My primary research interests are algorithms and statistical models for genomics.  I wish to understand how organisms have evolved at the molecular level.  Sequence alignment, particularly that of multiple whole genomes, is an active line of research.  Also of interest are analyses that are upstream or downstream of sequence alignment.  For example, upstream of alignment, I am interested in new technologies for the acquisition of whole-genome data.  Downstream, I develop methods that utilize alignments to make inferences about the function and evolution of genomic elements.

Mouse Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome. Nature 420:520-62, 2002.

Rat Genome Sequencing Project Consortium. Genome sequence of the Brown Norway rat yields insights inot mammalian evolution. Nature 428: 493-521, 2004.

Dewey C, Wu JQ, Cawley M, Alexandersson M, Gibbs R and Pachter L. Accurate identification of novel human genes through simultaneous gene prediction in human, mouse, and rat. Genome Research 14:661-664, 2004.

The ENCODE Project Consortium. The ENCODE (ENCyclopedia of DNA Elements) Project. Science 306:636-640, 2004.

International Chicken Genome Sequencing Consortium. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432:695-716, 2004

Dewey C and Woods K. Parametric Sequence Alignment, In, Algebraic Statistics for Computational Biology. L. Pachter and B. Sturmfels (Eds.), Cambridge University Press, November 2005, pp. 193-205.

Lall S, Grün D, Krek A, Chen K, Wang Y, Dewey C, Sood P, Colombo T, Bray N, MacMenamin P, Kao H, Gunsalus K, Pachter L, Piano F and Rajewsky N. A genome-wide map of conserved microRNA targets in C. elegans. Current Biology 16:460–471, 2006.

Dewey C and Pachter L. Evolution at the nucleotide level: the problem of multiple whole-genome alignment. Human Molecular Genetics 15:R51-R56, 2006.