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2013
Supple MA, Hines HM, Lavoie C, Ray D, Nielsen DM, Salazar C, Dasmahaptara K, McMillan WO and BA Counterman. 2013. Genomic architecture of adaptive color pattern divergence and convergence in Heliconius butterflies. Genome Research, doi:10.1101/gr.150615.112
Papa R, Kapan DD, Counterman BA, Maldonado K, Lindstrom DP, Reed RD, Nijhout HF, Hrbek T and WO McMillan. 2013. Multi-allelic major effect genes interact with minor effect QTLs to control adaptive color pattern variation in Heliconius erato. PLoS ONE, doi:10.1371/journal.pone.0057033
2012
Martin A, Papa R, Nadeau N, Hill RI, Counterman BA, Jiggins CD, Kronforst MR, Long AD, McMillan WO and RD Reed. 2012. Diversification of complex butterfly wing patterns by repeated regulatory evolution of a Wnt ligand. Proceedings of the National Academy of Sciences, USA, doi:10.1073/pnas.1204800109
The Heliconius Genome Consortium. 2012. A butterfly genome reveals promiscuous exchange of mimicry adaptations among species. Nature, 487(7405): 94-98. doi:10.1038/nature11041 (Open Access)
2011
Hines HM, Counterman BA, Papa R, Albuquerque De Moura P, Cardoso MZ, Linares M, Mallet J, Reed R, Jiggins CD, Kronforst MR and WO McMillan. 2011. A wing patterning gene redefines the mimetic history of Heliconius butterflies. Proceedings of the National Academy of Sciences, USA, 108(49). doi:10.1073/pnas.1110096108
Reed RD, Papa R, Martin A, Hines HM, Counterman BA, Pardo-Diaz C, Jiggins CD, Chamberlain NL, Kronforst MR, Chen R, Halder G, Nijhout HF and WO McMillan. 2011. Optix drives the repeated convergent evolution of butterfly wing pattern mimicry. Science, 333: 6046. doi:10.1126/science.1208227 
2010
Quek S-P, Counterman BA, Albuquerque De Moura P, Cardoso, MZ, Marshall CR, McMillan WO and MR Kronforst. 2010. Dissecting comimetic radiations in Heliconius reveals divergent histories of convergent butterflies. Proceedings of the National Academy of Sciences, USA, 107(16). doi:10.1073/pnas.0911572107 pdf
Counterman BA, Arajuo-Perez F, Hine, HM, Baxter SW, Morrison CM, Lindstrom DP, Papa R, Ferguson L, Joron M, Ffrench-Constant R, Smith C, Nielsen DM, Chen R, Jiggins CD, Reed RD, Halder G, Mallet J and WO McMillan. 2010. Genomic Hotspots for adaptation: population genetics of Mullerian mimicry in Heliconius erato. PLoS Genetics 6(2): e1000796. doi:10.1371/journal.pgen.1000796 pdf
Baxter SW, Nadeau N, Maroja L, Wilkinson P, Counterman BA, Dawson A, Beltran M, Perez-Espinoza S, Chamberlain N, Ferguson L, Clark R, Davidson C, Glithero R, Mallet J, WO McMillan, Kronforst M, Joron M, Ffrench-Constant R and CD Jiggins. 2010. Genomic Hotspots for adaptation: population genetics of Mullerian mimicry in the Heliconius melpomene clade. PLoS Genetics 6(2): e1000794. doi:10.1371/journal.pgen.1000794 pdf
2008
Papa R, Morrison CM, Walters JR, Counterman BA, Chen R, Halder G, Ferguson L, Chamberlain N, Ffrench-Constant R, Kapan DD, Jiggins CD, Reed RD and WO McMillan. 2008. Highly conserved gene order and numerous novel repetitive elements in genomic regions linked to wing pattern variation in Heliconius butterflies. BMC Genomics 9:345. doi:10.1186/1471-2164-9-345 pdf
2007
Ortíz-Barrientos D, Counterman BA and MA Noor. 2007. Gene expression divergence and the origin of species. Genetica 129: 71-81. doi:10.1007/s10709-006-0034-1 pdf
2006
Counterman BA, and MA Noor. 2006. Multilocus test for introgression between the cactophilic species Drosophila mojavensis and D. arizonae. American Naturalist 168: 682-696. http://www.jstor.org/stable/10.1086/508632 pdf
2005
Yang JY, Counterman BA, Eckert CG and SA Hodges. 2005. Microsatellite markers for evolutionary studies in Aquilegia. Molecular Ecology Notes 5: 317-320. doi:10.1111/j.1471-8286.2005.00913.x pdf
2004
Ortíz-Barrientos D, Counterman BA and MA Noor . 2004. The genetics of Reinforcement in Drosophila. PLoS Biology 2(12): e416. doi:10.1371/journal.pbio.0020416 pdf
Counterman BA, Ortíz-Barrientos D and MA Noor. 2004. Using comparative genomic data to test for fast-X evolution. Evolution 58: 656-660. doi:10.1111/j.0014-3820.2004.tb01688.x pdf
Stevison LS, Counterman BA and MA Noor. 2004. Molecular population genetics of X-linked accessory gland proteins in Drosophila pseudoobscura. Journal of Heredity 95: 114-118. doi:10.1093/jhered/esh027 pdf
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