FreeHi-C Spike-in Simulations for Benchmarking Differential Chromatin Interaction Detection.
Sign Up to like & getrecommendations! Published in 2020 at "Methods"
DOI: 10.1016/j.ymeth.2020.07.001
Abstract: High-throughput genome-wide chromatin conformation capture assay (Hi-C) is routinely used to profile long-range genomic interactions and three-dimensional organization of genomes. A key application of Hi-C is the comparative analysis of genomic interactions across different time… read more here.
Keywords: interaction detection; chromatin; chromatin interaction; differential chromatin ... See more keywords
Graph embedding and unsupervised learning predict genomic sub-compartments from HiC chromatin interaction data
Sign Up to like & getrecommendations! Published in 2020 at "Nature Communications"
DOI: 10.1038/s41467-020-14974-x
Abstract: Chromatin interaction studies can reveal how the genome is organized into spatially confined sub-compartments in the nucleus. However, accurately identifying sub-compartments from chromatin interaction data remains a challenge in computational biology. Here, we present Sub-Compartment… read more here.
Keywords: sub compartments; chromatin interaction; sub compartment; interaction data ... See more keywords
Chromatin Interaction Analyses Elucidate PRC2-bound Silencers’ Roles in Mouse Development
Sign Up to like & getrecommendations! Published in 2020 at "Nature genetics"
DOI: 10.1038/s41588-020-0581-x
Abstract: Lineage-specific gene expression is modulated by a balance between transcriptional activation and repression during animal development. Knowledge about enhancer-centered transcriptional activation has advanced considerably, but silencers and their roles in normal development remain poorly understood.… read more here.
Keywords: prc2 bound; chromatin interaction; bound silencers; development ... See more keywords
MIA-Sig: multiplex chromatin interaction analysis by signal processing and statistical algorithms
Sign Up to like & getrecommendations! Published in 2019 at "Genome Biology"
DOI: 10.1186/s13059-019-1868-z
Abstract: The single-molecule multiplex chromatin interaction data are generated by emerging 3D genome mapping technologies such as GAM, SPRITE, and ChIA-Drop. These datasets provide insights into high-dimensional chromatin organization, yet introduce new computational challenges. Thus, we… read more here.
Keywords: multiplex chromatin; chromatin; chromatin interaction; mia sig ... See more keywords
5C analysis of the Epidermal Differentiation Complex locus reveals distinct chromatin interaction networks between gene-rich and gene-poor TADs in skin epithelial cells
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DOI: 10.1371/journal.pgen.1006966
Abstract: Mammalian genomes contain several dozens of large (>0.5 Mbp) lineage-specific gene loci harbouring functionally related genes. However, spatial chromatin folding, organization of the enhancer-promoter networks and their relevance to Topologically Associating Domains (TADs) in these… read more here.
Keywords: chromatin interaction; gene; gene rich; edc locus ... See more keywords
Accurate Identification of DNA Replication Origin by Fusing Epigenomics and Chromatin Interaction Information
Sign Up to like & getrecommendations! Published in 2022 at "Research"
DOI: 10.34133/2022/9780293
Abstract: DNA replication initiation is a complex process involving various genetic and epigenomic signatures. The correct identification of replication origins (ORIs) could provide important clues for the study of a variety of diseases caused by replication.… read more here.
Keywords: chromatin interaction; replication; identification; dna replication ... See more keywords
Systematic analyses of genetic variants in chromatin interaction regions identified four novel lung cancer susceptibility loci
Sign Up to like & getrecommendations! Published in 2020 at "Journal of Cancer"
DOI: 10.7150/jca.35127
Abstract: Genome-wide association studies (GWAS) have reported 45 single-nucleotide polymorphisms (SNPs) that may contribute to the susceptibility of lung cancer, with the majority in non-coding regions. However, no study has ever systematically evaluated the association between… read more here.
Keywords: cancer; chromatin interaction; interaction regions; lung cancer ... See more keywords