Phát hiện các gen tuần hoàn từ các biểu hiện gen được lấy mẫu không đồng đều: Nghiên cứu so sánh

Spellman PT, Sherlock G, Zhang MQ, et al.: Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Molecular Biology of the Cell 1998,9(12):3273-3297. Whitfield ML, Sherlock G, Saldanha AJ, et al.: Identification of genes periodically expressed in the human cell cycle and their expression in tumors. Molecular Biology of the Cell 2002,13(6):1977-2000. 10.1091/mbc.02-02-0030. Arbeitman MN, Furlong EEM, Imam F, et al.: Gene expression during the life cycle of Drosophila melanogaster . Science 2002,297(5590):2270-2275. 10.1126/science.1072152 Giurcaneanu CD: Stochastic complexity for the detection of periodically expressed genes. Proceedings of IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS '07), Tuusula, Finland, June 2007 1-4. Ahdesmäki M, Lähdesmäki H, Pearson R, Huttunen H, Yli-Harja O: Robust detection of periodic time series measured from biological systems. BMC Bioinformatics 2005, 6, article 117: 1-18. Luan Y, Li H: Model-based methods for identifying periodically expressed genes based on time course microarray gene expression data. Bioinformatics 2004,20(3):332-339. 10.1093/bioinformatics/btg413 Lu X, Zhang W, Qin ZS, Kwast KE, Liu JS: Statistical resynchronization and Bayesian detection of periodically expressed genes. Nucleic Acids Research 2004,32(2):447-455. 10.1093/nar/gkh205 Wichert S, Fonkianos K, Strimmer K: Identifying periodically expressed trascripts in microarry time series data. Bioinformatics 2004,20(1):5-20. 10.1093/bioinformatics/btg364 Bowles T, Jakobsson A, Chambers J: Detection of cell-cyclic elements in mis-sampled gene expression data using a robust Capon estimator. Proceedings of IEEE International Conference on Acoustics, Speech and Signal Processing (ICASSP '04), Montreal, Canada, May 2004 5: 417-420. de Lichtenberg U, Jensen LJ, Fausbøll A, Jensen TS, Bork P, Brunak S: Comparison of computational methods for the identification of cell cycle-regulated genes. Bioinformatics 2005,21(7):1164-1171. 10.1093/bioinformatics/bti093 Stoica P, Moses RL: Introduction to Spectral Analysis. Prentice Hall, Upper Saddle River, NJ, USA; 1997. Lomb NR: Least-squares frequency analysis of unequally spaced data. Astrophysics and Space Science 1976,39(2):447-462. 10.1007/BF00648343 Scargle JD: Studies in astronomical time series analysis—II: statistical aspects of spectral analysis of unevenly spaced data. The Astrophysics Journal 1982, 263: 835-853. Glynn EF, Chen J, Mushegian AR: Detecting periodic patterns in unevenly spaced gene expression time series using Lomb-Scargle periodograms. Bioinformatics 2006,22(3):310-316. 10.1093/bioinformatics/bti789 Schwarzenberg-Czerny A: On the advantage of using analysis of variance for period search. Monthly Notices of the Royal Astronomical Society 1989, 241: 153-165. Ahdesmäki M, Lähdesmäki H, Gracey A, Shmulevich I, Yli-Harja O: Robust regression for periodicity detection in non-uniformly sampled time-course gene expression data. BMC Bioinformatics 2007, 8, article 233: 1-16. Stoica P, Sandgren N: Spectral analysis of irregularly-sampled data: paralleling the regularly-sampled data approaches. Digital Signal Processing 2006,16(6):712-734. 10.1016/j.dsp.2006.08.012 Wang Y, Stoica P, Li J, Marzetta TL: Nonparametric spectral analysis with missing data via the EM algorithm. Digital Signal Processing 2005,15(2):191-206. 10.1016/j.dsp.2004.10.004 "Supplementary Materials", prepared in Microsoft Excel[http://www.ee.tamu.edu/~wtzhao/Research.html] Eyer L, Bartholdi P: Variable stars: which Nyquist frequency? Astronomy and Astrophysics Supplement Series 1999,135(1):1-3. 10.1051/aas:1999102 Fan J, Yao Q: Nonlinear Time series: Nonparametric and Parametric Methods. Springer, New York, NY, USA; 2003. Fisher RA: Tests of significance in harmonic analysis. Proceedings of the Royal Society of London. Series A 1929,125(796):54-59. 10.1098/rspa.1929.0151 Brockwell PJ, Davis RA: Time Series Theory and Methods. 2nd edition. Springer, New York, NY, USA; 1987. Ahdesmaki M, Lahdesmaki H, Yli-Harja O: Roubust Fisher's test for peridocity detection in noisy biological time series. Proceedings of IEEE international Workshop on Genomic Signal Processing and Statistics (GENSIPS '07), Tuusula, Finland, June 2007 Storey JD: A direct approach to false discovery rates. Journal of the Royal Statistical Society. Series B 2002,64(3):479-498. 10.1111/1467-9868.00346 Storey JD:The positive false discovery rate: a Bayesian interpretation and the -value. Annals of Statistics 2003,31(6):2013-2035. 10.1214/aos/1074290335 de Lichtenberg U, Wernersson R, Jensen TS, et al.: New weakly expressed cell cycle-regulated genes in yeast. Yeast 2005,22(15):1191-1201. 10.1002/yea.1302 Reiter LT, Potocki L, Chien S, Gribskov M, Bier E: A systematic analysis of human disease-associated gene sequences in Drosophila melanogaster . Genome Research 2001,11(6):1114-1125. 10.1101/gr.169101 Cooper S: Rethinking synchronization of mammalian cells for cell cycle analysis. Cellular and Molecular Life Sciences 2003,60(6):1099-1106.