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Research focus:

Research in my group focuses on ecological and evolutionary functional genomics. We primarily use the model system Drosophila to understand the molecular mechanisms that underlie variation in genome-wide gene expression and the ultimate role it plays in shaping the phenotypic diversity of life.


Selected Publications:

Coolon, J. D.*, Stevenson, K. R.,McManus, C. J., Graveley, B. R., and P.J. Wittkopp*. (2015) Molecular mechanisms and evolutionary processes contributing to accelerated divergence of gene expression on the Drosophila X chromosome. (In Press at Molecular Biology and Evolution) * Corresponding authors

Coolon, J. D., McManus, C. J., Stevenson, K. R., Graveley, B. R., and P.J. Wittkopp. (2014) Tempo and mode of regulatory evolution in Drosophila. Genome Research, 24:797-808.

McManus, C. J., Coolon, J. D., Duff, M., Eiper-Mains, J., Wittkopp P.J., and B. R. Graveley. (2014) Evolution of splicing regulatory networks in Drosophila. Genome Research, 24:786-796.

Meiklejohn, C. D., Coolon, J. D., Hartl, D. L., and P. J. Wittkopp. (2014) The roles of cis- and trans regulation in the evolution of regulatory incompatibilities and sexually dimorphic gene expression. Genome Research, 24:84-95.

Coolon, J. D.,* Webb, W., and P. J. Wittkopp. (2013) Sex-specific effects of cis-regulatory variants in Drosophila melanogaster. Genetics. 195(4): 1419-1422.* Corresponding author, Chosen by editors as issue highlight

Stevenson, K. R., Coolon, J. D., and P. J. Wittkopp. (2013) Reliable estimates of allele-specific expression derived from RNA-seq data aligned to a single reference genome. BMC Genomics, 14:536. Given “Highly Accessed” designation from journal, Selected by Faculty of 1000

Coolon, J. D.*, Jones, K. L., T. C. Todd, J. L., J. M. Blair, and M. A. Herman. (2013) Long-term nitrogen amendment alters soil bacterial diversity and assemblage in tallgrass prairie. PLoS ONE 8(6): e67884. * Corresponding author

Coolon, J. D., and P. J. Wittkopp. (2012) cis and trans-regulation in Drosophila interspecific hybrids. Hybrid and Polyploid Genomics. Editors: Z. Jeffrey Chen and Jim Birchler, Wiley-Blackwell Publishing. Invited Book Chapter

Coolon, J. D.*, Stevenson, K. R., McManus, C. J., Graveley, B. R., and P.J. Wittkopp. (2012) Genomic imprinting absent in Drosophila melanogaster adult females. 2012. Cell Reports, 2(1):69-75. * Corresponding author

McManus, C. J., Coolon, J. D., Duff, M., Eiper-Mains, J., Graveley, B. R., and P.J. Wittkopp. (2010) Regulatory divergence in Drosophila revealed by mRNA-seq. Genome Research, 20:816-825. Selected by Faculty of 1000

Coolon, J. D., Jones, K. L., Narayanan, S., and S. M. Wisely. (2010) Microbial Ecological Response of the Intestinal Flora of Peromyscus maniculatus and P. leucopus to Heavy Metal Contamination. Molecular Ecology, 19 (supp1): 67-80. Next Generation Molecular Ecology special issue

Herman, M. H., Coolon, J. D., Jones, K. L. and T. C. Todd. (2009) Ecological Genomics of Nematode Community Interactions: Model and Non-model Approaches. Evolutionary Biology Concept, Modeling, and Application II. ed. Axelle Pontarotti. Springer Tiergartenstr. 17 69121 Heidelberg Germany. Invited Book Chapter

Coolon, J. D., Jones, K. L., Carr, B. C. #, Todd, T. C., and M. A. Herman. (2009) Caenorhabditis elegans genomic response to soil bacteria predicts environment-specific genetic effects on life history traits. PLoS Genetics. 5(6): e1000503. Selected by Faculty of 1000, # Undergraduate author

Jones, K. L., Todd, T. C., Wall-Beam, J. L. #, Coolon, J. D., Blair, J. M., and M. A. Herman. (2006) Molecular approach for assessing responses of microbial-feeding nematodes to burning and chronic nitrogen enrichment in a native grassland. Molecular Ecology, 15, 2601-2609.

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