Microarray analysis at single-molecule resolution

IEEE Transactions on Nanobioscience

Volumn 9, Issue 1, 2010, Pages 51-58

  Mureşan, Leila ^a   Jacak, Jarosław ^a   Klement, Erich Peter ^a   Hesse, Jan ^b   Schütz, Gerhard J ^a  

^a JOHANNES KEPLER UNIVERSITY LINZ   (Austria)

^b Upper Austrian Research GmbH   (Austria)

Author keywords

Microarrays; Single molecule imaging

Indexed keywords

A-SPOTS; BACKGROUND NOISE; BIOANALYTICAL; BOUND MOLECULES; CONCENTRATION RANGES; DATA ANALYSIS; DETECTION METHODS; DIFFRACTION LIMITED; FALSE NEGATIVES; FLUORESCENT MOLECULES; FOREGROUND/BACKGROUND; HIGH RESOLUTION; MATHEMATICAL TOOLS; MICROARRAY ANALYSIS; MICROARRAY DATA; MICROARRAY IMAGES; PIXEL INTENSITIES; RELATIVE ERRORS; SIMULATED IMAGES; SINGLE-MOLECULE DETECTION; SINGLE-MOLECULE IMAGING; SINGLE-MOLECULE RESOLUTION; SPATIAL STATISTICS; STATE-OF-THE-ART TECHNOLOGY; TARGET MOLECULE; TRACE AMOUNTS; UNDECIMATED WAVELET TRANSFORM;

MICROARRAYS; MOLECULES; SIGNAL TO NOISE RATIO; WAVELET TRANSFORMS;

DATA HANDLING;

ALGORITHM; ARTICLE; CHEMICAL STRUCTURE; FLUORESCENCE MICROSCOPY; IMAGE PROCESSING; METHODOLOGY; MICROARRAY ANALYSIS; PARTICLE SIZE; STATISTICAL MODEL;

ALGORITHMS; IMAGE PROCESSING, COMPUTER-ASSISTED; MICROARRAY ANALYSIS; MICROSCOPY, FLUORESCENCE; MODELS, MOLECULAR; MODELS, STATISTICAL; PARTICLE SIZE;

EID: 77950523793     PISSN: 15361241     EISSN: None     Source Type: Journal    
DOI: 10.1109/TNB.2010.2040627     Document Type: Article

References (29)

