Implicating candidate genes at GWAS signals by leveraging topologically associating domains
Sign Up to like & getrecommendations! Published in 2017 at "European Journal of Human Genetics"
DOI: 10.1038/ejhg.2017.108
Abstract: Genome-wide association studies (GWAS) have contributed significantly to the understanding of complex disease genetics. However, GWAS only report association signals and do not necessarily identify culprit genes. As most signals occur in non-coding regions of… read more here.
Keywords: associating domains; gwas signals; association; candidate genes ... See more keywords
On the existence and functionality of topologically associating domains
Sign Up to like & getrecommendations! Published in 2020 at "Nature Genetics"
DOI: 10.1038/s41588-019-0561-1
Abstract: Genomes across a wide range of eukaryotic organisms fold into higher-order chromatin domains. Topologically associating domains (TADs) were originally discovered empirically in low-resolution Hi-C heat maps representing ensemble average interaction frequencies from millions of cells.… read more here.
Keywords: chromatin domains; associating domains; functionality topologically; existence functionality ... See more keywords
LPAD: using network construction and label propagation to detect topologically associating domains from Hi-C data.
Sign Up to like & getrecommendations! Published in 2023 at "Briefings in bioinformatics"
DOI: 10.1093/bib/bbad165
Abstract: With the development of chromosome conformation capture technique, the study of spatial conformation of a genome based on Hi-C technique has made a quantum leap. Previous studies reveal that genomes are folded into hierarchy of… read more here.
Keywords: topologically associating; lpad using; associating domains; label propagation ... See more keywords
A critical assessment of topologically associating domain prediction tools
Sign Up to like & getrecommendations! Published in 2017 at "Nucleic Acids Research"
DOI: 10.1093/nar/gkx145
Abstract: Abstract Topologically associating domains (TADs) have been proposed to be the basic unit of chromosome folding and have been shown to play key roles in genome organization and gene regulation. Several different tools are available… read more here.
Keywords: assessment topologically; prediction tools; tad prediction; critical assessment ... See more keywords
A comparison of topologically associating domain callers based on Hi-C data.
Sign Up to like & getrecommendations! Published in 2022 at "IEEE/ACM transactions on computational biology and bioinformatics"
DOI: 10.1109/tcbb.2022.3147805
Abstract: Topologically associating domains (TADs) are local chromatin interaction domains, which have been shown to play an important role in gene expression regulation. TADs were originally discovered in the investigation of 3D genome organization based on… read more here.
Keywords: comparison topologically; associating domain; callers based; tad boundaries ... See more keywords
Topologically associating domains in the POLLED region are the same for Angus- and Brahman-specific Hi-C reads from F1 hybrid fetal tissue.
Sign Up to like & getrecommendations! Published in 2023 at "Animal genetics"
DOI: 10.1111/age.13322
Abstract: Horns, a form of headgear carried by Bovidae, have ethical and economic implications for ruminant production species such as cattle and goats. Hornless (polled) individuals are preferred. In cattle, four genetic variants (Celtic, Friesian, Mongolian… read more here.
Keywords: brahman; angus brahman; brahman specific; topologically associating ... See more keywords
KSHV Topologically Associating Domains in Latent and Reactivated Viral Chromatin
Sign Up to like & getrecommendations! Published in 2022 at "Journal of Virology"
DOI: 10.1128/jvi.00565-22
Abstract: The 3D architecture of chromatin allows for efficient arrangement, expression, and replication of genetic material. The genomes of all organisms studied to date have been found to be organized through some form of tiered domain… read more here.
Keywords: topologically associating; expression; kshv; associating domains ... See more keywords
Functional Similarities of Protein-Coding Genes in Topologically Associating Domains and Spatially-Proximate Genomic Regions
Sign Up to like & getrecommendations! Published in 2022 at "Genes"
DOI: 10.3390/genes13030480
Abstract: Topologically associating domains (TADs) are the structural and functional units of the genome. However, the functions of protein-coding genes existing in the same or different TADs have not been fully investigated. We compared the functional… read more here.
Keywords: functional similarities; topologically associating; protein coding; similarities protein ... See more keywords