nuclear landmarks yields random, yet precise, genome organization
The 3D organization of eukaryotic genomes plays an important role in genome function.
While significant progress has been made in deciphering the folding mechanisms of …
While significant progress has been made in deciphering the folding mechanisms of …
The magic of unraveling genome architecture and function
MP Cosma, MV Neguembor - Cell Reports, 2023 - cell.com
Over the last decades, technological breakthroughs in super-resolution microscopy have
allowed us to reach molecular resolution and design experiments of unprecedented …
allowed us to reach molecular resolution and design experiments of unprecedented …
SnapFISH: a computational pipeline to identify chromatin loops from multiplexed DNA FISH data
Multiplexed DNA fluorescence in situ hybridization (FISH) imaging technologies have been
developed to map the folding of chromatin fibers at tens of nanometers and up to several …
developed to map the folding of chromatin fibers at tens of nanometers and up to several …
[HTML][HTML] Comparing chromatin contact maps at scale: methods and insights
LM Gunsalus, E McArthur, K Gjoni, S Kuang… - Research …, 2023 - ncbi.nlm.nih.gov
Comparing chromatin contact maps is an essential step in quantifying how three-
dimensional (3D) genome organization shapes development, evolution, and disease …
dimensional (3D) genome organization shapes development, evolution, and disease …
UNADON: transformer-based model to predict genome-wide chromosome spatial position
Motivation The spatial positioning of chromosomes relative to functional nuclear bodies is
intertwined with genome functions such as transcription. However, the sequence patterns …
intertwined with genome functions such as transcription. However, the sequence patterns …