1. J. Hesse, J. Jacak, M. Kasper, G. Regl, T. Eichberger, M. Winklmayr, F. Aberger, M. Sonnleitner, R. Schlapak, S. Howorka, L. Muresan, A. Frischauf, and G. J. Sch ̈utz, "RNA expression profiling at the single molecule level," Genome Res., vol.16, pp. 1041-1045, 2006. (Pubitemid 44162263)
2. V. Nygaard, M. Holden, A. Løland, M. Langaas, O. Myklebost, and E. Hovig. (2005). Limitations of mRNA amplification from small-size cell samples. BMC Genomics. [Online]. vol.6, article no. 147. DOI: 10.1186/1471-2164-6-147. (Pubitemid 41631796)
3. J. Hesse, M. Sonnleitner, A. Sonnleitner, G. Freudenthaler, J. Jacak, O. H ̈oglinger, H. Schindler, and G. Sch ̈utz, "Single-molecule reader for high-throughput bioanalysis," Anal. Chem., vol.76, pp. 5960-5964, 2004. (Pubitemid 39313347)
4. M. Sonnleitner, G. Freudenthaler, J. Hesse, and G. J. Sch ̈uz, "Highthroughput scanning with single-molecule sensitivity," in Proc. SPIE, 2005, pp. 202-210.
5. P. Bajcsy, "An overview of DNA microarray grid alignment and foreground separation approaches," EURASIP J. Appl. Signal Process., vol.2006, pp. 1-13, 2006.
6. Y. H. Yang, M. J. Buckley, and T. Speed, "Analysis of cDNA microarray images," Briefings Bioinform., vol.2, pp. 341-349, 2001.
7. Y. H. Yang, J. Buckley, S. Dudoit, and T. P. Speed, "Comparison of methods for image analysis on cDNAmicroarray data," J. Comput.Graph. Stat., vol.11, pp. 108-136, 2002.
8. Y. Balagurunathan, N. Wang, E. R. Dougherty, D. Nguyen, Y. Chen, M. Bittner, J. Tent, and R. Carroll, "Noise factor analysis for cDNA microarrays," J. Biomed. Opt., vol.9, no.4, pp. 663-678, 2004.
9. J. Angulo, "Polar modelling and segmentation of genomic microarray spots using mathematical morphology," Image Anal. Stereol., vol.27, pp. 107-124, 2008.
10. E. Chudin, S. Kruglyak, S. Baker, S. Oeser, D. Barker, and T. McDaniel, "A model of technical variation of microarray signals," J. Comput. Biol., vol.13, no.4, pp. 996-1003, 2006. (Pubitemid 43941647)
11. E. Korn, J. Habermann, M. Upender, T. Ried, and L. McShane, "Objective method of comparing DNA microarray image analysis systems," Biotech., vol.36, no.6, pp. 960-967, 2004. (Pubitemid 38747359)
12. Q. Li, C. Fraley, R. Bumgarner, K. Yeung, and A. Raftery, "Donuts, scratches and blanks: robust model-based segmentation of microarray images," Bioinformatics, vol.21, no.12, pp. 2875-2882, 2005. (Pubitemid 40862287)
13. P. Sarder, A. Nehorai, P. H. Davis, and S. L. J. Stanley, "Estimating gene signals from noisy microarray images," IEEE Trans. Nanobiosci., vol.7, no.2, pp. 142-153, Jun. 2008. (Pubitemid 351835962)
14. J.-L. Starck, F. Murtagh, and A. Bijaoui, Image and Data Analysis: The Multiscale Approach. Cambridge, U.K.: Cambridge Univ. Press, 1998.
15. J.-C. Olivo-Marin, "Extraction of spots in biological images using multiscale products," Pattern Recog., vol.35, pp. 1989-1996, 2002.
16. S. Mallat, A Wavelet Tour of Signal Processing. San Francisco, CA: Academic, 1999.
17. J. L. Starck, J. Fadili, and F. Murtagh, "The undecimated wavelet decomposition and its reconstruction," IEEE Trans. Image Process., vol.16, no.2, pp. 297-309, Feb. 2007. (Pubitemid 46421673)
18. D. Donoho and I. Johnstone, "Ideal spatial adaptation via wavelet shrinkage," Biometrika, vol.81, pp. 425-455, 1994.
19. D. Donoho, "De noising by soft-thresholidng," IEEE Trans. Inf. Theory, vol.41, no.3, pp. 613-627, May 1995.
20. Y. Benjamini and Y. Hochberg, "Controlling the false discovery rate: A practical and powerful approach to multiple testing," J. Royal Stat. Soc. B, vol.57, no.1, pp. 289-300, 1995.
21. F. Abramovich and Y. Benjamini, "Adaptive thresholding of wavelet coefficients," Comput. Stat. Data Anal., vol.22, pp. 351-361, 1996. (Pubitemid 126395610)
22. I. Johnstone and B. Silverman, "Needles and strawin haystacks: Empirical Bayes estimates of possibly sparse sequences," Ann. Stat., vol.32, no.4, pp. 1594-1649, 2004. (Pubitemid 41250278)
23. I. Johnstone and B. Silverman, "Empirical Bayes selection of wavelet thresholds," Ann. Stat., vol.33, no.4, pp. 1700-1752, 2005. (Pubitemid 41423984)
24. J. Boulanger, J.-B. Sibarita, C. Kervrann, and P. Bouthemy, "Nonparametric regression for patch-based fluorescence microscopy image sequence denoising," in Proc. IEEE Int. Symp. Biomed. Imag.: Nano Macro (ISBI), 2008, pp. 748-751.
25. K. Blekas, N. P. Galatsanos, A. Likas, and I. E. Lagaris, "Mixture model analysis of DNA microarray images," IEEE Trans. Med. Imag., vol.24, no.7, pp. 901-909, Jul. 2005. (Pubitemid 41118468)
26. S. Fr ̈uhwirth-Schnatter, Finite Mixture and Markov Switching Models. New York: Springer-Verlag, 2006.
27. S. Byers and A. E. Raftery, "Nearest-neighbor clutter removal for estimating features in spatial point processes," J. Amer. Staistical Assoc., vol.93, pp. 577-584, 1998. (Pubitemid 128083888)
28. D. B. Murphy, Fundamentals of Light Microscopy and Electronic Imaging. New York: Willey-LISS, 2001.
29. Y. Chen, E. Dougherty, and M. Bittner, "Ratio-based decisions and the quantitative analysis of cDNAmicroarray images," J. Biomed.Opt., vol.2, no.4, pp. 364-374, 1997. (Pubitemid 127663500)