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Hi-C Data Analysis Methods and Protocols
This volume details a comprehensive set of methods and tools for Hi-C data processing, analysis, and interpretation. Chapters cover applications of...
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Tough Tissue Hi-C
The ability to decipher the three-dimensional chromosome folding in many eukaryotes is a major asset in molecular biology. It is not only required to...
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Epiphany: predicting Hi-C contact maps from 1D epigenomic signals
Recent deep learning models that predict the Hi-C contact map from DNA sequence achieve promising accuracy but cannot generalize to new cell types...
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Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C
Technology for measuring 3D genome topology is increasingly important for studying gene regulation, for genome assembly and for mapping of genome...
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GreenHill: a de novo chromosome-level scaffolding and phasing tool using Hi-C
Chromosome-level haplotype-resolved genome assembly is an important resource in molecular biology. However, current de novo haplotype assemblers...
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Characterizing chromatin interactions of regulatory elements and nucleosome positions, using Hi-C, Micro-C, and promoter capture Micro-C
BackgroundRegulatory elements such as promoters, enhancers, and insulators interact each other to mediate molecular processes. To capture chromatin...
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Comparative study on chromatin loop callers using Hi-C data reveals their effectiveness
BackgroundChromosome is one of the most fundamental part of cell biology where DNA holds the hierarchical information. DNA compacts its size by...
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Hi-C Data Formats
Processing, storing, and visualizing high-resolution Hi-C data required development of efficient data formats. A sparse matrix format saving only...
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Modification of the Hi-C Technology for Molecular Genetic Analysis of Formalin-Fixed Paraffin-Embedded Sections of Tumor Tissues
AbstractMolecular genetic analysis of tumor tissues is the most important step towards understanding the mechanisms of cancer development; it is also...
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Hi-C Analysis to Identify Genome-Wide Chromatin Structural Aberration in Cancer
Hi-C is a method that analyzes genome-wide chromatin structureGenome-wide chromatin structure using next-generation sequencerNext-generation...
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Identifying quantitatively differential chromosomal compartmentalization changes and their biological significance from Hi-C data using DARIC
BackgroundChromosomal compartmentalization plays a critical role in maintaining proper transcriptional programs in cell differentiation and...
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Visualizing and Annotating Hi-C Data
Epigenomics studies require the combined analysis and integration of multiple types of data and annotations to extract biologically relevant...
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Easy Hi-C: A Low-Input Method for Capturing Genome Organization
Chromosome conformation capture technology and its derivatives have been widely used to study genome organization. Among them, Hi-C (chromosome...
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Catch me if you can: capturing microbial community transformation by extracellular DNA using Hi-C sequencing
The transformation of environmental microorganisms by extracellular DNA is an overlooked mechanism of horizontal gene transfer and evolution. It...
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Hi-C sequencing unravels dynamic three-dimensional chromatin interactions in muntjac lineage: insights from chromosome fusions in Fea’s muntjac genome
Eukaryotes have varying numbers and structures of characteristic chromosomes across lineages or species. The evolutionary trajectory of species may...
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EndHiC: assemble large contigs into chromosome-level scaffolds using the Hi-C links from contig ends
BackgroundThe application of PacBio HiFi and ultra-long ONT reads have enabled huge progress in the contig-level assembly, but it is still...
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Hi-C analysis of genomic contacts revealed karyotype abnormalities in chicken HD3 cell line
BackgroundKaryotype abnormalities are frequent in immortalized continuous cell lines either transformed or derived from primary tumors. Chromosomal...
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Polymer Folding Simulations from Hi-C Data
In the absence of a clear molecular understanding of the mechanism that stabilizes specific contacts in interphasic chromatin, we resort to the...
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ParticleChromo3D: a Particle Swarm Optimization algorithm for chromosome 3D structure prediction from Hi-C data
BackgroundThe three-dimensional (3D) structure of chromatin has a massive effect on its function. Because of this, it is desirable to have an...
