Publications
Landry C.R.*, C. I. Castillo-Davis*, A. Ogura, Jun S. Liu, D. L. Hartl. 2007. Systems-level analysis and evolution of the phototransduction network in Drosophila. Proceedings of the National Academy of Sciences. 104(9):3283-3288. 
Ma, P., C. I. Castillo-Davis*, W. Zhong, J. S. Liu. 2006. A data-driven clustering method for time course gene expression data. Nucleic Acids Research. 34:1261-1269.
Castillo-Davis, C. I. 2005. The evolution of noncoding DNA: how much junk, how much func? Trends in Genetics. 21(10): 533-536.
Castillo-Davis, C. I., D. L. Hartl, and G. Achaz. 2004. cis-regulatory and protein evolution in orthologous and duplicate genes. Genome Research. 14(8):1530-1536 Supplementary material 1 Supplementary material 2
Castillo-Davis, C. I., T.B.C. Bedford*, D.L Hartl. 2004. Accelerated rates of intron gain/loss and protein evolution in duplicate genes in human and malaria parasites. Molecular Biology and Evolution. 21(7):1422-1427.
Castillo-Davis, C. I., R. J. Kulathinal*, F.A. Kondrashov, D.L Hartl. 2004. The functional genomic distribution of protein divergence in two animal phyla: coevolution, genomic conflict, and constraint. Genome Research. 14(5):802-811.
Castillo-Davis, C. I. and D. L. Hartl. 2003. Conservation, relocation and duplication in evolutionary genomics. Trends in Genetics. 19(11):593-597.
Ranz, J.M., C.I. Castillo-Davis, C.D. Meiklejohn, D.L. Hartl. 2003. Sex-dependent gene expression and the evolution of the Drosophila transcriptome. Science. 300 (5626): 1742-1745. Supplementary material 1
Castillo-Davis, C. I. and D. L. Hartl. 2003. GeneMerge- post-genomic analysis, data-mining and hypothesis testing. Bioinformatics. 19(7): 891-892.
Winzeler, E.A., C.I. Castillo-Davis, G. Oshiro, D. Liang, D.R. Richards, Y. Zhou, and D.L. Hartl. 2003. Genetic diversity in yeast assessed with whole-genome oligonucleotide arrays. Genetics. 163(1):79-89.
Hartl, D. L., C. D. Meiklejohn, C. I. Castillo-Davis, D. Cavalieri, J. M. Ranz and J. P. Townsend. 2003. Gene expression profiling in evolutionary genetics. Pp. 74-93. In The Evolution of Population Biology: Modern Synthesis. Eds. R. Singh, S. Jain and M. Uyenoyama. Academic Press, New York.
Castillo-Davis, C. I., S.L. Mekhedov, D. L. Hartl, E.V. Koonin, F.A. Kondrashov. 2002. Selection for short introns in highly expressed genes. Nature Genetics. 31(4): 415-418.
Castillo-Davis, C. I. and D. L. Hartl. 2002. Genome evolution and developmental constraint in C. elegans. Molecular Biology and Evolution. 19(5): 728-735.
Hajek, A.E., C.I. Castillo-Davis, C.C. Eastburn, F.M. Vermeylen. 2002. Deposition and germination of conidia of the entomopathogen Entomophaga maimaiga infecting larvae of the gypsy moth, Lymantria dispar. Journal of Invertebrate Pathology. 79: 37-43.