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* = corresponding author

Metzger BPH, Duveau F, Yuan D, Tryban S, Yang B, Wittkopp PJ.* 2016. Contrasting frequencies and effects of cis- and trans- regulatory mutations affecting gene expression. Molecular biology and Evolution, in press PDF.

Moczek, A.P., K.E. Sears, A. Stollewerk, P.J. Wittkopp, P. Diggle, I. Dworkin, C. Ledon-Rettig, D.Q. Mattus, D.Q., S. Roth, E. Abouheif, F.D. Brown, C-H. Chiu, C.S. Cohen, A.W. De Tomaso, S.F. Gilbert, B.K. Hall, A.C. Love, D.C. Lyons, T. Sanger, J. Smith, C. Specht, M. Vallejo-Marin, and C.G. Extavour. forthcoming. 2015. The significance and scope of evolutionary developmental biology: a vision for the 21st century. Evolution & Development PDF

Coolon, J.D*, K.R. Stevenson, C.J. McManus, B.R. Graveley, and P.J. Wittkopp*. cis- and trans-regulation contribute to accelerated divergence of gene expression on the Drosophila X chromosome. In revision at Molecular Biology and EvolutionDRAFT

Metzger,B.P.H.1, D.C. Yuan1, J.D. Gruber, F. Duveau and P.J. Wittkopp*(2015). Selection on noise constrains variation in a eukaryotic promoter. NaturePDF
1 These authors contributed equally to this work.

Duveau, F*., B.P.H. Metzger, J.D. Gruber, K. Mack, N. Sood, T. Brooks and P.J. Wittkopp*. (2014) Mapping small effect mutations in Saccharomyces cerevisiae: impacts of experimental design and mutational properties. G3: Genes, Genomics, Genetics July Vol.4. No. 7 1205-1216 PDF

Coolon, J.D., C.J., McManus, K. Stevenson, B.R. Graveley, and P.J. Wittkopp*. (2014) Tempo and mode of regulatory evolution in Drosophila. Genome Research, 24: 797-808 PDF 
Genome sequences, chain files, and custom scripts used in this work are available as supplmental resources from the Genome Research website.

McManus, C.J.*, J.D. Coolon, J. Eipper-Mains, P.J. Wittkopp, and B.R. Graveley* (2014) Evolution of Splicing Regulatory Networks in Drosophila. Genome Research, March 24, Epub ahead of print. PDF
Genome sequences for D. melanogaster, D. simulans, and D. sechellia used in this work can be downloaded here. For details, see readme file included with the download.

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. Genetics. 196, 557-67 PDF

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, 24, 84-9. PDF

Coolon, J.D.*, W. Webb, and P.J. Wittkopp. (2013) Sex-specific effects of cis-regulatory variants in Drosophila melanogaster. Genetics, 195, 1419-22. PDF

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
Highly accessed
Selected by Faculty of 1000

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). 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
Invited primer

Coolon, J.D. and P.J. Wittkopp*. (2013) “cis- and trans-regulation in interspecificDrosophila hybrids” in Polyploid and Hybrid Genomics, Wiley-Blackwell Publishing. Editors: Z. Jeffrey Chen and Jim Birchler. PDF
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
Cover Article

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, 8e1002497PDF
Selected by Faculty of 1000

Wittkopp, P.J.*, and G. Kalay. (2012) cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence. Nature Review Genetics, 13, 59-69.PDF Invited book chapter

Wittkopp, P.J.* (2011) Using pyrosequencing to measure allele-specific mRNA abundance and infer the effects of cis- and trans-regulatory differences. Methods Mol Biol. 772, 297-317. PDF Invited book chapter

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 inDrosophila americana. Heredity 106, 592-602. PDF

Wittkopp, P.J. (2010). Variable transcription factor binding: a mechanism of evolutionary change. PLoS Biology8, 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 Research20, 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- andtrans-regulatory variants on gene expression in D. melanogasterGenetics 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 Genetics40, 346-50. PDF

Wittkopp, P.J. (2007) Evolutionary Genetics: How flies get naked. Current Biology17, R881-R883. PDF Dispatch for McGregor et al 2007

Kohn, M.H. and P.J. Wittkopp (2007) Annotating ebony on the fly. Molecular Ecology16, 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. 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. Genetics171, 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.PDF Invited,"Visions & Reflections"

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 DrosophilaNature 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 DrosophilaTrends in Genetics, 19, 495-504. PDF

Wittkopp, P.J.*, B.L. Williams*, J.E. Selegue, and S.B. Carroll (2003) Drosophilapigmentation 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 DrosophilaCurrent 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



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