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March 26 INTRODUCTION Introduction to Microarray Technology link Large-Scale Gene Expression and Microarray Links and Resources link The WWW Virtual Library of Cell Biology link to gene expression March 28 TECHNOLOGY (Anbazhagan Ramaswamy, JHU) A Concise Guide to cDNA Microarray Analysis Hegde P, Qi R, Abernathy R, Gay C, Dharap S, Gaspard R, Earle-Hughes J, Snesrud E, Lee NH, and Quackenbush J Biotechniques (2000), 29(3):548-562 Link to PDF and html versions Expression profiling using cDNA microarrays. Duggan DJ, Bittner M, Chen Y, Meltzer P, Trent JM Science 1999 Jan 1;283(5398):83-7 Article(PDF) April 2 NORMALIZATION (Liz Garrett, JHU) Tutorial on the Loess curve--fitting approach. Development of a prostate cDNA microarray and statistical gene expression analysis package. Carlisle AJ, Prabhu VV, Elkahloun A, Hudson J, Trent JM, Linehan WM, Williams ED, Emmert-Buck MR, Liotta LA, Munson PJ, Krizman DB Mol Carcinog 2000 May;28(1):12-22 Article(PDF) Normalization for cDNA Microarray Data Y. H. Yang, S. Dudoit, P. Luu and T. P. Speed. UC Berkeley Tech Report December 2000 Article(PDF) April 4 IMAGING AND NORMALIZATION (Yidong Chen, NHGRI) Ratio-based decisions and the quantitative analysis of cDNA micro-array images Chen Y, Dougherty E, Bittner M Journal of Biomedical Optics 2:364 (1997) Article(PDF) Normalization for cDNA Microarray Data The ArrayDB database ArrayDB site at NHGRI Comparison of methods for image analysis on cDNA microarray data Y.H. Yang, M. J. Buckley, S. Dudoit and T.P.Speed UC Berkeley Tech Report November 2000 Article(PDF) April 9 REPLICATION Importance of replication in microarray gene expression studies: Statistical methods and evidence from repetitive cDNA hybridizations Lee ML, Kuo FC, Whitmore GA, Sklar J. Proc Natl Acad Sci U S A 2000 Aug 29;97(18):9834-9839 Article(PDF) Development of a prostate cDNA microarray and statistical gene expression analysis package Carlisle AJ, Prabhu VV, Elkahloun A, Hudson J, Trent JM, Linehan WM, Williams ED, Emmert-Buck MR, Liotta LA, Munson PJ, Krizman DB Mol Carcinog 2000 May;28(1):12-22 Article(PDF) Design and Analysis of Gene Expression Microarray Experiments Kerr K, Churchill, G Article, Presentation slides and Supplementary materials by Ulrich Mansmann April 11 ESTIMATING RATIOS On differential variability of expression ratios: Improving statistical inference about gene expression changes from microarray data. Newton, M.A., C.M. Kendziorski, C.S. Richmond, F.R. Blattner, and K.W. Tsui Journal of Computational Biology to appear Article(PDF) Determining Significant Fold Differences in Gene Expression Analysis Butte AJ, Ye J, Niederfellner G, Rett K, Häring HU, White MF, Kohane IS Pacific Symposium on Biocomputing 2001; 6:6-17 Article(PDF) Computational methods for the identification of differential and coordinated gene expression. Claverie, J Human Molecular Genetics Volume 8 (10), 1821-1832, 1999 Article(PDF) R commands used in class. April 16 OLIGONUCLEOTIDE ARRAYS Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection Cheng Li and Wing Hung Wong PNAS 98: 31-36 Link April 18 CLUSTERING: EISEN's APPROACH Cluster analysis and display of genome-wide expression patterns M.B. Eisen, P.T. Spellman, P.O. Brown, David Botstein PNAS Vol. 95, Issue 25, 14863-14868, December 8, 1998 Article(PDF) The transcriptional program in the response of human fibroblasts to serum. Iyer VR, Eisen MB, Ross DT, Schuler G, Moore T, Lee JCF, Trent JM, Staudt LM, Hudson J Jr, Boguski MS, Lashkari D, Shalon D, Botstein D, Brown PO Science 1999 Jan 1;283(5398):83-7 Article(PDF) April 23 CLUSTERING: GENE SHAVING