Microarray Analysis References

Speed Group Microarray Page (http://www.stat.berkeley.edu/users/terry/zarray/Html/papersindex.html)
The MGED Data Transformation and Normalization Working Group (http://www.dnachip.org/mged/normalization.html)
GEDA References for Microarray Analysis. http://bioinformatics.upmc.edu/Help/MicroarrayReferences.html.
Smyth, G.K., Y.H. Yang, and T. Speed. To Appear. Statistical issues in cDNA microarray data analysis. To appear in M.J. Brownstein and A.B. Khodursky (eds.). Functional Genomics: Methods and Protocols, Methods in Molecular Biology Series, Humana Press, Totowa, NJ, 2002. (PDF)
Chu, Tzu-Ming, Bruce Weir, and Russ Wolfinger. 2002. A systematic statistical linear modeling approach to oligonucleotide array experiments. Mathematical Biosciences 176, 35-51.
Chu, Tzu-Ming, Bruce Weir, and Russ Wolfinger. Submitted. Comparison of Li-Wong and loglinear mixed models for the statistical analysis of oligonucleotide arrays.
Wolfinger, R.D., G. Gibson, E.D. Wolfinger, L Bennett, H Hamadeh, P. Bushel, C. Afshari, and R.S. Paules. 2001. Assessing gene significance from cDNA microarray expression data via mixed models. Journal of Computational Biology, 8, 625-637.
http://statgen.ncsu.edu/ggibson/Manual.htm
http://users.utu.fi/esauusi/kurssit/microarrays/Turku2003.ppt
S. Bhattacharya, S. Patel, J. Lyons-Weiler. 2003. Significance Analysis of Microarray in the GEDA Web Application. Final draft: 6/25/03. (HTML)
Chiara Sabatti. 2001. Inference on Gene Expression Changes as Measured with DNA Microarrays. Chiara Sabatti, UCLA, DNA Microarray: Principles and Biotechnological Applications, UCLA September 10-13, 2001. (PDF)
Contacts: Korbinian Strimmer and Ludwig Fahrmeir. Statistical Analysis of Gene Expression Data: An Introduction. Summer 2002, Seminar course at the Department of Statistics, University of Munich. Presented by the Laboratory of Statistical Genetics and Bioinformatics. (HTML)
BIOSTATISTICS 140.688: STATISTICS FOR GENE EXPRESSION. CLASS SCHEDULE and READING LIST, SPRING 2003. (HTML)
References for Microarray Data Analysis. PubH 5470-2 (Spring 2002). (HTML)
Tibshirani Technical Reports. (HTML)
Virginia Goss Tusher, Robert Tibshirani, and Gilbert Chu. 2001. Significance analysis of microarrays applied to the ionizing radiation response. Proc. Natl. Acad. Sci. USA, 98 (9, April 24, 2001), 5116-5121. (PDF)
J. D. Storey and R. Tibshirani. 2003. Statistical significance for genomewide studies. PNAS, August 5, 2003; 100(16): 9440 - 9445. (PDF)
A. Reverter, K. A. Byrne, H. L. Bruce, Y. H. Wang, B. P. Dalrymple, and S. A. Lehnert. 2003. A mixture model-based cluster analysis of DNA microarray gene expression data on Brahman and Brahman composite steers fed high-, medium-, and low-quality diets J Anim Sci, August 1, 2003; 81(8): 1900 - 1910. (PDF)
C. Cheadle, M. P. Vawter, W. J. Freed, and K. G. Becker. 2003. Analysis of Microarray Data Using Z Score Transformation Mol. Diagn., May 1, 2003; 5(2): 73 - 81.
N.M. Svrakic, O. Nesic, M.R.K. Dasu, D. Herndon, and J.R. Perez-Polo. 2003. Statistical Approach to DNA Chip Analysis Recent Prog. Horm. Res., January 1, 2003; 58(1): 75 - 93.
J. P. Brody, B. A. Williams, B. J. Wold, and S. R. Quake. 2002. Significance and statistical errors in the analysis of DNA microarray data PNAS, October 1, 2002; 99(20): 12975 - 12978. (PDF)
M. D. W. Piper, P. Daran-Lapujade, C. Bro, B. Regenberg, S. Knudsen, J. Nielsen, and J. T. Pronk. 2002. Reproducibility of Oligonucleotide Microarray Transcriptome Analyses. AN INTERLABORATORY COMPARISON USING CHEMOSTAT CULTURES OF SACCHAROMYCES CEREVISIAE J. Biol. Chem., October 4, 2002; 277(40): 37001 - 37008. (PDF)
A. D. Strand, J. M. Olson, and C. Kooperberg. 2002. Estimating the statistical significance of gene expression changes observed with oligonucleotide arrays Hum. Mol. Genet., September 15, 2002; 11(19): 2207 - 2221.
X. L. Xu, J. M. Olson, and L. P. Zhao. 2002. A regression-based method to identify differentially expressed genes in microarray time course studies and its application in an inducible Huntington's disease transgenic model Hum. Mol. Genet., August 15, 2002; 11(17): 1977 - 1985.
