From time to time, scientific breakthroughs or new technologies are born that forever change the way we do science. Advances in high-throughput DNA sequencing represent such a breakthrough that has led us into the genomics era. Just in the past few years, we have obtained genomic sequences for scores of organisms from man to bacteria, and the accumulation of new genome sequences is continuing at a rapid pace. Based on these accomplishments, many investigators are turning their attention to the study of complex biological systems at molecular levels never before possible. This systems biology approach is particularly evident in the gene expression field, where the availability of microarrays containing DNA probes for all of the genes of an organism makes whole-cell gene expression profiling possible. However, with these new genomic methods come new challenges. Foremost among these challenges is the development of computational methods to analyse and interpret the masses of data generated by genomic experiments. To meet these needs, biologists have developed dialogues with scientists in other fields, predominantly computer scientists, statisticians, and mathematicians, and great