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Choosing panels of genomics assays using submodular optimization.

ABSTRACT: 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.

SUBMITTER: Wei K

PROVIDER: S-EPMC5111315 | biostudies-literature | 2016 Nov

REPOSITORIES: biostudies-literature

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Choosing panels of genomics assays using submodular optimization.

Wei Kai K Libbrecht Maxwell W MW Bilmes Jeffrey A JA Noble William Stafford WS

Genome biology 20161115 1

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 h ...[more]

PMID: 27846892

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