Jeff's Wish List for Paper Presentations

Clustering

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)

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)

Detecting Stable Clusters Using Principal Component Analysis
Asa Ben-Hur, Isabelle Guyon
    Article(PDF)

Two-way Clustering

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)

Double Conjugated Clustering Applied to Leukemia Microarray Data (2002)
Stanislav Busygin, Gerrit Jacobsen, Ewald Krämer, 2nd SIAM ICDM, Workshop on clustering high dimensional data
    Article(PDF)

Unsupervised feature selection via two-way ordering in gene expression analysis (2003)
Chris H.Q. Ding, Bioinformatics, Vol. 19 no. 10 2003, pages 1259–1266
    Article(PDF)

Dimensionality Reduction
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.

Curvilinear Distance Analysis vs. ISOMAP
John Aldo Lee, Amaury Lendasse, Michel Verleysen
ESANN' proceedings - European Symposium on Artificial Neural Networks Bruges (Belgium), 24-26 April 2002, ISBN 2-930307-02-1, pp. 185-192     Article(PDF)

Mapping physiological states from microarray expresson measurements(2002)
Gregory Stephanopoulos et al., Bioinformatics, Vol. 18, no. 8, 2002, pp. 1054-1063.
    Article(PDF)

Classification

Effective dimension reduction methods for tumor
classification using gene expression data (2003)

A. Antoniadis ., S. Lambert-Lacroix and F. Leblanc, Bioinformatics, Vol. 19 no. 5 2003, pages 563–570.
    Article(PDF)

New algorithms for multi-class cancer diagnosis
using tumor gene expression signatures (2003)
A. M. Bagirov ., B. Ferguson, S. Ivkovic, G. Saunders and
J. Yearwood, Bioinformatics, Vol. 19 no. 14 2003, pages 1800–1807.
    Article(PDF)

PCA disjoint models for multiclass cancer
analysis using gene expression data (2003)
S. Bicciato ., A. Luchini and C. Di Bello, Bioinformatics, Vol. 19 no. 5 2003, pages 571–578
    Article(PDF)