Eksi, S. E., Barmina, O., McCallough, C. L., Kopp, A., and Orenic, T. V. (2018). A Distalless-responsive enhancer of the Hox gene Sex combs reduced is required for segment- and sex-specific sensory organ development in Drosophila. PLoS Genetics (uncorrected proof).

Rice, G. R., Barmina, O., Hu, K., and Kopp, A. (2018). Evolving doublesex expression correlates with the origin and diversification of male sexual ornaments in the Drosophila immigrans species group. Evol Devel 20:78-88.


Allen, S.L., Delaney, E.K., Reddiex, Kopp, A. and Chenoweth, S.F. (2017). Single-molecule sequencing of the Drosophila serrata genome. G3 7: 781-788.

Kopp, A. (2016). Strong reproductive isolation among African species of the Drosophila montium subgroup. Drosophila Info Service 99: 33-35.


Yassin, A., Delaney, E.K., Reddiex, A.J., Seher, T.D., Bastide, H., Appleton, N.C., Lack, J.B., David, J.R., Chenoweth, S.F., Pool, J.E. and Kopp, A. (2016). The pdm3 locus is a hotspot for recurrent evolution of female-limited color dimorphism in Drosophila. Current Biology 26: 2412-2422.

Signor, S.A., Liu, Y., Rebeiz, M., and Kopp, A. (2016). Genetic convergence in the evolution of male-specific color patterns in Drosophila. Current Biology 26: 2423-2433.


Hoang, D., Kopp, A., and Chandler, J.A. (2015). Interactions between Drosophila and its natural yeast symbionts – Is Saccharomyces cerevisiae the right model for studying the fly-yeast relationship? PeerJ 3:e1116 https://dx.doi.org/10.7717/peerj.1116


Arbeitman, M.N., Kopp, A., Siegal, M.L., and van Doren, M. (2014). The genetics of sex: exploring differences. Genetics 197: 527-529.

Platchetzki, D. C., Pankey, M. S., Johnson, B. R., Ronne, E.J., Kopp, A, Grosberg, R.K. (2014). Gene co-expression modules underlying polymorphic and monomorphic zooids in the colonial hydrozoan, Hydractinia symbiolongicarpus. Int Comp Biol 54: 276-283.

Wexler, J. R., Plachetzki, D. C., and Kopp, A. 2014. Pan-metazoan phylogeny of the DMRT gene family: a framework for functional studies. Devel Genes Evol 224: 175-81

Chen, Z. et al (2014). Comparative validation of the D. melanogaster modENCODE transcriptome annotation. Genome Research 24: 1209–1223.

Atallah, J., Vurens, G., Mavong, S., Mutti, A., Hoang, D., and Kopp, A. (2014).  Sex-specific repression of dachshund is required for Drosophila sex comb development. Devel Biol 386: 440–447.

Atallah, J., Teixeira, L., Salazar, R., Zaragoza, G., and Kopp, A. (2014). The making of a pest: the evolution of a fruit-penetrating ovipositor in Drosophila suzukii and related species. Proc. R. Soc. B 281: 20132840.


Kopp, A. (2013). Evolutionary genetics: Large effect of a small RNA. Current Biology 23(6) R247-R249.

Bossuyt, W., Chen, C. L., Chen, Q., Sudol, M., Pan, D., Kopp, A., and Halder, G. (2013). An evolutionary shift in the regulation of the Hippo pathway between mice and flies. Oncogene 2013 Apr 8. doi: 10.1038/onc.2013.82.

Chandler, J.A., and James, P.M. (2013). Discovery of trypanosomatid parasites in globally distributed Drosophila species. PLoS ONE 8(4): e61937.


Kopp, A. (2012). Evolutionary genetics: No coming back from neverland. Current Biology 22: R1004-R1006.

Kopp, A. 2012. Dmrt genes in the development and evolution of sexual dimorphism. Trends in Genetics 28(4): 175-184.

Kopp, A. 2012. Rate variation in the evolution of development: a phylogenetic perspective. In: Singh, R. S., Xu, J., Kulathinal, R. J. (Editors) “Rapidly evolving genes and genetic systems”, pp 246 – 255. Oxford University Press, Oxford UK.

