[HTML][HTML] Understanding 3D genome organization by multidisciplinary methods
I Jerkovic, G Cavalli - Nature Reviews Molecular Cell Biology, 2021 - nature.com
Understanding how chromatin is folded in the nucleus is fundamental to understanding its
function. Although 3D genome organization has been historically difficult to study owing to a …
function. Although 3D genome organization has been historically difficult to study owing to a …
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 …
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 …
Open structural data in precision medicine
Three-dimensional protein structural data at the molecular level are pivotal for successful
precision medicine. Such data are crucial not only for discovering drugs that act to block the …
precision medicine. Such data are crucial not only for discovering drugs that act to block the …
Minimalistic 3D chromatin models: Sparse interactions in single cells drive the chromatin fold and form many-body units
J Liang, A Perez-Rathke - Current opinion in structural biology, 2021 - Elsevier
Computational three-dimensional chromatin modeling has helped uncover principles of
genome organization. Here, we discuss methods for modeling three-dimensional chromatin …
genome organization. Here, we discuss methods for modeling three-dimensional chromatin …
Hi-BDiSCO: folding 3D mesoscale genome structures from Hi-C data using brownian dynamics
The structure and dynamics of the eukaryotic genome are intimately linked to gene
regulation and transcriptional activity. Many chromosome conformation capture experiments …
regulation and transcriptional activity. Many chromosome conformation capture experiments …
Perspectives for the reconstruction of 3D chromatin conformation using single cell Hi-C data
PI Kos, AA Galitsyna, SV Ulianov… - PLoS Computational …, 2021 - journals.plos.org
Construction of chromosomes 3D models based on single cell Hi-C data constitute an
important challenge. We present a reconstruction approach, DPDchrom, that incorporates …
important challenge. We present a reconstruction approach, DPDchrom, that incorporates …
HiC-GNN: A generalizable model for 3D chromosome reconstruction using graph convolutional neural networks
V Hovenga, J Kalita, O Oluwadare - Computational and Structural …, 2023 - Elsevier
Chromosome conformation capture (3 C) is a method of measuring chromosome topology in
terms of loci interaction. The Hi-C method is a derivative of 3 C that allows for genome-wide …
terms of loci interaction. The Hi-C method is a derivative of 3 C that allows for genome-wide …
Principal curve approaches for inferring 3D chromatin architecture
Summary Three-dimensional (3D) genome spatial organization is critical for numerous
cellular processes, including transcription, while certain conformation-driven structural …
cellular processes, including transcription, while certain conformation-driven structural …