The 3D genome structure of single cells
The spatial organization of the genome in the cell nucleus is pivotal to cell function.
However, how the 3D genome organization and its dynamics influence cellular phenotypes …
However, how the 3D genome organization and its dynamics influence cellular phenotypes …
Chromatin compaction multiscale modeling: a complex synergy between theory, simulation, and experiment
Understanding the mechanisms that trigger chromatin compaction, its patterns, and the
factors they depend on, is a fundamental and still open question in Biology. Chromatin …
factors they depend on, is a fundamental and still open question in Biology. Chromatin …
[HTML][HTML] LncRNA-SLC16A1-AS1 induces metabolic reprogramming during Bladder Cancer progression as target and co-activator of E2F1
Long non-coding RNAs (lncRNAs) have emerged as integral components of E2F1-regulated
gene regulatory networks (GRNs), but their implication in advanced or treatment-refractory …
gene regulatory networks (GRNs), but their implication in advanced or treatment-refractory …
Fine-mapping of nuclear compartments using ultra-deep Hi-C shows that active promoter and enhancer elements localize in the active A compartment even when …
Megabase-scale intervals of active, gene-rich and inactive, gene-poor chromatin are known
to segregate, forming the A and B compartments. Fine mapping of the contents of these A …
to segregate, forming the A and B compartments. Fine mapping of the contents of these A …
3D genome reconstruction from partially phased Hi-C data
Abstract The 3-dimensional (3D) structure of the genome is of significant importance for
many cellular processes. In this paper, we study the problem of reconstructing the 3D …
many cellular processes. In this paper, we study the problem of reconstructing the 3D …
Identifying 3D genome organization in diploid organisms via euclidean distance geometry
The spatial organization of the genome in the cell nucleus plays an important role for gene
regulation, replication of the deoxyribonucleic acid (DNA), and genomic integrity. Through …
regulation, replication of the deoxyribonucleic acid (DNA), and genomic integrity. Through …
[HTML][HTML] Understanding three-dimensional chromatin organization in diploid genomes
Abstract The three-dimensional (3D) organization of chromatin in the nucleus of diploid
eukaryotic organisms has fascinated biologists for many years. Despite major progress in …
eukaryotic organisms has fascinated biologists for many years. Despite major progress in …
Does multi-way, long-range chromatin contact data advance 3D genome reconstruction?
AB Olshen, MR Segal - BMC bioinformatics, 2023 - Springer
Background Methods for inferring the three-dimensional (3D) configuration of chromatin
from conformation capture assays that provide strictly pairwise interactions, notably Hi-C …
from conformation capture assays that provide strictly pairwise interactions, notably Hi-C …
Inference of 3D genome architecture by modeling overdispersion of Hi-C data
Motivation We address the challenge of inferring a consensus 3D model of genome
architecture from Hi-C data. Existing approaches most often rely on a two-step algorithm …
architecture from Hi-C data. Existing approaches most often rely on a two-step algorithm …
Imputation-free reconstructions of three-dimensional chromosome architectures in human diploid single-cells using allele-specified contacts
Single-cell Hi-C analysis of diploid human cells is difficult because of the lack of dense
chromosome contact information and the presence of homologous chromosomes with very …
chromosome contact information and the presence of homologous chromosomes with very …