Compressive sensing DNA microarrays

A Compressive Sensing Microarray (CSM), based on the theory of Compressive Sensing (CS), is used to identify target organisms with fewer shared probes than a regular DNA microarray would require, with each probe identifying a group of targets. We propose an algorithm to design these group identifier probes by accounting for the constraints from CS theory as well as the biochemistry of probe-target DNA hybridization. The CSM alleviates three problems faced by traditional microarrays: (1) cross-hybridization events that lead to errors in array readout, (2) difficulty in sensing a large number of organisms while simultaneously miniaturizing the array, and (3) an inefficient utilization of the large number of array spots due to the sparsity of target type in a given sample. Finally we employ Belief Propagation as a CS-based recovery method to estimate target concentrations from the microarray intensities.

Authors: Mona A. Sheikh

Publications: Probe Design for Compressive Sensing Microarray (BIBM '08), Designing Compressive Sensing Microarrays (CAMSAP '07), DNA Array Decoding from Nonlinear Measurements by Belief Propagation (SSP '07)

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