DNA array decoding from nonlinear measurements by belief propagation

IEEE Workshop on Statistical Signal Processing Proceedings

Volumn , Issue , 2007, Pages 215-219

  Sheikh, Mona A ^a   Sarvotham, Shriram ^a   Milenkovic, Olgica ^b   Baraniuk, Richard G ^a  

^a Rice University   (United States)

^b UCB 450   (United States)

Author keywords

Belief propagation; Compressed sensing; DNA microarray; Saturated measurements

Indexed keywords

BACKPROPAGATION; BACKPROPAGATION ALGORITHMS; DECODING; DNA; GENES; NUCLEIC ACIDS; ORGANIC ACIDS; SIGNAL PROCESSING; SIGNAL RECONSTRUCTION; TECHNICAL PRESENTATIONS;

BELIEF PROPAGATION; COMPRESSED SENSING; DNA ARRAYS; DNA MICROARRAY; DNA MOLECULES; GREEDY ALGORITHMS; HIGH CONCENTRATIONS; LINEAR COMBINATIONS; NON LINEARITIES; NON-LINEAR MEASUREMENTS; NONLINEAR EFFECTS; ORIGINAL SIGNALS; SATURATED MEASUREMENTS; SIGNAL RECOVERIES; TARGET SIGNALS;

DNA SEQUENCES;

EID: 47049112174     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/SSP.2007.4301250     Document Type: Conference Paper

References (16)

1. "Affymetrix microarrays," http://www.affymetrix.com/products/ arrays/ specific/cexpress.affx.
2. A. Taylor, E. Turner, J. Townsend, J. Dettman, and D. Jacobson, "Eukaryotic microbes, species recognition and the geographic limits of species: examples from the kingdom fungi.," Phil. Trans. of the Royal Society of London Bio. Sciences, vol. 361, pp. 1947-1963, 2006.
3. M. Schienle, C. Paulus, A. Frey, F. Hofmann, B. Holzapfl, O. Schindler-Bauer, and R. Thewes, "A fully electronic DNA sensor with 128 positions and in-pixel A/D conversion," IEEE Journal of Solid-State Circuits, vol. 39, no. 12, 2004.
4. O. Milenkovic, R. Baraniuk, and T. Simunic-Rosing, "Compressed sensing meets bioinformatics: A novel DNA microarray design.," in Second Annual ITA Workshop, San Diego, California, January 2007.
5. L. Buck and R. Axel, "Nobel prize 2004," http://nobelprize.org/ nobel prizes/medicine/laureates/2004.
6. M. A. Sheikh, S. Sarvotham, O. Milenkovic, and R. G. Baraniuk, "Compressed sensing DNA microarrays," 2007, Technical Report ECE-0706.
7. S. Sarvotham, D. Baron, and R. G. Baraniuk, "Compressed sensing reconstruction via belief propagation," 2006, Technical Report ECE-06-01.
8. D. Z. Du and F. K. Hwang, Combinatorial group testing and its applications, World Scientific Publishing Co., 2000.
9. A. Schliep, D. Torney, and S. Rahmann, "Proceedings of the computational systems bioinformatics," 2003.
10. E. J. Candés and T. Tao, "Decoding by linear programming," IEEE Trans. Inform. Theory, vol. 51, pp. 4203-4215, Dec. 2005.
11. Y. Chen, C.C. Chou, X. Lu, E. Slate, K. Peck, W. Xu, E. Voit, and J. Almeida, "A multivariate prediction model for microarray cross-hybridization.," BMC Bioinformatics, vol. 7, no. 1, pp. 101-112, 2006.
12. "Clusters of orthologous groups - NCBI/NIH.," Available at http://www.ncbi.nlm.nih.gov/COG/.
13. S. Schwartz, W. J. Kent, A. Smith, Z. Zhang, R. Baertsch, R. C. Hardison, D. Haussler, and W. Miller, "Human-mouse alignments with blastz," January 2003.
14. B. Snel, P. Bork, and M. A. Huynen, "The identification of functional modules from the genomic association of genes.," PNAS, vol. 99, no. 9, pp. 5890-5895, 2002.
15. D. Hekstra, D. Taussig, A. Magnasco, and M. Naef, "Absolute mRNA concentrations from sequence-specific calibration of oligonucleotide arrays.," Nucleic Acids Research, vol. 31, pp. 1962-1968, 2003.
16. M. D. Kane, "Assesment of the sensitivity and specificity of oligonucleotide (50mer) microarrays.," Nucleic Acids Research, vol. 28, pp. 4552-4557, 2000.