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 …
Reconstruction of 3D genome architecture via a two-stage algorithm
MR Segal, HL Bengtsson - BMC bioinformatics, 2015 - Springer
Background The three-dimensional (3D) configuration of chromosomes within the eukaryote
nucleus is an important factor for several cellular functions, including gene expression …
nucleus is an important factor for several cellular functions, including gene expression …
HSA: integrating multi-track Hi-C data for genome-scale reconstruction of 3D chromatin structure
Genome-wide 3C technologies (Hi-C) are being increasingly employed to study three-
dimensional (3D) genome conformations. Existing computational approaches are unable to …
dimensional (3D) genome conformations. Existing computational approaches are unable to …
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) …
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 …
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 …
Manifold based optimization for single-cell 3D genome reconstruction
The three-dimensional (3D) structure of the genome is important for orchestration of gene
expression and cell differentiation. While mapping genomes in 3D has for a long time been …
expression and cell differentiation. While mapping genomes in 3D has for a long time been …
Si-C is a method for inferring super-resolution intact genome structure from single-cell Hi-C data
L Meng, C Wang, Y Shi, Q Luo - Nature Communications, 2021 - nature.com
There is a strong demand for methods that can efficiently reconstruct valid super-resolution
intact genome 3D structures from sparse and noise single-cell Hi-C data. Here, we develop …
intact genome 3D structures from sparse and noise single-cell Hi-C data. Here, we develop …
Large-scale reconstruction of 3D structures of human chromosomes from chromosomal contact data
Chromosomes are not positioned randomly within a nucleus, but instead, they adopt
preferred spatial conformations to facilitate necessary long-range gene–gene interactions …
preferred spatial conformations to facilitate necessary long-range gene–gene interactions …