Results 221 to 230 of about 243,805 (237)
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In-Nucleus Hi-C in Drosophila Cells
Journal of Visualized Experiments, 2021The genome is organized into topologically associating domains (TADs) delimited by boundaries that isolate interactions between domains. In Drosophila, the mechanisms underlying TAD formation and boundaries are still under investigation. The application of the in-nucleus Hi-C method described here helped to dissect the function of architectural protein
Ayerim, Esquivel-López +3 more
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Visualizing and Annotating Hi-C Data
2021Epigenomics studies require the combined analysis and integration of multiple types of data and annotations to extract biologically relevant information. In this context, sophisticated data visualization techniques are fundamental to identify meaningful patterns in the data in relation to the genomic coordinates.
Pal K, Ferrari F
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Computational Analysis of Hi-C Data
2020The chromatin organization in the 3D nuclear space is essential for genome functionality. This spatial organization encompasses different topologies at diverse scale lengths with chromosomes occupying distinct volumes and individual chromosomes folding into compartments, inside which the chromatin fiber is packed in large domains (as the topologically ...
Forcato M., Bicciato S.
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2021
Processing, storing, and visualizing high-resolution Hi-C data required development of efficient data formats. A sparse matrix format saving only nonzero values has become the norm. A "zoomable" matrix style also became popular, storing multiple resolutions in a single file for interactive visualization.
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Processing, storing, and visualizing high-resolution Hi-C data required development of efficient data formats. A sparse matrix format saving only nonzero values has become the norm. A "zoomable" matrix style also became popular, storing multiple resolutions in a single file for interactive visualization.
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2022
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 study the biological relevance of chromosome folding in cellular processes but also for the de novo assembly of genomes of nonmodel species.
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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 study the biological relevance of chromosome folding in cellular processes but also for the de novo assembly of genomes of nonmodel species.
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Proceedings of the eighteenth ACM SIGSOFT international symposium on Foundations of software engineering, 2010
In prior work we have developed an escape analysis to help developers identify sources of object churn (i.e., excessive use of temporaries) in large framework-based applications. We have developed Hi-C, an Eclipse plug-in that allows users to visualize, filter, and explore analysis results to aid them in diagnosis of object churn and in program ...
Marc Fisher II +2 more
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In prior work we have developed an escape analysis to help developers identify sources of object churn (i.e., excessive use of temporaries) in large framework-based applications. We have developed Hi-C, an Eclipse plug-in that allows users to visualize, filter, and explore analysis results to aid them in diagnosis of object churn and in program ...
Marc Fisher II +2 more
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Science, 2017
Genome Assembly Most genomes sequenced today are determined through the generation of short sequenced bits of DNA that are computationally pieced together like a jigsaw puzzle. This has resulted in the need for funds and additional data to fill in gaps in order to fully assemble the many chromosomes that make up a eukaryotic genome.
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Genome Assembly Most genomes sequenced today are determined through the generation of short sequenced bits of DNA that are computationally pieced together like a jigsaw puzzle. This has resulted in the need for funds and additional data to fill in gaps in order to fully assemble the many chromosomes that make up a eukaryotic genome.
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Read Mapping for Hi-C Analysis
Hi-C is a popular ligation-based technique to detect 3D physical chromosome structure within the nucleus using cross-linking and next-generation sequencing. As an unbiased genome-wide assay based on chromosome conformation capture, it provides rich insights into chromosome structure, dynamic chromosome folding and interactions, and the regulatory stateSimon Thomas, Kelly +3 more
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Methods for the Differential Analysis of Hi-C Data
2021The 3D organization of chromatin within the nucleus enables dynamic regulation and cell type-specific transcription of the genome. This is true at multiple levels of resolution: on a large scale, with chromosomes occupying distinct volumes (chromosome territories); at the level of individual chromatin fibers, which are organized into compartmentalized ...
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