Results 31 to 40 of about 243,805 (237)
DLO Hi-C Tool for Digestion-Ligation-Only Hi-C Chromosome Conformation Capture Data Analysis [PDF]
Genes, 2019 Abstract Background 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 genome organizations and gene regulation ...
Hong, Ping +6 more
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Revisiting the use of structural similarity index in Hi-C [PDF]
Nature Genetics, 2021 Abstract Identification of dynamic changes in chromatin conformation is a fundamental task in genetics. In 2020, Galan et al. 1 presented CHESS (Comparison of Hi-C Experiments using Structural Similarity), a novel computational algorithm designed for systematic identification of ...
Hanjun Lee +3 more
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Hi-C 2.0: An optimized Hi-C procedure for high-resolution genome-wide mapping of chromosome conformation [PDF]
Methods, 2016 ABSTRACT 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 chromatin interactions reflecting topological chromatin structures into digital information (counts of pair-wise interactions). Here, we describe an updated protocol
Houda Belaghzal +2 more
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Hi–C interaction graph analysis reveals the impact of histone modifications in chromatin shape
Applied Network Science, 2021 Chromosome conformation capture experiments such as Hi–C map the three-dimensional spatial organization of genomes in a genome-wide scale. Even though Hi–C interactions are not biased towards any of the histone modifications, previous analysis has ...
Emre Sefer
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Software tools for visualizing Hi-C data [PDF]
Genome Biology, 2016 Abstract Recently developed, high-throughput assays for measuring the three-dimensional configuration of DNA in the nucleus have provided unprecedented insights into the relationship between DNA 3D configuration and function. However, accurate interpretation of data from assays such as ChIA-PET and Hi-C is challenging because the data ...
Galip Gürkan Yardımcı +1 more
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Role of lamins in 3D genome organization and global gene expression
Nucleus, 2019 Genome-wide mapping of lamin-B1-genome interactions has shown that gene-poor and transcriptionally inactive genomic regions are associated with the nuclear lamina.
Youngjo Kim, Xiaobin Zheng, Yixian Zheng
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HUGIn: Hi-C Unifying Genomic Interrogator [PDF]
Bioinformatics, 2017 Abstract Motivation High throughput chromatin conformation capture (3C) technologies, such as Hi-C and ChIA-PET, have the potential to elucidate the functional roles of non-coding variants. However, most of published genome-wide unbiased chromatin organization studies have used cultured cell ...
Joshua S. Martin +7 more
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A Multigraph-Based Representation of Hi-C Data
Genes, 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 ...
Diána Makai +3 more
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Massively multiplex single-cell Hi-C [PDF]
Nature Methods, 2017 We present single-cell combinatorial indexed Hi-C (sciHi-C), a method that applies combinatorial cellular indexing to chromosome conformation capture. In this proof of concept, we generate and sequence six sciHi-C libraries comprising a total of 10,696 single cells.
Vijay Ramani +8 more
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, 2020 Technology advance during the past decade has greatly expanded our understanding of the higher-order structure of the genome. The various chromosome conformation capture (3C)-based techniques such as Hi-C have provided the most widely used tools for interrogating three-dimensional (3D) genome organization. We recently developed a Hi-C variant, DNase Hi-
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