Gene shaving' as a method for identifying distinct sets of genes with similar expression patterns T Hastie1, R Tibshirani, M B Eisen, A Alizadeh, R Levy, L Staudt, W C Chan, D Botstein, P Brown Genome Biology 1(2):research0003.1-0003.21 Article(PDF) Additional material Slide presentation in .ps April 25 BICLUSTERING Coupled two-way clustering analysis of gene microarray data Gad Getz, Erel Levine, and Eytan Domany PNAS Vol. 97, Issue 22, 12079-12084, October 24, 2000 PNAS Abstract page (including PDF) Plaid Models for Gene Expression Data L Lazzeroni, A Owen Stanford University Tech Report ResearchIndex link and Author's site with slides, software etc April 30 CLUSTERING: OVERVIEW OF ALTERNATIVE APPROACHES Clustering in an Object-Oriented Environment Anja Struyf, Mia Hubert, and Peter Rousseeuw JSS Article(PDF) and more Peter Rousseeuw, Anja Struyf and Mia Hubert R Functions for cluster analysis CRAN website Download and User Manual Stat Soft documentation and tutorial on clustering algorithms. Admissible Clustering Procedures L Fisher, J van Ness Biometrika JSTOR page to paper An Analysis of Recent Work on Clustering Algorithms Daniel Fasulo University of Washington Tech Report Article(PDF) May 2 SINGULAR VALUE DECOMPOSITION and PCA's Singular value decomposition for genome-wide expression data processing and modeling Alter, O., P. Brown, and D. Botstein PNAS 97 (18), 10101-10106, 2000 Article(PDF) Orly Alter's website, which includes supplementary figures, data, matlab code, and a realvideo lecture. Tutorial on Principal Components Analysis Link May 7 BINARY CLASSIFICATION A Tutorial on Logistic Regression Y So SAS tutorial Article(PDF) Stat Soft documentation and tutorial on discriminant analysis. Classification R J Henery Machine Learning, Neural and Statistical Classification Chapter (PS) Flexible discriminant analysis by optimal scoring Hastie, T., Tibshirani, R. & Buja, A. Journal of the American Statistical Association (1994) 89: 1255-1270 Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling Alizadeh AA, Eisen MB, Davis RE, Ma C, Lossos IS, Rosenwald A, Boldrick JC, Sabet H, Tran T, Yu X, Powell JI, Yang L, Marti GE, Moore T, Hudson J Jr, Lu L, Lewis DB, Tibshirani R, Sherlock G, Chan WC, Greiner TC, Weisenburger DD, Armitage JO, Warnke R, Staudt LM, et al. Nature 2000 Feb 3;403(6769):503-11 Article(PDF) May 9 CLASSIFICATION TREES Stat Soft documentation and tutorial on classification trees. Building Classification Models: ID3 and C4.5. Link Machine Learning of Rules and Trees C Feng, D Michie Machine Learning, Neural and Statistical Classification Chapter (PS) May 14 COMPARISON OF CLASSIFIERS Methods of Comparison for classifiers R J Henery Machine Learning, Neural and Statistical Classification Chapter (PS) Comparison of Discrimination Methods for the Classification of Tumors Using Gene Expression Data S. Dudoit, J. Fridlyand, and T. P. Speed UC Berkeley Tech Report June 2000 Article(PDF) Data Analysis and Modelling of DNA Microarrays in Genetic Expression Profiling Presentation (PS and PDF) May 16 UNSUPERVISED MOLECULAR CLASSIFICATION Molecular Classification of Cutaneous Malignant Melanoma by Gene Expression Profiling. M. Bittner, P. Meltzer, Y. Chen, Y. Jiang, E. Seftor, M. Hendrix, M. Radmacher, R. Simon, Z. Yakhini, A. Ben-Dor, E. Dougherty, E. Wang, F. Marincola, C. Gooden, J. Lueders, A. Glatfelter, P. Pollock, E. Gillanders, D. Leja, K. Dietrich, C., M. Berens, D. Alberts, V. Sondak, N. Hayward, and J. Trent Nature 406: 536-540 (2000) Article(PDF) Supplemental Information SITES WITH ADDITIONAL LITERATURE
SOFTWARE SITES
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