Results 251 to 260 of about 2,265,648 (271)

TADShop: systematic benchmarking and identification of topologically associating domains

Nature Methods
Topologically associating domains (TADs) are structural units of chromatin organization. Their definition and identification rely on computational analyses of chromosome conformation capture data. Here we systematically assessed and compared 43 TAD identification strategies, none of which excelled in all tests, often displaying conflicting results.
Pumin Li, Andras Hatos, Miljan Petrovic, Gian Marco Franceschini, Luca Nanni, Daniele Tavernari, Giovanni Ciriello   +6 more
openaire   +3 more sources

A Review of Methods to Quantify the Genomic Similarity of Topological Associating Domains

Journal of Computational Biology, 2019
Abstract Topologically associating domains (TADs) are the most fundamental elements and significant structures of the eukaryotic genome. Currently, algorithms have been developed to find the TADs. But few algorithms are reported to compare the similarity of TADs between genomes.
Yufang Li, Aoshen Wu, Gang Liu, Lei Liu
openaire   +2 more sources

A functional variant in the boundary of a topological association domain is associated with pancreatic cancer risk

Molecular Carcinogenesis, 2019
AbstractAs the proper binding of CCCTC‐binding factor (CTCF) in the boundaries of topological association domains (TADs) was important for chromatin structures and gene regulation, we hypothesized that single nucleotide polymorphisms (SNPs) affecting CTCF binding in TAD boundaries might contribute to pancreatic cancer (PC) susceptibility.
Shufang Mei, Juntao Ke, Jianbo Tian, Pingting Ying, Nan Yang, Xiaoyang Wang, Danyi Zou, Xiating Peng, Yang Yang, Ying Zhu, Yajie Gong, Rong Zhong, Jiang Chang, Xiaoping Miao   +13 more
openaire   +2 more sources

Automatic Association of Cross-Domain Network Topology

2022 IEEE International Conference on Trust, Security and Privacy in Computing and Communications (TrustCom), 2022
Sai Han, Zelin Wang, Guangquan Wang, Qiukeng Fang, Hongbing Ma, Lin Lin, Lexi Xu, Heng Zhang   +7 more
openaire   +1 more source

TADBay: A Bayesian Construction of Topologically Associated Domains

2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2022
Carlos Soto 0002, Darshan W. Bryner, Audrey Dalgarno, Nicola Neretti, Anuj Srivastava   +4 more
openaire   +2 more sources

Self-organization of a chromatin fibril into topologically-associated domains

Russian Journal of Bioorganic Chemistry, 2017
A number of recent experimental approaches demonstrated that a three-dimensional organization of the eukaryotic genome play an important role in the regulation of its activity. One of the most important results was a discovery of the genome separation into relatively independent topologically-associated domains (TADs).
S. V. Razin, A. A. Gavrilov, P. Kos, S. V. Ulianov   +3 more
openaire   +1 more source

Topologically Associating Domains in 3D Chromatin Organization

The spatial organization of the genome within the nucleus is crucial in regulating gene expression, DNA replication, and other cellular processes. Topologically Associating Domains (TADs) is a important feature, and is the compartmentalization of the genome into discrete regulatory clusters. The review goes through biophysical and mathematical models
Murari Ambati, Abdullah Choudhary
openaire   +1 more source

Transcription factors locations analysis in topological associated domains

2021
Blanchette, Mathieu (Supervisor)
openaire   +1 more source

Spectral methods for the detection and characterization of Topologically Associated Domains

2019
VCU Theses and ...
openaire   +1 more source

Methods for the Analysis of Topologically Associating Domains (TADs)

Methods in Molecular Biology, 2022
Daniele Tavernari, Giovanni Ciriello, Marie Zufferey   +2 more
exaly