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.



Work Title Representation of Chromosome Conformations Using a Shape Alphabet Across Modeling Methods
Open Access
  1. Carlos Soto
  2. Audrey Dalgarno
  3. Darshan Bryner
  4. Benjamin McLaughlin
  5. Nicola Neretti
  6. Anuj Srivastava
License In Copyright (Rights Reserved)
Work Type Article
  1. 2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)
Publication Date January 14, 2021
Publisher Identifier (DOI)
Deposited November 14, 2022




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Work History

Version 1

  • Created
  • Added Representation_of_Chromosome_Conformations_Using_a_Shape_Alphabet_Across_Modeling_Methods.pdf
  • Added Creator Carlos Soto
  • Added Creator Audrey Dalgarno
  • Added Creator Darshan Bryner
  • Added Creator Benjamin McLaughlin
  • Added Creator Nicola Neretti
  • Added Creator Anuj Srivastava
  • Published