* = corresponding author
Coolon, J.D.*, W. Webb, and P.J. Wittkopp. (2013) Sex-specific effects of cis-regulatory variants in Drosophila melanogaster. Genetics, advance early online publication. PDF
He, B.Z.*, M.Z. Ludwig, D.A. Dickerson, L. Barse, B. Arun, S-Y. Park, N.A. Tamarina, S.B. Selleck, P.J. Wittkopp, G.I. Bell, and M. Kreitman* (2013) Effect of Natural Genetic Variation on Phenotype in a Drosophila Model of Diabetes-Associated Misfolded Human Proinsulin. In revision. DRAFT
Coolon, J.D., C.J., McManus, K. Stevenson, B.R. Graveley, and P.J. Wittkopp*. (2013) Tempo and mode of regulatory evolution in Drosophila. In revision.
McManus, C.J.*, J.D. Coolon, J. Eipper-Mains, P.J. Wittkopp, and B.R. Graveley* (2013) Evolution of Splicing Regulatory Networks in Drosophila. In revision.
Meiklejohn, C. D*., Coolon, J., D. L. Hartl, and P. J. Wittkopp. (2013) The roles of cis- and trans-regulation in the evolution of regulatory incompatibilities and sexually dimorphic gene expression. Genome Research, in press.
Stevenson, K., J.D. Coolon, and P.J., Wittkopp. (2013) Sources of bias in measures of allele-specific expression derived from RNA-seq data aligned to a single reference genome. BMC Genomics, 14: 536.PDF
Scripts used in this work can be downloaded here and instructions for using them here.
Wittkopp, P.J.* (2013) "Evolution of Gene Expression" in The Princeton Guide to Evolution (Editor-in-chief, Jonathan Losos; Second editor, Hopi Hoekstra), in press. PDF
Invited book chapter
Wittkopp, P.J. (2013) Population Genetics and a Study of Speciation using Next-Generation Sequencing: An Educational Primer for Use with “Patterns of Transcriptome Divergence in the Male Accessory Gland of Two Closely Related Species of Field Crickets”. Genetics 193, 671-675. PDF
Coolon, J.D. and P.J. Wittkopp*. (2013) “cis- and trans-regulation in interspecific Drosophila hybrids” in Polyploid and Hybrid Genomics, Wiley-Blackwell Publishing. Editors: Z. Jeffrey Chen and Jim Birchler, In press.
Invited book chapter
Coolon, J.D.*, K. Stevenson, C.J., McManus, B. Graveley, and P.J. Wittkopp. (2012) Genomic imprinting absent in Drosophila melanogaster adult females, Cell Reports 2,69-75. PDF
Cooley, A.M.*, L. Shefner, W.N. McLaughlin, E.E. Stewart, and P.J. Wittkopp. (2012) The ontogeny of color: Developmental origins of divergent pigmentation in Drosophila americana and D. novamexicana. Evolution and Development 14, 317-325. PDF
Gruber, J.D., K. Vogel, G. Kalay, and P.J. Wittkopp*. (2012) Contrasting Properties of Gene-specific Regulatory, Coding, and Copy Number Mutations in Saccharomyces cerevisiae: Frequency, Effects and Dominance. PLoS Genetics, 8, e1002497. PDF
Selected by Faculty of 1000
Kalay, G. and P.J. Wittkopp (2011). Nomadic enhancers: tissue-specific cis-regulatory elements of yellow have divergent genomic positions among Drosophila species. PLoS Genetics 6, e1001222 PDF
Wittkopp, P.J., G. Smith-Winberry, L.L. Arnold, E. M. Thompson, A. M. Cooley, D. Yuan, Q. Song, and B.F. McAllister (2010). Local adaptation for body color in Drosophila americana. Heredity 106, 592-602. PDF
Wittkopp, P.J. (2010). Variable transcription factor binding: a mechanism of evolutionary change. PLoS Biology, 8, e1000342. PDF
McManus, C.J., J.D. Coolon, M. Duff, J. Eiper-Mains, B.R. Graveley, and P.J. Wittkopp (2010). Regulatory divergence in Drosophila revealed by mRNA-Seq. Genome Research, 20, 816-825. PDF.
