Probe design for compressive sensing DNA microarrays

Wei Dai, Olgica Milenkovic, Mona A. Sheikh, Richard G. Baraniuk

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Compressive Sensing Microarrays (CSM) are DNA-based sensors that operate using the principle of compressive sensing (CS). 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 group of targets. We study the problem of designing CS probes that simultaneously account for both the constraints from group testing theory and the biochemistry of probe-target DNA hybridization. Our results show 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, experiments show that out-of-equilibrium datasets are usually as accurate as those obtained from equilibrium conditions. Consequently, one can use CSMs in applications for which only short hybridization times are allowed.

Original languageEnglish (US)
Title of host publicationProceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008
Pages163-169
Number of pages7
DOIs
StatePublished - Dec 1 2008
Event2008 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008 - Philadelphia, PA, United States
Duration: Nov 3 2008Nov 5 2008

Publication series

NameProceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008

Other

Other2008 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008
CountryUnited States
CityPhiladelphia, PA
Period11/3/0811/5/08

ASJC Scopus subject areas

  • Molecular Biology
  • Information Systems
  • Biomedical Engineering

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  • Cite this

    Dai, W., Milenkovic, O., Sheikh, M. A., & Baraniuk, R. G. (2008). Probe design for compressive sensing DNA microarrays. In Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008 (pp. 163-169). [4684888] (Proceedings - IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2008). https://doi.org/10.1109/BIBM.2008.56