Publications

* = corresponding author

Duveau, F., W. Toubiana, and P.J. Wittkopp. 2017 Fitness effects of cis-regulatory variants in the Saccharomyces cerevisiae TDH3 promoter, Molecular Biology and Evolution, PDF

Metzger, B.P.H., P. J. Wittkopp, and J.D. Coolon*. 2017 Dissecting the evolution of gene regulation among Saccharomyces yeast reveals common patterns and mechanisms underlying the evolution of gene expression. Genome Biology and Evolution, in press.

Yang, B. and P. J. Wittkopp*. 2017 Structure of the transcriptional regulatory network correlates with regulatory divergence in Drosophila. Molecular Biology and Evolution, in press. PDF

Andrade López, J. M., Lanno, S. M., Auerbach, J. M., Moskowitz, E. C., Sligar, L. A., Wittkopp, P. J., and J. D. Coolon*. 2016. Genetic basis of octanoic acid resistance in Drosophila sechellia: functional analysis of a fine-mapped region. Molecular Ecology, in press. PDF

Massey, J., Wittkopp, P.J. 2016. The genetic basis of pigmentation differences within and between Drosophila species. Curr Top Dev Biol. 2016; 119: 27–61.  PDF

Wittkopp, P.J. 2016. Voices: Big Questions in Evolution. Cell 166, 528-29. Invited opinion PDF

Kalay, G., R. Lusk, M. Dome, K. Hens, B. Deplancke and P.J. Wittkopp*. 2016. Potential direct regulators of the Drosophila yellow gene identified by yeast one-hybrid and RNAi screens. G3: Genes, Genomics, Genetics 13, 3419-343. PDF

Lamb, A.M., Walker, E.A., and Wittkopp PJ.* 2016. Tools and strategies for scarless allele replacement in Drosophila using CRISPR/Cas9. Fly. PDF

John, A.V., Sramkoski L.L., Walker E.A., Cooley A.M., and Wittkopp PJ.* 2016. Sensitivity of allelic divergence to genomic position: Lessons from the Drosophila tan gene. G3: Genes, Genomics, Genetics. PDF

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  PDF.

Moczek AP, Sears, KE, Stollewerk A, Wittkopp PJ, Diggle P, Dworkin I, Ledon-Rettig C, Matus DQ, Roth S, Abouheif E, Brown FD, Chiu C, Cohen CS, De Tomaso AW, Gilbert SF, Hall B, Love A, Lyons DC, Sanger T, Smith J, Specht C, Vallejo-Marin M, Extavour CG 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*. (2015) Molecular mechanisms and evolutionary processes contributing to accelerated divergence of gene expression on the Drosophila X chromosome. Molecular Biology and Evolution, in press. DRAFT

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. Nature. PDF 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 supplemental 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, 24: 786-796 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 Genomics14: 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 interspecific Drosophila 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 & Evolution207, 462-470. PDF

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