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Compensatory trans-regulatory alleles minimizing variation in TDH3 expression are common within Saccharomyces cerevisiae.

Metzger BPH, Wittkopp PJ.

Evol Lett. 2019 Aug 29;3(5):448-461. doi: 10.1002/evl3.137. eCollection 2019 Oct.


The yellow gene influences Drosophila male mating success through sex comb melanization.

Massey JH, Chung D, Siwanowicz I, Stern DL, Wittkopp PJ.

Elife. 2019 Oct 15;8. pii: e49388. doi: 10.7554/eLife.49388.


Empirical measures of mutational effects define neutral models of regulatory evolution in Saccharomyces cerevisiae.

Hodgins-Davis A, Duveau F, Walker EA, Wittkopp PJ.

Proc Natl Acad Sci U S A. 2019 Oct 15;116(42):21085-21093. doi: 10.1073/pnas.1902823116. Epub 2019 Sep 30.


Pleiotropic Effects of ebony and tan on Pigmentation and Cuticular Hydrocarbon Composition in Drosophila melanogaster.

Massey JH, Akiyama N, Bien T, Dreisewerd K, Wittkopp PJ, Yew JY, Takahashi A.

Front Physiol. 2019 May 1;10:518. doi: 10.3389/fphys.2019.00518. eCollection 2019.


Corrigendum: Tempo and mode of regulatory evolution in Drosophila.

Coolon JD, McManus CJ, Stevenson KR, Graveley BR, Wittkopp PJ.

Genome Res. 2018 Nov;28(11):1766. doi: 10.1101/gr.244087.118. No abstract available.


Fitness effects of altering gene expression noise in Saccharomyces cerevisiae.

Duveau F, Hodgins-Davis A, Metzger BP, Yang B, Tryban S, Walker EA, Lybrook T, Wittkopp PJ.

Elife. 2018 Aug 20;7. pii: e37272. doi: 10.7554/eLife.37272.


Effects of mutation and selection on plasticity of a promoter activity in Saccharomyces cerevisiae.

Duveau F, Yuan DC, Metzger BPH, Hodgins-Davis A, Wittkopp PJ.

Proc Natl Acad Sci U S A. 2017 Dec 26;114(52):E11218-E11227. doi: 10.1073/pnas.1713960115. Epub 2017 Dec 19.


Fitness Effects of Cis-Regulatory Variants in the Saccharomyces cerevisiae TDH3 Promoter.

Duveau F, Toubiana W, Wittkopp PJ.

Mol Biol Evol. 2017 Nov 1;34(11):2908-2912. doi: 10.1093/molbev/msx224.


Evolutionary Dynamics of Regulatory Changes Underlying Gene Expression Divergence among Saccharomyces Species.

Metzger BPH, Wittkopp PJ, Coolon JD.

Genome Biol Evol. 2017 Apr 1;9(4):843-854. doi: 10.1093/gbe/evx035.


Structure of the Transcriptional Regulatory Network Correlates with Regulatory Divergence in Drosophila.

Yang B, Wittkopp PJ.

Mol Biol Evol. 2017 Jun 1;34(6):1352-1362. doi: 10.1093/molbev/msx068.


Genetic basis of octanoic acid resistance in Drosophila sechellia: functional analysis of a fine-mapped region.

Andrade López JM, Lanno SM, Auerbach JM, Moskowitz EC, Sligar LA, Wittkopp PJ, Coolon JD.

Mol Ecol. 2017 Feb;26(4):1148-1160. doi: 10.1111/mec.14001. Epub 2017 Feb 4.


Potential Direct Regulators of the Drosophila yellow Gene Identified by Yeast One-Hybrid and RNAi Screens.

Kalay G, Lusk R, Dome M, Hens K, Deplancke B, Wittkopp PJ.

G3 (Bethesda). 2016 Oct 13;6(10):3419-3430. doi: 10.1534/g3.116.032607.


Tools and strategies for scarless allele replacement in Drosophila using CRISPR/Cas9.

Lamb AM, Walker EA, Wittkopp PJ.

Fly (Austin). 2017 Jan 2;11(1):53-64. doi: 10.1080/19336934.2016.1220463. Epub 2016 Aug 5.


Sensitivity of Allelic Divergence to Genomic Position: Lessons from the Drosophila tan Gene.

John AV, Sramkoski LL, Walker EA, Cooley AM, Wittkopp PJ.

G3 (Bethesda). 2016 Sep 8;6(9):2955-62. doi: 10.1534/g3.116.032029.


The Genetic Basis of Pigmentation Differences Within and Between Drosophila Species.

Massey JH, Wittkopp PJ.

Curr Top Dev Biol. 2016;119:27-61. doi: 10.1016/bs.ctdb.2016.03.004. Epub 2016 Apr 25. Review.


Contrasting Frequencies and Effects of cis- and trans-Regulatory Mutations Affecting Gene Expression.

Metzger BP, Duveau F, Yuan DC, Tryban S, Yang B, Wittkopp PJ.