Kronforst, M. R., Barsh, G. S, Kopp, A., Mallet, J., Monteiro, A., Mullen, S. P., Protas, M., Rosenblum, E. B., Schneider, C. J., and Hoekstra, H. E. 2012. Unraveling the thread of nature’s tapestry: the genetics of diversity and convergence in animal pigmentation. Pigment Cell and Melanoma Research 25: 411 – 433.

Chandler, J. S., Eisen, J., and Kopp, A. 2012. Yeast communities of diverse Drosophila species: Comparison of two symbiont groups in the same hosts. Appl. Environ. Microbiol. vol. 78 no. 20 7327-7336 .

Atallah, J., Watabe, H., and Kopp, A. 2012. Many ways to make a novel structure: a new mode of sex comb development in Drosophilidae. Evol Devel 14(6): 476-483.

Signor, S. A., Seher, T. D., and Kopp, A. 2012. Genomic resources for multiple species in the Drosophila ananassae species group. Fly 7(1) 47-56.

Seher, T.D., Ng, C.S., Signor, S.A., Podlaha, O., Barmina, O., and Kopp, A.. Genetic basis of a violation of Dollo’s law: re-evolution of rotating sex combs in Drosophila bipectinata. Genetics vol. 192 no. 4 1465-1475


Chandler, J., Morgan Lang, J., Bhatnagar, S., Jonathan A. Eisen, J.A., Kopp, A. 2011. Bacterial Communities of Diverse Drosophila Species: Ecological Context of a Host-Microbe Model System. PLOS Genetics; 9(7): e1002272.

Tanaka, K., Barmina, O., Sanders, L., Arbeitman, M., Kopp, A. 2011. Evolution of Sex-Specific Traits through Changes in HOX-Dependent doublesex Expression. PLOS Biology August; 9(8): e1001131.

Kopp, A. 2011. Drosophila sex combs as a model of evolutionary innovations. Evolution and Development 13:6, 504–522.

Bickel, R.D., Kopp, A., Nuzhdin, S.V., (2011). Composite Effects of Polymorphisms near Multiple Regulatory Elements Create a Major-Effect QTL. PLoS Genetics 7(1): e1001275


Kaczmarczyk, A.N., and Kopp, A. (2010). Germline stem cell maintenance as a proximate mechanism of life-history trade-offs? Bioessays 33(1): 5-12

Arbeitman, M.N., Kopp, A., Siegal, M.L., and Van Doren, M. (2010). Everything You Always Wanted to Know about Sex…in Flies. Sexual Development (6): 315-320

Syed, Z., Kopp, A., Kimbrell, D., and Leal, W. (2010). Bombykol receptors in the silkworm moth and the fruit fly. PNAS 107-20: 9436-9439


Bickel, R.D., Schackwitz, W.S., Pennacchio, L.A., Nuzhdin, S.V., and Kopp, A. (2009). Contrasting Patterns of Sequence Evolution at the Functionally Redundant bric a brac Paralogs in Drosophila melanogaster. Journal of Molecular Evolution 69:194-202

Kopp, A. (2009). Metamodels and phylogenetic replication: A systematic approach to the evolution of developmental pathways. Evolution 63-11: 2771-2789

Matsuda, M., Ng, C.-S., Doi, M., Kopp, A. and Tobari, Y. (2009). Evolution in the Drosophila ananassae species subgroup. Fly 3 (2): 1-13.

Tanaka, K., Barmina, O., and Kopp, A. (2009). Distinct developmental mechanisms underly the evolutionary diversification in Drosophila: sex combs. PNAS 106: 4764-4769

Telonis-Scott, M. Kopp, A. Wayne, M.L., Nuzhdin, S.V., and McIntyre, L.M. (2009). Sex-specific splicing in Drosophila: Widespread occurance, tissue-specificity, and evolutionary conservation. Genetics 181: 421-434.


Ng, C.-S., Hamilton, A.M., Frank, A., Barmina, O., and Kopp, A. (2008). Genetic Basis of sex-specific color patterns in Drosophila malerkotliana. Genetics 180: 421-429

Williams, T.M., Selegue, J., Werner, T., Gompel, N., Kopp, A., and Carrol, S.B. (2008). The regulation and evolution of a genetic switch controlling sexually dimorphic traits in Drosophila. Cell 134: 610-623

Ng, C.-S., and Kopp, A. (2008). Sex combs are important for male mating success in Drosophila melanogaster. Behav Genet 38: 195-201


