UMMS Affiliation

Program in Bioinformatics and Integrative Biology

Publication Date

2019-08-28

Document Type

Article

Disciplines

Artificial Intelligence and Robotics | Biochemistry | Computational Biology | Genetic Phenomena | Genomics | Molecular Biology | Theory and Algorithms

Abstract

Semi-automated genome annotation methods such as Segway take as input a set of genome-wide measurements such as of histone modification or DNA accessibility and output an annotation of genomic activity in the target cell type. Here we present annotations of 164 human cell types using 1615 data sets. To produce these annotations, we automated the label interpretation step to produce a fully automated annotation strategy. Using these annotations, we developed a measure of the importance of each genomic position called the "conservation-associated activity score." We further combined all annotations into a single, cell type-agnostic encyclopedia that catalogs all human regulatory elements.

Keywords

Chromatin, Genomics, Machine learning

Rights and Permissions

© The Author(s). 2019 Open Access: This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

DOI of Published Version

10.1186/s13059-019-1784-2

Source

Genome Biol. 2019 Aug 28;20(1):180. doi: 10.1186/s13059-019-1784-2. Link to article on publisher's site

Journal/Book/Conference Title

Genome biology

Related Resources

Link to Article in PubMed

PubMed ID

31462275

Creative Commons License

Creative Commons Attribution 4.0 License
This work is licensed under a Creative Commons Attribution 4.0 License.

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