Therese Biedl, Brona Brejova, Erik D. Demaine, Angele M. Hamel, Tomas Vinar. Optimal Arrangement of Leaves in the Tree Representing Hierarchical Clustering of Gene Expression Data. Technical Report CS-2001-14, University of Waterloo, April 2001.

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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