Reading list:
These are the papers we plan to discuss in each session:
 Biology and Technology
 Expression Indices
 Li, C., and W.H. Wong. 2001. Modelbased analysis of oligonucleotide
arrays: expression index computation and outlier detection.
PNAS 98:3136.
 Naef, F., D.A. Lim, N. patil, and M.O. Magnasco. 2001.
From features to expression: highdensity oligonucleotide
array analysis revisited.
Preprint.
 Irizarry, R.A., B. Hobbs, F. Collin, Y.S. BeazerBarclay,
K.J. Antonellis, U. Scherf, and T.P. Speed.
2002. Exploration, normalization, and summaries of high density
oligonucleotide array probe level data.
Preprint.
 Normalisation
 Schadt, E.E., C. Li, C. Su, and W. H. Wong. 2000.
Analyzing highdensity oligonucleotide gene expression array data.
J. Cellul. Biochem. 80:192202
(reprint).
 Yang, Y.H., S. Dudoit, P. Lu, and T.P. Speed. 2001.
Normalization for cDNA microarray data.
Proc. Int.
Symp. Biomedical Optics. 2026 January, 2001, San Jose.
(preprint)
 Yang, Y.H., S. Dudoit, P. Lu, D.M. Lin, V. Peng, J. Ngai,
and T.P. Speed. 2002. Normalization for cDNA microarray data:
a robust composite method addressing single and multiple slide
systematic variation.
Nucl. Acids Res. 30(4):e15.
 Differential Expression I
 Chen, Y., E.D. Dougherty, and M.L. Bittner. 1997.
Ratiobased decisions and the quantitative analysis of
cDNA microarray images.
J. Biomed. Optics 2:364374.
 Newton, M.A., C.M. Kendziorski, C.S. Richmond, F.R. Blattner,
and K.W. Tsui. 2001.
On differential variability of expression ratios: improving
statistical inference about gene expression changes from
microarray data.
J. Comp. Biol. 8:3752.
 Ting Lee, M.L., F.C. Kuo, G.A. Whitmore, and J. Sklar. 2000.
Importance of replication in microarray gene expression studies:
statistical methods and evidence from repetitive cDNA hybridizations.
PNAS 97:98349839.
 Differential Expression II
 Dudoit, S., Y.H Yang, M.C. Callow, and T.P. Speed. 2002.
Statistical methods for identifying differentially expressed
genes in replicated cNDA microarray experiments.
Statistika Sinica 12(1).
(preprint)
 Goss Tusher, V., R. Tibshirani, and G. Chu. 2001.
Significance analysis of microarrays applied to the
ionizing radiation response.
PNAS 98:51165121.
 Lönnstedt, I., and T.P. Speed. 2002.
Replicated microarray data.
Statistika Sinica 12(1).
(preprint)
 Differential Expression III
 Efron, B., R. Tibshirani, J.D. Storey, and V. Tusher. 2001.
Empirical Bayes analysis of a microarray experiment.
JASA 96:11511160.
 Efron, B., J.D. Storey, and R. Tibshirani. 2001.
Microarrays empirical Bayes methods, and false discovery rates.
Technical Report 200123B/217
(Dept. of Statistics, Stanford).
 Efron, B. 2001. Robbins, empirical Bayes, and microarrays.
Technical Report 200130B/219
(Dept. of Statistics, Stanford).
 ANOVA
 Kerr, M.K, M. Martin, and G.A. Churchill. 2000.
Analysis of variance for gene expression microarray data.
J. Comp. Biol. 7:819837.
(preprint)
 Kerr, M.K, and G.A. Churchill. 2001. Statistical design and the analysis
of gene expression microarray data.
Genet. Res. Camb. 77:123128.
 Kerr, M.K., C.A. Afshari, L. Bennet, P. Bushel, J. Martinez, N.J. Walker,
and G.A. Churchill. 2002.
Statistika Sinica 12(1).
(preprint)
 Clustering I
 Tamayo, P., D. Slonim, J. Mesirov, Q. Zhu, S. Kitareewan, E. Dmitrovsky,
E.S. Lander, and T.R. Golub. 1999. Interpreting patterns of gene expression with
selforganizing maps: methods and application to hematopoietic
differentiation.
PNAS 96:29072912.
 Yeung, K.Y., C. Fraley, A. Murua, A.E. Raftery, and W.L. Ruzzo. 2001.
Modelbased clustering and data transformations for gene expression
data.
Bioinformatics 17:977987.
 Fraley, C., and A.E. Raftery. 1998. How many clusters? Which
clustering method? Answers via modelbased cluster analysis.
The Computer Journal 41:578588.
 Clustering II
 Eisen, M.B., P.T. Spellman, P.O. Brown, and D. Botstein. 1998.
Cluster analysis and display of genomewide expression patterns.
PNAS 95:1486314868.
 Herrero, J., A. Valencia, and J. Dopazo. 2001. A hierarchical
unsupervised growing neural network for clustering gene
expression patterns.
Bioinformatics 17:126136.
 Kerr, M.K., and G.A. Churchill. 2001. Bootstrapping cluster
analysis: assessing the reliability of conclusions from microarray
experiments.
PNAS 98:89618965.
 Data and Dimension Reduction
 Alter, O., P.O. Brown, and D. Botstein. 2000. Singular value
decomposition for genomewide expression data processing and
modelling.
PNAS97:1010110106
 Yeung, K.Y., and W.L. Ruzzo. 2001. Principal component analysis
for clustering gene expression data.
Bioinformatics 17:763774.
 Hastie, T., R. Tibshirani, M.B. Eisen, A. Alizadeh, R. Levy, L. Staudt,
W.C. Chan, D. Botstein, and P. Brown. 2000.
'Gene shaving' as a method for
identifying distinct sets of genes with similar expression patterns.
Genome Biology 1(2):research0003.0003.21
 Classification I
 Golub, T.R., D.K. Slonim, P. Tamayo, C. Huard, M. Gaasenbeek,
J.P. Mesirov, H. Coller, M.L. Loh, J.R. Downing, M.A. Caligiuri,
C.D. Bloomfield, and E.S. Lander. 1999.
Molecular classification of cancer: class discovery and class
prediction by gene expression monitoring.
Science 286:531537.
 Slonim, D.K., P. Tamayo, J.P. Mesirov, T.R. Golub, and E.S. Lander.
2000. Class prediction and discovery using gene expression data.
Proceedings RECOMB IV:263271.
(reprint)
 Yeang, C.H., S. Ramaswamy, P. Tamayo, S. Mukherjee, R.M. Rifkin,
M. Angelo, M. Reich, E.S. Lander, J. Mesirov, and T. Golub. 2001.
Molecular classification of multiple tumor types.
Bioinformatics 17:S316S322.
 Classification II
Most of these papers are downloadable from within the network of the
University of Munich. (You may need to configure your browser properly
 see the proxy guide
at the LRZ). If you have
problems or prefer to copy an article please contact us.
