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Title: Representation of Chromosome Conformations Using a Shape Alphabet Across Modeling Methods
Despite enormous structural variability exhibited in 3D chromosomal conformations at a global scale, there is a significant commonality of structures visible at smaller, local levels. We hypothesize that chromosomal conformations are representable as concatenations of a handful of prototypical shapelets, termed shape letters. This is akin to expressing complicated sentences in a language using only a small set of letters. Our goal is to organize the vast variability of 3D chromosomal conformation by constructing a set of predominant shape letters, termed a shape alphabet, using statistical shape analysis of curvelets taken from training conformations. This paper utilizes conformations generated from Integrative Genome Modeling to develop a shape alphabet as follows: it first segments 3D conformations into curvelets according to their Topologically Associated Domains. It then clusters these segments, estimates mean shapes, and refines and reorders these shapes into a Chromosome Shape Alphabet. The paper demonstrates effectiveness of this construction by successfully representing independent test conformations taken from IGM and other methods such as SIMBA3D, both symbolically and structurally, using the constructed alphabet.  more » « less
Award ID(s):
1953087 1853209
NSF-PAR ID:
10339552
Author(s) / Creator(s):
; ; ; ; ;
Date Published:
Journal Name:
2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
Page Range / eLocation ID:
151 to 156
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
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