相关论文: From Hi-C Contact Map to Three-dimensional Organiz…
The principles that govern the organization of genomes, which are needed for a deeper understanding of how chromosomes are packaged and function in eukaryotic cells, could be deciphered if the three-dimensional (3D) structures are known.…
Several experiments show that the three dimensional (3D) organization of chromosomes affects genetic processes such as transcription and gene regulation. To better understand this connection, researchers developed the Hi-C method that is…
The population-averaged contact maps generated by the chromosome conformation capture technique provide important information about the average frequency of contact between pairs of chromatin loci as a function of the genetic distance…
Hi-C experiments are used to infer the contact probabilities between loci separated by varying genome lengths. Contact probability should decrease as the spatial distance between two loci increases. However, studies comparing Hi-C and FISH…
Modern biological techniques such as Hi-C permit to measure probabilities that different chromosomal regions are close in space. These probabilities can be visualised as matrices called contact maps. In this paper, we introduce a…
The statistical properties of intra-chromosome maps obtained by a genome-wide chromosome conformation capture method (Hi-C) are described in the framework of the hierarchical crumpling model of heteropolymer chain with quenched disorder in…
The three-dimensional organisation of chromosomes can be probed using methods such as Capture-C. However it is unclear how such population level data relates to the organisation within a single cell, and the mechanisms leading to the…
To better understand DNA's 3D folding in cell nuclei, researchers developed chromosome capture methods such as Hi-C that measure the contact frequencies between all DNA segment pairs across the genome. As Hi-C data sets often are massive,…
Researchers developed chromosome capture methods such as Hi-C to better understand DNA's 3D folding in nuclei. The Hi-C method captures contact frequencies between DNA segment pairs across the genome. When analyzing Hi-C data sets, it is…
To understand the nature of a cell, one needs to understand the structure of its genome. For this purpose, experimental techniques such as Hi-C detecting chromosomal contacts are used to probe the three-dimensional genomic structure. These…
It is widely believed that the folding of the chromosome in the nucleus has a major effect on genetic expression. For example co-regulated genes in several species have been shown to colocalize in space despite being far away on the DNA…
We present a minimal computational model, which allows very fast, on-the-fly construction of three dimensional haploid interphase genomes from single cell Hi-C contact maps using the HOOMD-blue molecular dynamics package on graphics…
How long threadlike eukaryotic chromosomes fit tidily in the small volume of the nucleus without significant entanglement is just beginning to be understood, thanks to major advances in experimental techniques. Several polymer models, which…
The three-dimensional organization of chromatin, on the length scale of a few genes, is crucial in determining the functional state - accessibility and the amount of gene expression - of the chromatin. Recent advances in chromosome…
While bacterial chromosomes were long thought to be amorphous, recent experiments reveal pronounced organizational features. However, the extent of bacterial chromosome organization remains unclear. Here, we develop a fully data-driven…
Understanding the three-dimensional (3D) structure of the genome is essential for elucidating vital biological processes and their links to human disease. To determine how the genome folds within the nucleus, chromosome conformation capture…
Chromosomes are crumpled polymer chains further folded into a sequence of stochastic loops via loop extrusion. While extrusion has been verified experimentally, the particular means by which the extruding complexes bind DNA polymer remains…
Three-dimensional (3D) chromatin structure is closely related to genome function, in particular transcription. However, the folding path of the chromatin fiber in the interphase nucleus is unknown. Here, we systematically measured the 3D…
Phase separation in polymer solutions often correlates with single-chain and two-chain properties, such as the single-chain radius of gyration, Rg, and the pairwise second virial coefficient, B22. However, recent studies have shown that…
Inspired by recent advances in the chromosome capture techniques, a method is proposed to study the structural organization of systems of polymers rings with topological constraints.To this purpose, the system is divided into compartments…