Mol Biol Evol. 2016 May;33(5):1131-46. doi: 10.1093/molbev/msw011. Epub 2016 Jan 18.


Molecular Mechanisms and Evolutionary Processes Contributing to Accelerated Divergence of Gene Expression on the Drosophila X Chromosome.

Coolon JD, Stevenson KR, McManus CJ, Yang B, Graveley BR, Wittkopp PJ.

Mol Biol Evol. 2015 Oct;32(10):2605-15. doi: 10.1093/molbev/msv135. Epub 2015 Jun 2.


The significance and scope of evolutionary developmental biology: a vision for the 21st century.

Moczek AP, Sears KE, Stollewerk A, Wittkopp PJ, Diggle P, Dworkin I, Ledon-Rettig C, Matus DQ, Roth S, Abouheif E, Brown FD, Chiu CH, Cohen CS, Tomaso AW, Gilbert SF, Hall B, Love AC, Lyons DC, Sanger TJ, Smith J, Specht C, Vallejo-Marin M, Extavour CG.

Evol Dev. 2015 May-Jun;17(3):198-219. doi: 10.1111/ede.12125.


Selection on noise constrains variation in a eukaryotic promoter.

Metzger BP, Yuan DC, Gruber JD, Duveau F, Wittkopp PJ.

Nature. 2015 May 21;521(7552):344-7. doi: 10.1038/nature14244. Epub 2015 Mar 16.


Mapping small effect mutations in Saccharomyces cerevisiae: impacts of experimental design and mutational properties.

Duveau F, Metzger BP, Gruber JD, Mack K, Sood N, Brooks TE, Wittkopp PJ.

G3 (Bethesda). 2014 Apr 29;4(7):1205-16. doi: 10.1534/g3.114.011783.


Tempo and mode of regulatory evolution in Drosophila.

Coolon JD, McManus CJ, Stevenson KR, Graveley BR, Wittkopp PJ.

Genome Res. 2014 May;24(5):797-808. doi: 10.1101/gr.163014.113. Epub 2014 Feb 24. Erratum in: Genome Res. 2018 Nov;28(11):1766.


Evolution of splicing regulatory networks in Drosophila.

McManus CJ, Coolon JD, Eipper-Mains J, Wittkopp PJ, Graveley BR.

Genome Res. 2014 May;24(5):786-96. doi: 10.1101/gr.161521.113. Epub 2014 Feb 10.


Effect of genetic variation in a Drosophila model of diabetes-associated misfolded human proinsulin.

He BZ, Ludwig MZ, Dickerson DA, Barse L, Arun B, Vilhjálmsson BJ, Jiang P, Park SY, Tamarina NA, Selleck SB, Wittkopp PJ, Bell GI, Kreitman M.

Genetics. 2014 Feb;196(2):557-67. doi: 10.1534/genetics.113.157800. Epub 2013 Nov 26. Erratum in: Genetics. 2014 Apr;196(4):1357. Jiang, Pengyao [added].


Sex-specific effects of cis-regulatory variants in Drosophila melanogaster.

Coolon JD, Webb W, Wittkopp PJ.

Genetics. 2013 Dec;195(4):1419-22. doi: 10.1534/genetics.113.156331. Epub 2013 Oct 4.


The roles of cis- and trans-regulation in the evolution of regulatory incompatibilities and sexually dimorphic gene expression.

Meiklejohn CD, Coolon JD, Hartl DL, Wittkopp PJ.

Genome Res. 2014 Jan;24(1):84-95. doi: 10.1101/gr.156414.113. Epub 2013 Sep 16.


Sources of bias in measures of allele-specific expression derived from RNA-sequence data aligned to a single reference genome.

Stevenson KR, Coolon JD, Wittkopp PJ.

BMC Genomics. 2013 Aug 7;14:536. doi: 10.1186/1471-2164-14-536.


Genomic imprinting absent in Drosophila melanogaster adult females.

Coolon JD, Stevenson KR, McManus CJ, Graveley BR, Wittkopp PJ.

Cell Rep. 2012 Jul 26;2(1):69-75. doi: 10.1016/j.celrep.2012.06.013. Epub 2012 Jul 20.


The ontogeny of color: developmental origins of divergent pigmentation in Drosophila americana and D. novamexicana.

Cooley AM, Shefner L, McLaughlin WN, Stewart EE, Wittkopp PJ.

Evol Dev. 2012 Jul;14(4):317-25. doi: 10.1111/j.1525-142X.2012.00550.x.


Contrasting properties of gene-specific regulatory, coding, and copy number mutations in Saccharomyces cerevisiae: frequency, effects, and dominance.

Gruber JD, Vogel K, Kalay G, Wittkopp PJ.

PLoS Genet. 2012 Feb;8(2):e1002497. doi: 10.1371/journal.pgen.1002497. Epub 2012 Feb 9.


Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence.

Wittkopp PJ, Kalay G.

