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
Descripción
Sumario: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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