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Schadt, E., C. Li, B. Eliss, and W. H. Wong. Feature extraction and normalization algorithms for high-density oligonucleotide gene expression array data. J. Cell. Biochem. 84(S37),120–125, 2002. (regarding Non-linear baseline normalization)
Tavazoie, S., Hughes, J. D., Campbell, M. J., Cho, R. J., and Church, G. M. Systematic determination of genetic network architecture. Nat Genet, 22: 281-285, 1999. (regarding K-Means clustering algorithm)
Tamayo, P., Slonim, D., Mesirov, J., Zhu, Q., Kitareewan, S., Dmitrovsky, E., Lander, E. S., and Golub, T. R. Interpreting patterns of gene expression with self-organizing maps: methods and application to hematopoietic differentiation. Proc Natl Acad Sci U S A, 96, 2907-2912, 1999. (regarding SOM clustering algorithm)
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Tanay, A. Sharan, R. and Shamir, R. Discovering statistically significant biclusters in gene expression data. Bioinformatics, 18(1), 136-144, 2002. (regarding the SAMBA biclustering algorithm)
Elkon, R., Linhart, C. Sharan, R. Samir, R. and Shiloh, Y. Genome-Wide In Silico Identification of Transcriptional Regulators Controlling the Cell Cycle in Human Cells. Genome Research, Vol. 13(5), pp. 773-780, 2003. (regarding the PRIMA algorithm)
Eisen, M. B., Spellman, P. T. et al. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A 95(25), 14863-8, 1998. (regarding the agglomerative algorithm for hierarchical clustering)
Harbison, C.T., D.B. Gordon, T.I. Lee, N.J. Rinaldi, K.D. Macisaac, T.W. Danford, N.M. Hannett, J.B. Tagne, D.B. Reynolds, J. Yoo, E.G. Jennings, J. Zeitlinger, D.K. Pokholok, M. Kellis, P.A. Rolfe, K.T. Takusagawa, E.S. Lander, D.K. Gifford, E. Fraenkel, and R.A. Young. 2004. Transcriptional regulatory code of a eukaryotic genome. Nature 431: 99-104. (regarding some of the TF binding site profiles that were used to generate the supplied yeast TF fingerprint files)
Spellman, P. T., Sherlock, G., et al. Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization. Mol Biol Cell 9(12), 3273-97, 1998. (Regarding expressionData1.txt sample input file)