||Wittkopp, P.J., S.B. Carroll, and A. Kopp (2003) Evolution in Black and White: Genetic control of pigment patterns in Drosophila. Trends in Genetics, 19, 495-504.
Wittkopp, P.J, B.L. Williams, J.E. Selegue, and S.B. Carroll (2003) Drosophila pigmentation evolution: divergent genotypes underlying convergent phenotypes. Proc Natl Acad Sci U.S.A., 100, 1808-1813
Drapeau, M.D., A. Radovic, P.J. Wittkopp, and A. Long (2003) A gene necessary for normal male courtship, yellow, acts downstream of fruitless in the Drosophila melanogaster larval brain. J. of Neurobiology, 55, 53-72.
Wittkopp, P.J., K. Vaccaro and S.B. Carroll (2002) Evolution of yellow gene regulation and pigmentation patterns in Drosophila. Current Biology, 12, 1547-1556.
Radovic, A, P.J. Wittkopp, A.D. Long, and M.D. Drapeau (2002) Immunohistochemical colocalization of Yellow and male-specific Fruitless in Drosophila melanogaster neuroblasts. Biochemical and Biophysical Research Communications, 293, 1262-1264.
Wittkopp, P.J., J.R. True, and S.B. Carroll (2002) Reciprocal functions of the Drosophila Yellow and Ebony proteins in the development and evolution of pigment patterns. Development, 129, 1849-1858.
Halder G. H., P. J. Polaczyk, M.E. Kraus, A. Hudson, J. Kim, A. Laughon, and S.B. Carroll (1998) The Vestigial and Scalloped proteins act together to directly regulate wing-specific gene expression in response to signaling proteins. Genes & Development, 12:3900-3909.
Polaczyk, P.J., R. Gasparini, and G. Gibson (1998) Naturally occurring genetic variation affects Drosophila photoreceptor determination. Development, Genes & Evolution 207, 462-470.
||Wittkopp, P.J., B.K. Haerum, and A.G. Clark. (2008). Independent effects of cis- and trans-regulatory variation on gene expression in Drosophila melanogaster, Genetics 178, 1831-5.
Wittkopp, P.J., B.K. Haerum, and A.G. Clark. (2008) Genetic basis of regulatory variation within and between Drosophila species. Nature Genetics 40, 346-50.
Wittkopp, P.J. (2007) Evolutionary genetics: how flies get naked. Current Biology 17, R881-3.
Kohn, M.H. and P.J. Wittkopp. (2007) Annotating ebony on the fly. Molecular Ecology, 16, 2831-3.
Davis, GK, Srinivasan, D, Wittkopp, PJ and DL Stern (2007) The function and regulation of Ultrabithorax in the legs of Drosophila melanogaster. Developmental Biology 308, 621-631.
Wittkopp, P.J. (2007). Variable gene expression in eukaryotes: a network perspective. Journal of Experimental Biology, 210, 1567-1575.
Fay, J.C. and P.J. Wittkopp (2007). Evaluating the role of natural selection in the evolution of gene regulation. Heredity, 100, 191-199
Wittkopp, P.J., B.K. Haerum, and A.G. Clark (2006). Parent-of-origin effects on mRNA levels in Drosophila melanogaster are not caused by genomic imprinting. Genetics, 173, 1817-1821.
Wittkopp, P.J. (2006) Evolution of cis-regulatory sequence and function in diptera. Heredity 97, 139-147
Landry, C.R, P.J. Wittkopp, C. Taubes, J.M. Ranz, A.G. Clark, and D.L. Hartl (2005). Compensatory cis-trans regulation and dysregulation of gene expression in hybrids between species. Genetics 171, 1813-1822.
Wittkopp, P.J. (2005) Genomic sources of regulatory variation in cis and in trans. Cellular and Molecular Life Sciences 62, 1779-83.
Gompel, N, B. Prud’homme, P.J. Wittkopp, V.A. Kassner, and S.B. Carroll (2005) Chance caught on the wing: cis-regulatory evolution and the origin of pigment patterns in Drosophila. Nature 433, 481-487.
Wittkopp, P.J., Haerum, B.K. and A.G. Clark (2004) Evolutionary divergence of cis and trans gene regulation. Nature, 430, 85-88.