Paper by Erik D. Demaine

Therese Biedl, Broňa Brejová, Erik D. Demaine, Angèle M. Hamel, and Tomáš Vinař, “Optimal Arrangement of Leaves in the Tree Representing Hierarchical Clustering of Gene Expression Data”, Technical Report 2001-14, Department of Computer Science, University of Waterloo, April 2001.

In this paper, we study how to present gene expression data to display similarities by trying to find a linear ordering of genes such that genes with similar expression profiles will be close in this ordering. In general, finding the best possible order is intractable. Therefore we assume that hierarchical clustering has been applied to the gene expression profiles and show that the best order respecting the clustering can be computed efficiently. We perform experiments comparing the optimal order to several other methods. The implementation of the algorithm, as well as a simple program for viewing hierarchically clustered expression array data and the complete results of our experiments are available at

Detailed results, source code, and running times

The paper is 12 pages.

The paper is available in PostScript (4386k), gzipped PostScript (640k), and PDF (556k).
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Related papers:
GeneExpression_WABI2002 (K-ary Clustering with Optimal Leaf Ordering for Gene Expression Data)

See also other papers by Erik Demaine.
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Last updated May 16, 2024 by Erik Demaine.