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1.  Measuring gene expression divergence: the distance to keep 
Biology Direct  2010;5:51.
Gene expression divergence is a phenotypic trait reflecting evolution of gene regulation and characterizing dissimilarity between species and between cells and tissues within the same species. Several distance measures, such as Euclidean and correlation-based distances have been proposed for measuring expression divergence.
We show that different distance measures identify different trends in gene expression patterns. When comparing orthologous genes in eight rat and human tissues, the Euclidean distance identified genes uniformly expressed in all tissues near the expression background as genes with the most conserved expression pattern. In contrast, correlation-based distance and generalized-average distance identified genes with concerted changes among homologous tissues as those most conserved. On the other hand, correlation-based distance, Euclidean distance and generalized-average distance highlight quite well the relatively high similarity of gene expression patterns in homologous tissues between species, compared to non-homologous tissues within species.
Different trends exist in the high-dimensional numeric data, and to highlight a particular trend an appropriate distance measure needs to be chosen. The choice of the distance measure for measuring expression divergence can be dictated by the expression patterns that are of interest in a particular study.
This article was reviewed by Mikhail Gelfand, Eugene Koonin and Subhajyoti De (nominated by Sarah Teichmann).
PMCID: PMC2928186  PMID: 20691088
2.  Evolutionary history of bacteriophages with double-stranded DNA genomes 
Biology Direct  2007;2:36.
Reconstruction of evolutionary history of bacteriophages is a difficult problem because of fast sequence drift and lack of omnipresent genes in phage genomes. Moreover, losses and recombinational exchanges of genes are so pervasive in phages that the plausibility of phylogenetic inference in phage kingdom has been questioned.
We compiled the profiles of presence and absence of 803 orthologous genes in 158 completely sequenced phages with double-stranded DNA genomes and used these gene content vectors to infer the evolutionary history of phages. There were 18 well-supported clades, mostly corresponding to accepted genera, but in some cases appearing to define new taxonomic groups. Conflicts between this phylogeny and trees constructed from sequence alignments of phage proteins were exploited to infer 294 specific acts of intergenome gene transfer.
A notoriously reticulate evolutionary history of fast-evolving phages can be reconstructed in considerable detail by quantitative comparative genomics.
Open peer review
This article was reviewed by Eugene Koonin, Nicholas Galtier and Martijn Huynen.
PMCID: PMC2222618  PMID: 18062816
3.  Similarity searches in genome-wide numerical data sets 
Biology Direct  2006;1:13.
We present psi-square, a program for searching the space of gene vectors. The program starts with a gene vector, i.e., the set of measurements associated with a gene, and finds similar vectors, derives a probabilistic model of these vectors, then repeats search using this model as a query, and continues to update the model and search again, until convergence. When applied to three different pathway-discovery problems, psi-square was generally more sensitive and sometimes more specific than the ad hoc methods developed for solving each of these problems before.
This article was reviewed by King Jordan, Mikhail Gelfand, Nicolas Galtier and Sarah Teichmann.
PMCID: PMC1489924  PMID: 16734895

Results 1-3 (3)