Jeff A. Bilmes's Publications

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Choosing panels of genomics assays using submodular optimization

Kai Wei, Maxwell W. Libbrecht, Jeffrey A. Bilmes, and William Stafford Noble. Choosing panels of genomics assays using submodular optimization. Genome Biology, 17(1):229, 2016.

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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.

@Article{wei2016genomicselection,
author="Wei, Kai and Libbrecht, Maxwell W. and Bilmes, Jeffrey A. and Noble, William Stafford",
title="Choosing panels of genomics assays using submodular optimization",
journal="Genome Biology",
year="2016",
volume="17",
number="1",
pages="229",
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.",
issn="1474-760X",
doi="10.1186/s13059-016-1089-7",
url="http://dx.doi.org/10.1186/s13059-016-1089-7",
}

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