Nat Rev Genet. 2011 Dec 6;13(1):59-69. doi: 10.1038/nrg3095. Review.


Using pyrosequencing to measure allele-specific mRNA abundance and infer the effects of cis- and trans-regulatory differences.

Wittkopp PJ.

Methods Mol Biol. 2011;772:297-317. doi: 10.1007/978-1-61779-228-1_18.


Nomadic enhancers: tissue-specific cis-regulatory elements of yellow have divergent genomic positions among Drosophila species.

Kalay G, Wittkopp PJ.

PLoS Genet. 2010 Nov 24;6(11):e1001222. doi: 10.1371/journal.pgen.1001222.


Local adaptation for body color in Drosophila americana.

Wittkopp PJ, Smith-Winberry G, Arnold LL, Thompson EM, Cooley AM, Yuan DC, Song Q, McAllister BF.

Heredity (Edinb). 2011 Apr;106(4):592-602. doi: 10.1038/hdy.2010.90. Epub 2010 Jul 7.


Key considerations for measuring allelic expression on a genomic scale using high-throughput sequencing.

Fontanillas P, Landry CR, Wittkopp PJ, Russ C, Gruber JD, Nusbaum C, Hartl DL.

Mol Ecol. 2010 Mar;19 Suppl 1:212-27. doi: 10.1111/j.1365-294X.2010.04472.x.


Regulatory divergence in Drosophila revealed by mRNA-seq.

McManus CJ, Coolon JD, Duff MO, Eipper-Mains J, Graveley BR, Wittkopp PJ.

Genome Res. 2010 Jun;20(6):816-25. doi: 10.1101/gr.102491.109. Epub 2010 Mar 30. Erratum in: Genome Res. 2014 Jun;24(6):1051.


Variable transcription factor binding: a mechanism of evolutionary change.

Wittkopp PJ.

PLoS Biol. 2010 Mar 23;8(3):e1000342. doi: 10.1371/journal.pbio.1000342.


Intraspecific polymorphism to interspecific divergence: genetics of pigmentation in Drosophila.

Wittkopp PJ, Stewart EE, Arnold LL, Neidert AH, Haerum BK, Thompson EM, Akhras S, Smith-Winberry G, Shefner L.

Science. 2009 Oct 23;326(5952):540-4. doi: 10.1126/science.1176980.


Development and evolution of insect pigmentation: genetic mechanisms and the potential consequences of pleiotropy.

Wittkopp PJ, Beldade P.

Semin Cell Dev Biol. 2009 Feb;20(1):65-71. doi: 10.1016/j.semcdb.2008.10.002. Epub 2008 Oct 14. Review.


Regulatory changes underlying expression differences within and between Drosophila species.

Wittkopp PJ, Haerum BK, Clark AG.

Nat Genet. 2008 Mar;40(3):346-50. doi: 10.1038/ng.77. Epub 2008 Feb 17.


Independent effects of cis- and trans-regulatory variation on gene expression in Drosophila melanogaster.

Wittkopp PJ, Haerum BK, Clark AG.

Genetics. 2008 Mar;178(3):1831-5. doi: 10.1534/genetics.107.082032. Epub 2008 Feb 3.


Evolutionary genetics: how flies get naked.

Wittkopp PJ.

Curr Biol. 2007 Oct 23;17(20):R881-3. Review.


The function and regulation of Ultrabithorax in the legs of Drosophila melanogaster.

Davis GK, Srinivasan DG, Wittkopp PJ, Stern DL.

Dev Biol. 2007 Aug 15;308(2):621-31. Epub 2007 Jun 12.


Annotating ebony on the fly.

Kohn MH, Wittkopp PJ.

Mol Ecol. 2007 Jul;16(14):2831-3.


Evaluating the role of natural selection in the evolution of gene regulation.

Fay JC, Wittkopp PJ.

Heredity (Edinb). 2008 Feb;100(2):191-9. Epub 2007 May 23. Review.


Variable gene expression in eukaryotes: a network perspective.

Wittkopp PJ.

J Exp Biol. 2007 May;210(Pt 9):1567-75. Review.


Evolution of cis-regulatory sequence and function in Diptera.

Wittkopp PJ.

Heredity (Edinb). 2006 Sep;97(3):139-47. Epub 2006 Jul 19. Review.


Parent-of-origin effects on mRNA expression in Drosophila melanogaster not caused by genomic imprinting.

Wittkopp PJ, Haerum BK, Clark AG.

Genetics. 2006 Jul;173(3):1817-21. Epub 2006 May 15.


Compensatory cis-trans evolution and the dysregulation of gene expression in interspecific hybrids of Drosophila.

Landry CR, Wittkopp PJ, Taubes CH, Ranz JM, Clark AG, Hartl DL.

Genetics. 2005 Dec;171(4):1813-22. Epub 2005 Sep 2.


Genomic sources of regulatory variation in cis and in trans.

Wittkopp PJ.

Cell Mol Life Sci. 2005 Aug;62(16):1779-83. Review.


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