Population-based 3D genome structure analysis reveals driving forces in spatial genome organization

H Tjong, W Li, R Kalhor, C Dai, S Hao… - Proceedings of the …, 2016 - National Acad Sciences
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 …

Producing genome structure populations with the dynamic and automated PGS software

N Hua, H Tjong, H Shin, K Gong, XJ Zhou, F Alber - Nature protocols, 2018 - nature.com
Chromosome conformation capture technologies such as Hi-C are widely used to
investigate the spatial organization of genomes. Because genome structures can vary …

[HTML][HTML] Extensive heterogeneity and intrinsic variation in spatial genome organization

EH Finn, G Pegoraro, HB Brandão, AL Valton… - Cell, 2019 - cell.com
Several general principles of global 3D genome organization have recently been
established, including non-random positioning of chromosomes and genes in the cell …

Bayesian inference of spatial organizations of chromosomes

M Hu, K Deng, Z Qin, J Dixon, S Selvaraj… - PLoS computational …, 2013 - journals.plos.org
Knowledge of spatial chromosomal organizations is critical for the study of transcriptional
regulation and other nuclear processes in the cell. Recently, chromosome conformation …

Sci-Hi-C: a single-cell Hi-C method for mapping 3D genome organization in large number of single cells

V Ramani, X Deng, R Qiu, C Lee, CM Disteche… - Methods, 2020 - Elsevier
The highly dynamic nature of chromosome conformation and three-dimensional (3D)
genome organization leads to cell-to-cell variability in chromatin interactions within a cell …

Iterative correction of Hi-C data reveals hallmarks of chromosome organization

M Imakaev, G Fudenberg, RP McCord, N Naumova… - Nature …, 2012 - nature.com
Extracting biologically meaningful information from chromosomal interactions obtained with
genome-wide chromosome conformation capture (3C) analyses requires the elimination of …

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

J Dekker, MA Marti-Renom, LA Mirny - Nature Reviews Genetics, 2013 - nature.com
How DNA is organized in three dimensions inside the cell nucleus and how this affects the
ways in which cells access, read and interpret genetic information are among the longest …

PHi-C: deciphering Hi-C data into polymer dynamics

S Shinkai, M Nakagawa, T Sugawara… - NAR genomics and …, 2020 - academic.oup.com
Genomes are spatiotemporally organized within the cell nucleus. Genome-wide
chromosome conformation capture (Hi-C) technologies have uncovered the 3D genome …

Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation

H Belaghzal, J Dekker, JH Gibcus - Methods, 2017 - Elsevier
Chromosome conformation capture-based methods such as Hi-C have become mainstream
techniques for the study of the 3D organization of genomes. These methods convert …

Analysis methods for studying the 3D architecture of the genome

F Ay, WS Noble - Genome biology, 2015 - Springer
The rapidly increasing quantity of genome-wide chromosome conformation capture data
presents great opportunities and challenges in the computational modeling and …