English (United Kingdom)

https://curated-unify.zendy.io/wp-json/zendy-region/v1/featured_content/oa?rat=en

https://curated-unify.zendy.io/wp-json/zendy-region/v1/highlighted_journal/

Global: Zendy Plus annual

Presents the access of premium content as premium feature

Premium Content

Presents the keyphrase highlighting as premium feature

Keyphrase Highlighting

Presents the summarisation as premium feature

Summarisation

Insights

Presents the pdf analysis as premium feature

PDF Analysis

Presents the zaia usage as premium feature

ZAIA

Global: Zendy Tools annual

Global: Zendy Free Plan

Global: Zendy Tools monthly

Global: Zendy Plus monthly

How chromosomes fold and how distal genomic elements interact with one another at a genomic scale have been actively pursued in the past decade following the seminal work describing the Chromosome Conformation Capture (3C) assay. Essentially, 3C-based technologies produce two-dimensional (2D) contact maps that capture interactions between genomic fragments. Accordingly, a plethora of analytical methods have been proposed to take a 2D contact map as input to recapitulate the underlying whole genome three-dimensional (3D) structure of the chromatin. However, their performance in terms of several factors, including data resolution and ability to handle contact map features, have not been sufficiently evaluated. This task is taken up in this article, in which we consider several recent and/or well-regarded methods, both optimization-based and model-based, for their aptness of producing 3D structures using contact maps generated based on a population of cells. These methods are evaluated and compared using both simulated and real data. Several criteria have been used. For simulated data sets, the focus is on accurate recapitulation of the entire structure given the existence of the gold standard. For real data sets, comparison with distances measured by Florescence in situ Hybridization and consistency with several genomic features of known biological functions are examined.

Evaluation and comparison of methods for recapitulation of 3D spatial chromatin structures