Choosing panels of genomics assays using submodular optimization

Due to the high cost of sequencing-based genomics assays such as ChIP-seq and DNase-seq, the epigenomic characterization of a cell type is typically carried out using a small panel of assay types. Deciding a priori which assays to perform is, thus, a critical step in many studies. We present the sub...

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Detalles Bibliográficos
Autores principales: Wei, Kai, Libbrecht, Maxwell W., Bilmes, Jeffrey A., Noble, William Stafford
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2016
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5111315/
https://www.ncbi.nlm.nih.gov/pubmed/27846892
http://dx.doi.org/10.1186/s13059-016-1089-7
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author Wei, Kai
Libbrecht, Maxwell W.
Bilmes, Jeffrey A.
Noble, William Stafford
author_facet Wei, Kai
Libbrecht, Maxwell W.
Bilmes, Jeffrey A.
Noble, William Stafford
author_sort Wei, Kai
collection PubMed
description Due to the high cost of sequencing-based genomics assays such as ChIP-seq and DNase-seq, the epigenomic characterization of a cell type is typically carried out using a small panel of assay types. Deciding a priori which assays to perform is, thus, a critical step in many studies. We present the submodular selection of assays (SSA), a method for choosing a diverse panel of genomic assays that leverages methods from submodular optimization. More generally, this application serves as a model for how submodular optimization can be applied to other discrete problems in biology. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-016-1089-7) contains supplementary material, which is available to authorized users.
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spelling pubmed-51113152016-11-25 Choosing panels of genomics assays using submodular optimization Wei, Kai Libbrecht, Maxwell W. Bilmes, Jeffrey A. Noble, William Stafford Genome Biol Method Due to the high cost of sequencing-based genomics assays such as ChIP-seq and DNase-seq, the epigenomic characterization of a cell type is typically carried out using a small panel of assay types. Deciding a priori which assays to perform is, thus, a critical step in many studies. We present the submodular selection of assays (SSA), a method for choosing a diverse panel of genomic assays that leverages methods from submodular optimization. More generally, this application serves as a model for how submodular optimization can be applied to other discrete problems in biology. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13059-016-1089-7) contains supplementary material, which is available to authorized users. BioMed Central 2016-11-15 /pmc/articles/PMC5111315/ /pubmed/27846892 http://dx.doi.org/10.1186/s13059-016-1089-7 Text en © The Author(s) 2016 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.
spellingShingle Method
Wei, Kai
Libbrecht, Maxwell W.
Bilmes, Jeffrey A.
Noble, William Stafford
Choosing panels of genomics assays using submodular optimization
title Choosing panels of genomics assays using submodular optimization
title_full Choosing panels of genomics assays using submodular optimization
title_fullStr Choosing panels of genomics assays using submodular optimization
title_full_unstemmed Choosing panels of genomics assays using submodular optimization
title_short Choosing panels of genomics assays using submodular optimization
title_sort choosing panels of genomics assays using submodular optimization
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5111315/
https://www.ncbi.nlm.nih.gov/pubmed/27846892
http://dx.doi.org/10.1186/s13059-016-1089-7
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AT noblewilliamstafford choosingpanelsofgenomicsassaysusingsubmodularoptimization

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