Kopp, A., Barmina, O., Hamilton, A. Higgins, L., and Jones, C. (2007). Evolution of gene expression in the Drosophila olfactory system. Mol Biolo Evol 25: 1081-1092

Wayne, M.L., Telonis-Scott, M., Bono, L., Harshman, L., Kopp, A., Nuzhdin, S.V., and McIntyre, L.M. (2007). Simpler mode of inheritence of transcriptional variation in male Drosophila melanogaster. PNAS 104: 18577-18582

Barmina, O. and Kopp, A. (2007). Sex-specific regulation of a HOX gene associated with rapid morphological evolution. Devel Biol 311: 277-286


McIntyre, L.M., Genissel, A. Wasterman, R.L., Bono, L., Telonis, M., Wayne, M.L., Harshman, L., Vacha, S., Kopp, A., and Nuzhdin, S.V. (2006). Sex-specific expression of alternative transcripts in Drosophila. Genome Biology 7:R79

Kopp, A. (2006). Basal relationships in the Drosophila melanogaster species group. Mol Phyl Evol 39:787-798

Kopp, A., Barmina, O., and Frank, A. (2006). Interspecific divergence and intrachomasomal recombination of Y-chromosomal genes in Drosophila. Mol. Phyl. Evol 38:731-741.


Kopp, A., Frank, A., and Fu, J. (2005). Historical biogeography of Drosophila simulans based on Y-chromosomal sequences. Mol. Phyl. Evol 38:355-362.

Siegel A, Lee S, Kopp A. 2005. New mutants report: morphological markers in Drosophila malerkotliana and D. bipectinata. Dros. Inf. Serv. 87: 110-112.

Barmina O., Gonzalo, M., McIntyre, L., Kopp, A. (2005). Sex- and segment-specific modulation of gene expression profiles in Drosophila. Developmental Biology 288: 528-544.

Kopp, A., Barmina O. (2005). Evolutionary history of the Drosophila bipectinata species complex. Genet. Res., Camb. 85: 23-46.

Kopp, A., Frank A. (2005). Speciation in progress? A continuum of reproductive isolation in Drosophila bipectinata species. Genetica 125:55-68.


Kopp, A. (2004). Making a better worm. Nature Genetics 36: 213-214.

Gibson, G., Riley-Berger, R., Harshman, L., Kopp, A., Vacha, S., Nuzhdin, S., Wayne, M. (2004). Extensive sex-specific non-additivity of gene expression in Drosophila melanogaster. Genetics 167: 1791-1799.


Wittkopp, P. J., Carroll, S. B. and Kopp, A. (2003). Evolution in black and white: Genetic control of pigment patterns in Drosophila. Trends Genet. 19: 495-504.

Kopp, A., Graze, R., Xu, S., Carroll, S. B. and S. Nuzhdin, 2003. Quantitative trait loci responsible for variation in sexually dimorphic traits in Drosophila melanogaster. Genetics 163: 771-787.


Kopp, A. and J. True, 2002. Phylogeny of the Oriental Drosophila melanogaster species group: a multi-locus reconstruction. Syst. Biol. 51: 786-805.

Kopp, A. and J. True, 2002. Evolution of male sexual characters in the Oriental Drosophila melanogaster species group. Evol. Devel 4: 274-291.

Kopp, A. and I. Duncan, 2002. Anteroposterior patterning in adult abdominal segments of Drosophila. Devel. Biol. 242: 15-30.


True, J. R., A. Kopp and S. B. Carroll, 2001. Prophenoloxidase as a reporter for analysis of gene expression in Drosophila. BioTechniques 30: 1004-9.

2000 and earlier

Kopp, A, I. Duncan, D. Godt and S. B. Carroll, 2000. Genetic control and evolution of sexually dimorphic characters in Drosophila. Nature 408: 553-559.

Kopp, A., R. Blackman and I. Duncan, 1999. Wingless, Decapentaplegic and EGF Receptor signaling pathways interact to specify dorso-ventral pattern in the adult abdomen of Drosophila. Development 126: 3495-507.

Kopp, A., M. A. T. Muskavitch and I. Duncan, 1997. The roles of hedgehog and engrailed in patterning the adult abdominal segments of Drosophila. Development 124, 3703-3714.

Kopp, A. and I. Duncan, 1997. Control of cell fate and polarity in the adult abdominal segments of Drosophila by optomotor-blind. Development 124, 3715-3726.