N. Kaminski and N. Friedman. 2002. Practical Approaches to Analyzing Results of Microarray Experiments Am. J. Respir. Cell Mol. Biol., August 1, 2002; 27(2): 125 - 132. (PDF)
Y. Xu, F. M. Selaru, J. Yin, T. T. Zou, V. Shustova, Y. Mori, F. Sato, T. C. Liu, A. Olaru, S. Wang, M. C. Kimos, K. Perry, K. Desai, B. D. Greenwald, M. J. Krasna, D. Shibata, J. M. Abraham, and S. J. Meltzer. 2002. Artificial Neural Networks and Gene Filtering Distinguish Between Global Gene Expression Profiles of Barrett's Esophagus and Esophageal Cancer Cancer Res., June 1, 2002; 62(12): 3493 - 3497. (PDF)
K.-H. Pan, C.-J. Lih, and S. N. Cohen. 2002. Analysis of DNA microarrays using algorithms that employ rule-based expert knowledge PNAS, February 19, 2002; 99(4): 2118 - 2123. (PDF)
J. S. Rao and M. Bond. 2001. Microarrays : Managing the Data Deluge Circ. Res., June 22, 2001; 88(12): 1226 - 1227. (PDF)
C. Kooperberg, S. Sipione, M. LeBlanc, A. D. Strand, E. Cattaneo, and J. M. Olson. 2002. Evaluating test statistics to select interesting genes in microarray experiments Hum. Mol. Genet., September 15, 2002; 11(19): 2223 - 2232.
Morrison DA, Ellis JT. 2003. The design and analysis of microarray experiments: applications in parasitology. DNA AND CELL BIOLOGY 22 (6): 357-394 JUN 2003. (HTML)
Xu RH, Li XC. 2003. A comparison of parametric versus permutation methods with applications to general and temporal microarray gene expression data. BIOINFORMATICS 19 (10): 1284-1289 JUL 1 2003. (HTML)
Ge YC, Dudoit S, Speed TP. 2003. Resampling-based multiple testing for microarray data analysis. TEST 12 (1): 1-77 JUN 2003. (HTML
Hariharan R. 2003. The analysis of microarray data. PHARMACOGENOMICS 4 (4): 477-497 JUL 2003. (HTML)
Ishwaran H, Rao JS. 2003. Detecting differentially expressed genes in microarrays using Bayesian model selection. JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION 98 (462): 438-455 JUN 2003. (HTML)
Zhao YL, Pan W. 2003. Modified nonparametric approaches to detecting differentially expressed genes in replicated microarray experiments. BIOINFORMATICS 19 (9): 1046-1054 JUN 12 2003. (HTML)
Xiang ZY, Yang YN, Ma XJ, Ding W. 2003. Microarray expression profiling: Analysis and applications. CURRENT OPINION IN DRUG DISCOVERY & DEVELOPMENT 6 (3): 384-395 MAY 2003. (HTML)
Dobbin K, Shih JH, Simon R. 2003. Statistical design of reverse dye microarrays. BIOINFORMATICS 19 (7): 803-810 MAY 1 2003. (HTML)
He YDD, Dai HY, Schadt EE, Cavet G, Edwards SW, Stepaniants SB, Duenwald S, Kleinhanz R, Jones AR, Shoemaker DD, Stoughton RB. 2003. Microarray standard data set and figures of merit for comparing data processing methods and experiment designs. BIOINFORMATICS 19 (8): 956-965 MAY 22 2003. (HTML)
Svrakic NM, Nesic O, Dasu MRK, Herndon D, Perez-Polo JR. 2003. Statistical approach to DNA chip analysis. RECENT PROGRESS IN HORMONE RESEARCH 58: 75-93 2003. (HTML)
Cui XQ, Churchill GA. 2003. Statistical tests for differential expression in cDNA microarray experiments. GENOME BIOLOGY 4 (4): art. no. 210 2003. (HTML)
Efron B. 2003. Robbins, empirical Bayes and microarrays. ANNALS OF STATISTICS 31 (2): 366-378 APR 2003. (HTML)
Khodarev NN, Park J, Kataoka Y, Nodzenski E, Hellman S, Roizman B, Weichselbaum RR, Pelizzari CA. 2003. Receiver operating characteristic analysis: a general tool for DNA array data filtration and performance estimation. GENOMICS 81 (2): 202-209 FEB 2003. (HTML)
Craig BA, Black MA, Doerge RW. 2003. Gene expression data: The technology and statistical analysis. JOURNAL OF AGRICULTURAL BIOLOGICAL AND ENVIRONMENTAL STATISTICS 8 (1): 1-28 MAR 2003. (HTML)
Lee KE, Sha NJ, Dougherty ER, Vannucci M, Mallick BK. 2003. Gene selection: a Bayesian variable selection approach. BIOINFORMATICS 19 (1): 90-97 JAN 2003. (HTML)
Marchal K, Engelen K, De Brabanter J, Aert S, De Moor B, Ayoubi T, Van Hummelen P. 2002. Comparison of different methodologies to identify differentially expressed genes in two-sample cDNA microarrays. JOURNAL OF BIOLOGICAL SYSTEMS 10 (4): 409-430 DEC 2002. (HTML)
Butte A. 2002. The use and analysis of microarray data. NATURE REVIEWS DRUG DISCOVERY 1 (12): 951-960 DEC 2002. (HTML)

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