Compressive Sensing DNA Microarrays

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Title: Compressive Sensing DNA Microarrays
Authors: Dai, W
Sheikh, MA
Milenkovic, O
Baraniuk, RG
Item Type: Journal Article
Abstract: Compressive sensing microarrays (CSMs) are DNA-based sensors that operate using group testing and compressive sensing (CS) principles. In contrast to conventional DNA microarrays, in which each genetic sensor is designed to respond to a single target, in a CSM, each sensor responds to a set of targets. We study the problem of designing CSMs that simultaneously account for both the constraints from CS theory and the biochemistry of probe-target DNA hybridization. An appropriate cross-hybridization model is proposed for CSMs, and several methods are developed for probe design and CS signal recovery based on the new model. Lab experiments suggest that in order to achieve accurate hybridization profiling, consensus probe sequences are required to have sequence homology of at least 80% with all targets to be detected. Furthermore, out-of-equilibrium datasets are usually as accurate as those obtained from equilibrium conditions. Consequently, one can use CSMs in applications in which only short hybridization times are allowed.
Issue Date: 13-Jan-2009
Date of Acceptance: 23-Oct-2008
ISSN: 1687-4153
Publisher: Hindawi Publishing Corporation
Journal / Book Title: Eurasip Journal on Bioinformatics and Systems Biology
Volume: 2009
Copyright Statement: Copyright © 2009 Wei Dai et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Publication Status: Published
Article Number: 162824
Appears in Collections:Faculty of Engineering
Electrical and Electronic Engineering

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