ChromeBat: A Bio-Inspired Approach to 3D Genome Reconstruction

With the advent of Next Generation Sequencing and the Hi-C experiment, high quality genome-wide contact data are becoming increasingly available. These data represents an empirical measure of how a genome interacts inside the nucleus. Genome conformation is of particular interest as it has been expe...

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Autores principales:	Brandon Collins, Oluwatosin Oluwadare, Philip Brown
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	Hi-C 3D chromosome structure bat algorithm chromosome conformation capture 3D genome Genetics QH426-470
Acceso en línea:	https://doaj.org/article/eccfe16108b34c969cd52308ec59af00
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id	oai:doaj.org-article:eccfe16108b34c969cd52308ec59af00
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spelling	oai:doaj.org-article:eccfe16108b34c969cd52308ec59af002021-11-25T17:41:35ZChromeBat: A Bio-Inspired Approach to 3D Genome Reconstruction10.3390/genes121117572073-4425https://doaj.org/article/eccfe16108b34c969cd52308ec59af002021-11-01T00:00:00Zhttps://www.mdpi.com/2073-4425/12/11/1757https://doaj.org/toc/2073-4425With the advent of Next Generation Sequencing and the Hi-C experiment, high quality genome-wide contact data are becoming increasingly available. These data represents an empirical measure of how a genome interacts inside the nucleus. Genome conformation is of particular interest as it has been experimentally shown to be a driving force for many genomic functions from regulation to transcription. Thus, the Three Dimensional-Genome Reconstruction Problem (3D-GRP) seeks to take Hi-C data and produces a complete physical genome structure as it appears in the nucleus for genomic analysis. We propose and develop a novel method to solve the Chromosome and Genome Reconstruction problem based on the Bat Algorithm (BA) which we called ChromeBat. We demonstrate on real Hi-C data that ChromeBat is capable of state-of-the-art performance. Additionally, the domain of Genome Reconstruction has been criticized for lacking algorithmic diversity, and the bio-inspired nature of ChromeBat contributes algorithmic diversity to the problem domain. ChromeBat is an effective approach for solving the Genome Reconstruction Problem.Brandon CollinsOluwatosin OluwadarePhilip BrownMDPI AGarticleHi-C3D chromosome structurebat algorithmchromosome conformation capture3D genomeGeneticsQH426-470ENGenes, Vol 12, Iss 1757, p 1757 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Hi-C 3D chromosome structure bat algorithm chromosome conformation capture 3D genome Genetics QH426-470
spellingShingle	Hi-C 3D chromosome structure bat algorithm chromosome conformation capture 3D genome Genetics QH426-470 Brandon Collins Oluwatosin Oluwadare Philip Brown ChromeBat: A Bio-Inspired Approach to 3D Genome Reconstruction
description	With the advent of Next Generation Sequencing and the Hi-C experiment, high quality genome-wide contact data are becoming increasingly available. These data represents an empirical measure of how a genome interacts inside the nucleus. Genome conformation is of particular interest as it has been experimentally shown to be a driving force for many genomic functions from regulation to transcription. Thus, the Three Dimensional-Genome Reconstruction Problem (3D-GRP) seeks to take Hi-C data and produces a complete physical genome structure as it appears in the nucleus for genomic analysis. We propose and develop a novel method to solve the Chromosome and Genome Reconstruction problem based on the Bat Algorithm (BA) which we called ChromeBat. We demonstrate on real Hi-C data that ChromeBat is capable of state-of-the-art performance. Additionally, the domain of Genome Reconstruction has been criticized for lacking algorithmic diversity, and the bio-inspired nature of ChromeBat contributes algorithmic diversity to the problem domain. ChromeBat is an effective approach for solving the Genome Reconstruction Problem.
format	article
author	Brandon Collins Oluwatosin Oluwadare Philip Brown
author_facet	Brandon Collins Oluwatosin Oluwadare Philip Brown
author_sort	Brandon Collins
title	ChromeBat: A Bio-Inspired Approach to 3D Genome Reconstruction
title_short	ChromeBat: A Bio-Inspired Approach to 3D Genome Reconstruction
title_full	ChromeBat: A Bio-Inspired Approach to 3D Genome Reconstruction
title_fullStr	ChromeBat: A Bio-Inspired Approach to 3D Genome Reconstruction
title_full_unstemmed	ChromeBat: A Bio-Inspired Approach to 3D Genome Reconstruction
title_sort	chromebat: a bio-inspired approach to 3d genome reconstruction
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/eccfe16108b34c969cd52308ec59af00
work_keys_str_mv	AT brandoncollins chromebatabioinspiredapproachto3dgenomereconstruction AT oluwatosinoluwadare chromebatabioinspiredapproachto3dgenomereconstruction AT philipbrown chromebatabioinspiredapproachto3dgenomereconstruction
_version_	1718412138833248256

ChromeBat: A Bio-Inspired Approach to 3D Genome Reconstruction

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