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LeNup: learning nucleosome positioning from DNA sequences with improved convolutional neural networks

LeNup: learning nucleosome positioning from DNA sequences with improved convolutional neural... MotivationNucleosome positioning plays significant roles in proper genome packing and its accessibility to execute transcription regulation. Despite a multitude of nucleosome positioning resources available on line including experimental datasets of genome-wide nucleosome occupancy profiles and computational tools to the analysis on these data, the complex language of eukaryotic Nucleosome positioning remains incompletely understood.ResultsHere, we address this challenge using an approach based on a state-of-the-art machine learning method. We present a novel convolutional neural network (CNN) to understand nucleosome positioning. We combined Inception-like networks with a gating mechanism for the response of multiple patterns and long term association in DNA sequences. We developed the open-source package LeNup based on the CNN to predict nucleosome positioning in Homo sapiens, Caenorhabditis elegans, Drosophila melanogaster as well as Saccharomyces cerevisiae genomes. We trained LeNup on four benchmark datasets. LeNup achieved greater predictive accuracy than previously published methods.Availability and implementationLeNup is freely available as Python and Lua script source code under a BSD style license from https://github.com/biomedBit/LeNup.Supplementary informationSupplementary data are available at Bioinformatics online. http://www.deepdyve.com/assets/images/DeepDyve-Logo-lg.png Bioinformatics Oxford University Press

LeNup: learning nucleosome positioning from DNA sequences with improved convolutional neural networks

Bioinformatics , Volume 34 (10): 8 – Jan 10, 2018
8 pages

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References (88)

Publisher
Oxford University Press
Copyright
© The Author(s) 2018. Published by Oxford University Press.
ISSN
1367-4803
eISSN
1460-2059
DOI
10.1093/bioinformatics/bty003
Publisher site
See Article on Publisher Site

Abstract

MotivationNucleosome positioning plays significant roles in proper genome packing and its accessibility to execute transcription regulation. Despite a multitude of nucleosome positioning resources available on line including experimental datasets of genome-wide nucleosome occupancy profiles and computational tools to the analysis on these data, the complex language of eukaryotic Nucleosome positioning remains incompletely understood.ResultsHere, we address this challenge using an approach based on a state-of-the-art machine learning method. We present a novel convolutional neural network (CNN) to understand nucleosome positioning. We combined Inception-like networks with a gating mechanism for the response of multiple patterns and long term association in DNA sequences. We developed the open-source package LeNup based on the CNN to predict nucleosome positioning in Homo sapiens, Caenorhabditis elegans, Drosophila melanogaster as well as Saccharomyces cerevisiae genomes. We trained LeNup on four benchmark datasets. LeNup achieved greater predictive accuracy than previously published methods.Availability and implementationLeNup is freely available as Python and Lua script source code under a BSD style license from https://github.com/biomedBit/LeNup.Supplementary informationSupplementary data are available at Bioinformatics online.

Journal

BioinformaticsOxford University Press

Published: Jan 10, 2018

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