Selected by Faculty of 1000
Fontanillas, P., C.R. Landry, P.J. Wittkopp, C. Russ, J.D. Gruber, C. Nusbaum, and D.L. Hartl. (2010) Key considerations for measuring allelic expression on a genomic scale using high-throughput sequencing. Molecular Ecology, 19 (Suppl. 1), 212–227. PDF
Next Generation Molecular Ecology special issue Editorial
Wittkopp, P.J., E.E. Stewart, A.H. Neidert, B.K. Haerum, L.L. Arnold, E. M. Thompson, G. Smith-Winberry, and L. Shefner (2009). Intraspecific polymorphism to interspecific divergence: genetics of pigmentation in Drosophila. Science 326, 540-544. PDF
Wittkopp, P.J. and P. Beldade (2009). Development and evolution of insect pigmentation: genetic mechanisms and the potential consequences of pleiotropy. Seminars in Cell and Developmental Biology 20, 65-71.PDF Invited review, Pigment Cell Development special issue
Wittkopp, P.J., B.K. Haerum, and A.G. Clark (2008). Independent effects of cis- and trans-regulatory variants on gene expression in D. melanogaster. Genetics 178, 1831-5. PDF
Wittkopp, P.J., B.K. Haerum, and A. Clark (2008) Genetic basis of regulatory variation within and between Drosophila species, Nature Genetics, 40, 346-50. PDF
Wittkopp, P.J. (2007) Evolutionary Genetics: How flies get naked. Current Biology 17, R881-R883. PDF Dispatch for McGregor et al 2007
Kohn, M.H. and P.J. Wittkopp (2007) Annotating ebony on the fly. Molecular Ecology 16, 2831-3. PDF News and Views for Pool and Aquadro 2007
Davis, G.K., D. Srinivasan, P.J. Wittkopp, and D.L. Stern (2007) The function and regulation of Ultrabithorax in the legs of Drosophila melanogaster. Developmental Biology 308, 621-631. PDF
Wittkopp, P.J. (2007) Variable gene expression in eukaryotes: a network perspective. J. Experimental Biology 210 , 1567-1575. PDF Invited Review, Post-genomic Comparative Physiology Special Issue
Fay, J. and P.J. Wittkopp (2007) Evaluating the role of natural selection in the evolution of gene regulation. Heredity, May 23 Epub ahead of print. PDF Invited Review, Ecological and Evolutionary Functional Genomics Special Issue
Wittkopp, P.J., B.K. Haerum, and A. Clark (2006) Parent-of-origin effects on mRNA expression in Drosophila melanogaster not caused by genomic imprinting. Genetics 173, 1817-1821. PDF
Wittkopp, P.J. (2006) Evolution of cis-regulatory sequence and function in diptera. Heredity 97, 139-147. Invited review PDF Invited Review, Evo-Devo Special Issue
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 PDF
Wittkopp, P.J. (2005) Genomic sources of regulatory variation in cis and in trans. Cellular and Molecular Life Sciences 62 , 1779-83.[Invited,"Visions & Reflections"PDF
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. (*=co-first authors) PDF News &Views
Wittkopp, P.J., B.K. Haerum, and A.G. Clark (2004) Evolutionary divergence of cis and trans gene regulation. Nature, 430, 85-88. PDF
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. PDF
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 (* = co-first authors) PDF
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. (*=co-first authors) PDF
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. PDF
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. PDF
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. (*=co-first authors) PDF
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. (* = co-first authors) PDF
Polaczyk, P.J., R. Gasparini, and G. Gibson (1998) Naturally occurring genetic variation affects Drosophila photoreceptor determination. Development, Genes & Evolution 207, 462-470. PDF