My Bibliography

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Chakraborty M, Lara AG, Dang A, McCulloch KJ, Rainbow D, Carter D, Ngo LT, Solares EA, Said I, Corbett-Detig R, Gilbert LE, Emerson JJ, Briscoe AD. Sex-linked gene traffic underlies the acquisition of sexually dimorphic UV color vision in Heliconius butterflies. Proc Natl Acad Sci U S A. Forthcoming; 120. doi: 10.1073/pnas.2301411120.

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Liao Y, Wang J, Zhu Z, Liu Y, Chen J, Zhou Y, Liu F, Lei J, Gaut BS, Cao B, Emerson JJ, Chen C. The 3D architecture of the pepper genome and its relationship to function and evolution. Nat Commun. 2022 Jun 16;13(1):3479. doi: 10.1038/s41467-022-31112-x. PubMed PMID: 35710823; PubMed Central PMCID: PMC9203530.

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Durkin SM, Chakraborty M, Abrieux A, Lewald KM, Gadau A, Svetec N, Peng J, Kopyto M, Langer CB, Chiu JC, Emerson JJ, Zhao L. Behavioral and Genomic Sensory Adaptations Underlying the Pest Activity of Drosophila suzukii. Mol Biol Evol. 2021 May 19;38(6):2532-2546. doi: 10.1093/molbev/msab048. PubMed PMID: 33586767; PubMed Central PMCID: PMC8136512.

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Liao Y, Zhang X, Chakraborty M, Emerson JJ. Topologically associating domains and their role in the evolution of genome structure and function in Drosophila. Genome Res. 2021 Mar;31(3):397-410. doi: 10.1101/gr.266130.120. Epub 2021 Feb 9. PubMed PMID: 33563719; PubMed Central PMCID: PMC7919452.

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Chakraborty M, Chang CH, Khost DE, Vedanayagam J, Adrion JR, Liao Y, Montooth KL, Meiklejohn CD, Larracuente AM, Emerson JJ. Evolution of genome structure in the Drosophila simulans species complex. Genome Res. 2021 Mar;31(3):380-396. doi: 10.1101/gr.263442.120. Epub 2021 Feb 9. PubMed PMID: 33563718; PubMed Central PMCID: PMC7919458.

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Chakraborty M, Ramaiah A, Adolfi A, Halas P, Kaduskar B, Ngo LT, Jayaprasad S, Paul K, Whadgar S, Srinivasan S, Subramani S, Bier E, James AA, Emerson JJ. Hidden genomic features of an invasive malaria vector, Anopheles stephensi, revealed by a chromosome-level genome assembly. BMC Biol. 2021 Feb 10;19(1):28. doi: 10.1186/s12915-021-00963-z. PubMed PMID: 33568145; PubMed Central PMCID: PMC7876825.

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Kou Y, Liao Y, Toivainen T, Lv Y, Tian X, Emerson JJ, Gaut BS, Zhou Y. Evolutionary Genomics of Structural Variation in Asian Rice (Oryza sativa) Domestication. Mol Biol Evol. 2020 Dec 16;37(12):3507-3524. doi: 10.1093/molbev/msaa185. PubMed PMID: 32681796; PubMed Central PMCID: PMC7743901.

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Adolfi A, Gantz VM, Jasinskiene N, Lee HF, Hwang K, Terradas G, Bulger EA, Ramaiah A, Bennett JB, Emerson JJ, Marshall JM, Bier E, James AA. Efficient population modification gene-drive rescue system in the malaria mosquito Anopheles stephensi. Nat Commun. 2020 Nov 3;11(1):5553. doi: 10.1038/s41467-020-19426-0. PubMed PMID: 33144570; PubMed Central PMCID: PMC7609566.

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Heras J, Chakraborty M, Emerson JJ, German DP. Genomic and biochemical evidence of dietary adaptation in a marine herbivorous fish. Proc Biol Sci. 2020 Feb 26;287(1921):20192327. doi: 10.1098/rspb.2019.2327. Epub 2020 Feb 19. PubMed PMID: 32070255; PubMed Central PMCID: PMC7062031.

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Chakraborty M, Emerson JJ, Macdonald SJ, Long AD. Structural variants exhibit widespread allelic heterogeneity and shape variation in complex traits. Nat Commun. 2019 Oct 25;10(1):4872. doi: 10.1038/s41467-019-12884-1. PubMed PMID: 31653862; PubMed Central PMCID: PMC6814777.

