Submodular Selection of Assays v0.1

Submodular-Selection-of-Assays (SSA)

Please see the following manuscript for more details: Kai Wei * , Maxwell W. Libbrecht * , Jeffrey A Bilmes, William S. Noble. "Evaluation and selection of panels of genomics assays." Submitted.

Get the most recent version on github: https://github.com/melodi-lab/Submodular-Selection-of-Assays

Abstract: Due to the high cost of sequencing-based genomics assays such as ChIP-seq and DNase-seq, 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 submodular selection of assays (SSA), a method for choosing a diverse panel of genomic assays that leverages methods from the field of submodular optimization. More generally, this application serves as a model for how submodular optimization can be applied to other discrete problems in biology.