TY - JOUR
T1 - Compressive sensing DNA microarrays
AU - Dai, Wei
AU - Sheikh, Mona A.
AU - Milenkovic, Olgica
AU - Baraniuk, Richard G.
N1 - Funding Information:
This work was supported by NSF Grants CCF 0821910 and CCF 0809895. The authors also gratefully acknowledge many useful discussions with Xiaorong Wu from the University of Colorado at Denver School of Medicine.
PY - 2009
Y1 - 2009
N2 - 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.
AB - 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.
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U2 - 10.1155/2009/162824
DO - 10.1155/2009/162824
M3 - Article
C2 - 19158952
AN - SCOPUS:59849117352
SN - 1687-4145
VL - 2009
JO - Eurasip Journal on Bioinformatics and Systems Biology
JF - Eurasip Journal on Bioinformatics and Systems Biology
M1 - 162824
ER -