Active Research Evolutionary genomics of Drosophila Genetic diversity of P. falciparum Evolution of hybrid incompatibilities Evolution of gene expression Natural selection and protein evolution   Past Research Evolution of novel gene functions Bioinformatics Selective sweep C-value paradox Transposable element mariner Structure and sequence of the Drosophila genome Genome structure and evolution in D. virilis Cosuppression of transposable elements Molecular evolution in enteric bacteria Gregor Mendel

Evolutionary theory and bioinformatics Our laboratory is also very active in evolutionary theory as well as in the development and implementation of bioinformatics tools for analyzing genomic sequence and gene expression data from an evolutionary perspective. There are rich opportunities for research in these rapidly expanding areas of evolutionary biology. Contributions in bioinformatics include methods for analyzing data from gene expression arrays and mapping differences in expression onto functional categories of genes, as well as mining genomic sequence data for patterns of genome evolution in orthologs and paralogs, evolutionary forces affecting intron size and number, rates and patterns of evolution of genes expressed at various times in development, and differential selection in relation to sex.   PDF Lemos, B., C. D. Meiklejohn, and D. L. Hartl. 2004. Regulatory evolution across the protein interaction network. Nat. Genet. 36: 1059-1060.     PDF Castillo-Davis, C. I., D. L. Hartl, and G. Achaz. 2004. cis-regulatory and protein evolution in orthologous and duplicate genes. Genome Res. 14: 1530-1536.     PDF Castillo-Davis, C. I., F. A. Kondrashov, D. L. Hartl, and R. J. Kulathinal. 2004. The functional genomic distribution of protein divergence in two animal phyla: coevolution, genomic conflict, and constraint. Genome Res. 14: 802-811.     PDF Castillo-Davis, C. I., and D. L. Hartl, 2003 Conservation, relocation and duplication in genome evolution. Trends Genet. 19(11) 593-597.     PDF Castillo-Davis, C. I., and D. L. Hartl, 2003 GeneMerge--post-genomic analysis, data mining, and hypothesis testing. Bioinformatics 19(7): 891-892.     PDF Townsend, J. P., and D. L. Hartl, 2002 Bayesian analysis of gene expression levels: statistical quantification of relative mRNA level across multiple strains or treatments. Genome Biol. 3: research0071.1 - 0071.16.     PDF Meiklejohn, C. D., and D. L. Hartl, 2002 A single mode of canalization. Trends Ecol. Evol. 17: 468-473.     PDF Castillo-Davis, C. I., S. L. Mekhedov, D. L. Hartl, E. V. Koonin, and F. A. Kondrashov, 2002 Selection for shorter introns in highly expressed genes. Nature Genet. 31: 415-418.     PDF Grosu, P., J. P. Townsend, D. L. Hartl and D. Cavalieri, 2002 Pathway Processor: A tool for integrating whole-genome expression results into metabolic networks. Genome Research 12: 1121-1126.     PDF Castillo-Davis, C. I., and D. L. Hartl, 2002 Genome evolution and developmental constraint in Caenorhabditis elegans. Mol. Biol. Evol. 19: 728-735.