Choosing panels of genomics assays using submodular optimization. Issue 1 (December 2016)

• Record Type: Journal Article
• Authors: Wei, Kai; Libbrecht, Maxwell W.; Bilmes, Jeffrey A.; Noble, William Stafford
• Is Part Of: Genome biology. Volume 17:Issue 1(2016)
• Page Start: 1
• Page End: 15
• Publication Date: 2016-12
• Subjects: Genomics assays -- Submodularity -- Discrete optimization; Genomes -- Periodicals; Biology -- Periodicals; Molecular biology -- Periodicals; 572.8633
• DOI: 10.1186/s13059-016-1089-7
• Languages: English
• ISSNs: 1474-760X

Abstract

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.