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Zhang X, Emerson JJ. Inferring Compensatory Evolution of cis- and trans-Regulatory Variation. Trends Genet. 2019 Jan;35(1):1-3. doi: 10.1016/j.tig.2018.11.003. Epub 2018 Nov 29. Review. PubMed PMID: 30503570; PubMed Central PMCID: PMC8244802.

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Solares EA, Chakraborty M, Miller DE, Kalsow S, Hall K, Perera AG, Emerson JJ, Hawley RS. Rapid Low-Cost Assembly of the Drosophila melanogaster Reference Genome Using Low-Coverage, Long-Read Sequencing. G3 (Bethesda). 2018 Oct 3;8(10):3143-3154. doi: 10.1534/g3.118.200162. PubMed PMID: 30018084; PubMed Central PMCID: PMC6169397.

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Chakraborty M, VanKuren NW, Zhao R, Zhang X, Kalsow S, Emerson JJ. Hidden genetic variation shapes the structure of functional elements in Drosophila. Nat Genet. 2018 Jan;50(1):20-25. doi: 10.1038/s41588-017-0010-y. Epub 2017 Dec 18. PubMed PMID: 29255259; PubMed Central PMCID: PMC5742068.

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Emerson JJ. Evolution: A Paradigm Shift in Snake Sex Chromosome Genetics. Curr Biol. 2017 Aug 21;27(16):R800-R803. doi: 10.1016/j.cub.2017.06.079. PubMed PMID: 28829965.

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Long M, Emerson JJ. Meiotic Sex Chromosome Inactivation: Compensation by Gene Traffic. Curr Biol. 2017 Jul 10;27(13):R659-R661. doi: 10.1016/j.cub.2017.05.077. PubMed PMID: 28697367.

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Chakraborty M, Baldwin-Brown JG, Long AD, Emerson JJ. Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage. Nucleic Acids Res. 2016 Nov 2;44(19):e147. doi: 10.1093/nar/gkw654. Epub 2016 Jul 25. PubMed PMID: 27458204; PubMed Central PMCID: PMC5100563.

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Schaefke B, Emerson JJ, Wang TY, Lu MY, Hsieh LC, Li WH. Inheritance of gene expression level and selective constraints on trans- and cis-regulatory changes in yeast. Mol Biol Evol. 2013 Sep;30(9):2121-33. doi: 10.1093/molbev/mst114. Epub 2013 Jun 22. PubMed PMID: 23793114.

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Vicoso B, Emerson JJ, Zektser Y, Mahajan S, Bachtrog D. Comparative sex chromosome genomics in snakes: differentiation, evolutionary strata, and lack of global dosage compensation. PLoS Biol. 2013;11(8):e1001643. doi: 10.1371/journal.pbio.1001643. Epub 2013 Aug 27. PubMed PMID: 24015111; PubMed Central PMCID: PMC3754893.

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Pool JE, Corbett-Detig RB, Sugino RP, Stevens KA, Cardeno CM, Crepeau MW, Duchen P, Emerson JJ, Saelao P, Begun DJ, Langley CH. Population Genomics of sub-saharan Drosophila melanogaster: African diversity and non-African admixture. PLoS Genet. 2012;8(12):e1003080. doi: 10.1371/journal.pgen.1003080. Epub 2012 Dec 20. PubMed PMID: 23284287; PubMed Central PMCID: PMC3527209.

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Cardoso-Moreira M, Emerson JJ, Clark AG, Long M. Drosophila duplication hotspots are associated with late-replicating regions of the genome. PLoS Genet. 2011 Nov;7(11):e1002340. doi: 10.1371/journal.pgen.1002340. Epub 2011 Nov 3. PubMed PMID: 22072977; PubMed Central PMCID: PMC3207856.

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Nikaido M, Sasaki T, Emerson JJ, Aibara M, Mzighani SI, Budeba YL, Ngatunga BP, Iwata M, Abe Y, Li WH, Okada N. Genetically distinct coelacanth population off the northern Tanzanian coast. Proc Natl Acad Sci U S A. 2011 Nov 1;108(44):18009-13. doi: 10.1073/pnas.1115675108. Epub 2011 Oct 24. PubMed PMID: 22025696; PubMed Central PMCID: PMC3207662.

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Emerson JJ, Li WH. The genetic basis of evolutionary change in gene expression levels. Philos Trans R Soc Lond B Biol Sci. 2010 Aug 27;365(1552):2581-90. doi: 10.1098/rstb.2010.0005. PubMed PMID: 20643748; PubMed Central PMCID: PMC2935095.

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Emerson JJ, Hsieh LC, Sung HM, Wang TY, