Results 11 to 20 of about 2,360,372 (228)

Computational analysis of hi-c data

, 2021
The chromatin organization in the 3D nuclear space is essential for genome functionality. This spatial organization encompasses different topologies at diverse scale lengths with chromosomes occupying distinct volumes and individual chromosomes folding ...
Forcato M., Bicciato S.
core   +4 more sources

The DLO Hi-C Tool for Digestion-Ligation-Only Hi-C Chromosome Conformation Capture Data Analysis [PDF]

Genes, 2020
It is becoming increasingly important to understand the mechanism of regulatory elements on target genes in long-range genomic distance. 3C (chromosome conformation capture) and its derived methods are now widely applied to investigate three-dimensional (
Hao Jiang, Gang Cao, Qian Xu, Weize Xu, Ping Hong, Guoliang Li, Da Lin   +6 more
core   +4 more sources

Galaxy HiCExplorer 3: a web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization [PDF]

Nucleic Acids Research, 2020
International audienceThe Galaxy HiCExplorer provides a web service at https://hicexplorer.usegalaxy.eu. It enables the integrative analysis of chromosome conformation by providing tools and computational resources to pre-process, analyse and visualize ...
Manke, Thomas, Wolff, Joachim, Grüning, Bjorn, Rabbani, Leily, Richard, Gautier, Grüning, Björn A., Backofen, Rolf, Gilsbach, Ralf   +7 more
core   +5 more sources

Measuring the reproducibility and quality of Hi-C data

Genome Biology, 2017
Hi-C is currently the most widely used assay to investigate the 3D organization of the genome and to study its role in gene regulation, DNA replication, and disease.
Qunhua Li, Hakan Ozadam, Mark Gerstein, James Taylor, Galip Gürkan Yardımcı, Abhijit Chakraborty, Ye Zhang, Ferhat Ay, William S. Noble, Tao Yang, Anshul Kundaje, Fan Song, Arya Kaul, Oana Ursu, Bryan R. Lajoie, Koon-Kiu Yan, Feng Yue, Michael E.G. Sauria, Job Dekker   +18 more
core   +5 more sources

Comparison of computational methods for Hi-C data analysis [PDF]

Nature Methods, 2017
Hi-C is a genome-wide sequencing technique used to investigate 3D chromatin conformation inside the nucleus. Computational methods are required to analyze Hi-C data and identify chromatin interactions and topologically associating domains (TADs) from ...
Livi, Carmen Maria, Silvio Bicciato, NICOLETTI, CHIARA, Ferrari, Francesco, Carmen Maria Livi, Francesco Ferrari, Pal, Koustav, Chiara Nicoletti, FORCATO, Mattia, BICCIATO, Silvio, Mattia Forcato, Koustav Pal   +11 more
core   +7 more sources

Methods for comparative ChIA-PET and Hi-C data analysis.

Methods, 2020
The three-dimensional architecture of chromatin in the nucleus is important for genome regulation and function. Advanced high-throughput sequencing-based methods have been developed for capturing chromatin interactions (Hi-C, genome-wide chromosome ...
Tang, Zhonghui, Capurso, Dan, Ruan, Yijun   +2 more
core   +4 more sources

Unsupervised embedding of single-cell Hi-C data [PDF]

Bioinformatics, 2018
Single-cell Hi-C (scHi-C) data promises to enable scientists to interrogate the 3D architecture of DNA in the nucleus of the cell, studying how this structure varies stochastically or along developmental or cell cycle axes.
Galip Gürkan Yardımcı, Jie Liu, Dejun Lin, William Stafford Noble   +3 more
core   +3 more sources

Benchmarking alignment strategies for Hi-C reads in metagenomic Hi-C data. [PDF]

Genome Biol
Abstract Background Metagenomics combined with High-throughput Chromosome Conformation Capture (Hi-C) offers a powerful approach to study microbial communities by linking genomic content with spatial interactions.
Wang Y, Zuo W, Huang J, Sun F, Du Y.
europepmc   +3 more sources

Significance in scale space for Hi-C data. [PDF]

Bioinformatics
Abstract Motivation Hi-C technology has been developed to profile genome-wide chromosome conformation. So far Hi-C data have been generated from a large compendium of different cell types and different tissue types. Among different chromatin conformation units, chromatin loops were found to play a key
Liu R, Zhang Z, Won H, Marron JS.
europepmc   +3 more sources

A Multigraph-Based Representation of Hi-C Data. [PDF]

Genes (Basel), 2022
Chromatin–chromatin interactions and three-dimensional (3D) spatial structures are involved in transcriptional regulation and have a decisive role in DNA replication and repair. To understand how individual genes and their regulatory elements function within the larger genomic context, and how the genome reacts to environmental stimuli, the linear ...
Makai D, Cseh A, Sepsi A, Makai S.
europepmc   +4 more sources