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  • Ulitsky I, Maron-Katz A, Shavit S, Sagir D, Linhart C, Elkon R, Tanay A, Sharan R, Shiloh Y, Shamir R. Expander: from expression microarrays to networks and functions. Nature Protocols Vol 5, pp 303 - 322, 2010 .
  • Shamir R, Maron-Katz A, Tanay A, Linhart C, Steinfeld I, Sharan R, Shiloh Y, Elkon R. EXPANDER-an integrative program suite for microarray data analysis. BMC Bioinformatics. 2005 Sep 21;6:232.
  • Sharan, R., Maron-Katz, A. and Shamir, R.  CLICK and EXPANDER: A System for Clustering and Visualizing Gene Expression Data. Bioinformatics Vol. 19 No. 14 pp. 1787-1799 (2003): pdf 
  • CLICK: Shamir , R. and Sharan, R. CLICK: A Clustering Algorithm with Applications to Gene Expression Analysis. Proceedings ISMB 2000, pp. 307-316 (2000): postscript
  • HCS: E. Hartuv, A. Schmitt, J. Lange, S. Meier-Ewert, H. Lehrach and R. Shamir. An algorithm for clustering cDNA fingerprints. Genomics 66(3), pp. 249-256, 2000. pdf
  • K-Means, CLICK, Hierarchical Clustering, SOM: Shamir, R. and Sharan, R. Algorithmic Approaches to Clustering Gene Expression Data. in Current Topics in Computational Biology, T. Jiang, T. Smith, Y. Xu, M.Q. Zhang editors., MIT Press, pp. 269-299 (2002): postscript pdf
  • Hierarchical Clustering, SOM, and CLICK: Sharan, R., Elkon, R. and Shamir, R. Cluster Analysis and its Applications to Gene Expression Data. in Ernst Schering workshop on Bioinformatics and Genome Analysis, Springer Verlag (2001): pdf 
  • SAMBA: A. Tanay, R. Sharan, R. Shamir. Discovering Statistically Significant Biclusters in Gene Expression Data  Proceedings of ISMB 2002, Bioinformatics Vol. 18 Suppl. 1 S136--S144, (2002)
  • PRIMA: R. Elkon, C. Linhart, R. Sharan, R. Shamir, and Y. Shiloh. Genome-Wide In Silico Identification of Transcriptional Regulators Controlling the Cell Cycle in Human Cells. Genome Research, Vol. 13(5), pp. 773-780, (2003).
  • TANGO: A. Tanay. The TANGO program technical note. Unpublished text (2003)