Results 41 to 50 of about 8,821,447 (199)

Correction to: GSDB: a database of 3D chromosome and genome structures reconstructed from Hi-C data [PDF]

BMC Molecular and Cell Biology, 2020
An amendment to this paper has been published and can be accessed via the original article.
Oluwatosin Oluwadare, Max Highsmith, Douglass Turner, Erez Lieberman Aiden, Jianlin Cheng   +4 more
openaire   +3 more sources

Ki-67 is a PP1-interacting protein that organises the mitotic chromosome periphery [PDF]

, 2014
Copyright @ 2014 Booth et al. This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.When the nucleolus ...
Elizabeth Petfalski, Vagnarelli, Paola, David Tollervey, Earnshaw, William C, Imamoto, N, Petfalski, Elizabeth, Sanchez-Pulido, Luis, Giulia Vargiu, Takagi, M, Luis Sanchez-Pulido, Tollervey, David, Ponting, Chris P, Petfalski, E, Ponting, CP, Vargiu, Giulia, Tollervey, D, Naoko Imamoto, Ponting, Chris P.; id_orcid, Earnshaw, William C., Daniel G Booth, Vagnarelli, P, Kumiko Samejima, Imamoto, Naoko, Booth, Daniel G, William C Earnshaw, Masatoshi Takagi, Samejima, Kumiko, Sanchez-Pulido, L, Vargiu, G, Booth, Daniel G., Chris P Ponting, Paola Vagnarelli, Takagi, Masatoshi, Samejima, K, Earnshaw, WC   +34 more
core   +1 more source

3D chromosome structure reconstruction using graph convolutional neural networks

, 2022
Chromosome conformation capture (3C) is a method of measuring chromosome topology in terms of loci interaction. The Hi-C method is a derivative of 3C that allows for genome-wide quantification of chromosome interaction. From such interaction data, it is possible to infer the three-dimensional (3D) structure of the underlying ...
Van Hovenga, , Jugal Kalita, Oluwatosin Oluwadare   +2 more
openaire   +1 more source

HiCognition: a visual exploration and hypothesis testing tool for 3D genomics

Genome Biology, 2023
Genome browsers facilitate integrated analysis of multiple genomics datasets yet visualize only a few regions at a time and lack statistical functions for extracting meaningful information.
Christoph C. H. Langer, Michael Mitter, Roman R. Stocsits, Daniel W. Gerlich   +3 more
doaj   +1 more source

Network concepts for analyzing 3D genome structure from chromosomal contact maps [PDF]

EPJ Nonlinear Biomedical Physics, 2016
The recent experimental technique of chromosome conformational capture gives an in-vivo access to pairwise contact frequencies between genomic loci. We present how network analysis can be exploited to extract information from genome-wide contact maps. We recently proposed to use graph distance for deriving a complete distance matrix from sparse contact
Morlot, Jean-Baptiste, Mozziconacci, Julien, Lesne, Annick   +2 more
openaire   +2 more sources

RNA surveillance controls 3D genome structure via stable cohesin-chromosome interaction [PDF]

, 2021
Summary The 3D architecture that the genome is folded into is regulated by CTCF, which determines domain borders, and cohesin, which generates interactions within domains. However, organisms lacking CTCF have been reported to still have cohesin-mediated 3D structures with strong borders.
Yujin Chun, Sungwook Han, Taemook Kim, Yoonjung Choi, Daeyoup Lee   +4 more
openaire   +1 more source

Inferential Structure Determination of Chromosomes from Single-Cell Hi-C Data. [PDF]

PLoS Computational Biology, 2016
Chromosome conformation capture (3C) techniques have revealed many fascinating insights into the spatial organization of genomes. 3C methods typically provide information about chromosomal contacts in a large population of cells, which makes it difficult
Simeon Carstens, Michael Nilges, Michael Habeck   +2 more
doaj   +1 more source

Delta integrates 3D physical structure with topology and genomic data of chromosomes [PDF]

, 2017
Abstract Motivation The regulation of gene transcription and DNA replication are tightly associated with the 3D chromosomal structures and genomic features, e.g. epigenetic marks, transcription factor bindings and non-coding RNAs.
Tang, Bixia, Li, Feifei, Li, Jing, Zhao, Wenming, Zhang, Zhihua   +4 more
openaire   +1 more source

EVRC: Reconstruction of chromosome 3D structure models using Error-Vector Resultant algorithm with Clustering coefficient

Bioinformatics, 2023
Abstract Reconstruction of 3D structure models is of great importance for the study of chromosome function. In this paper, we present a novel reconstruction algorithm, called EVRC, which utilizes co-clustering coefficients and error-vector resultant for chromosome 3D structure reconstruction.
Xiao Wang, Wei-Cheng Gu, Jie Li, Bin-Guang Ma   +3 more
openaire   +2 more sources

Evolutionary patterns and functional effects of 3D chromatin structures in butterflies with extensive genome rearrangements

Nature Communications
Chromosome rearrangements may distort 3D chromatin architectures and thus change gene regulation, yet how 3D chromatin structures evolve in insects is largely unknown.
Botong Zhou, Ping Hu, Guichun Liu, Zhou Chang, Zhiwei Dong, Zihe Li, Yuan Yin, Zunzhe Tian, Ge Han, Wen Wang, Xueyan Li   +10 more
doaj   +1 more source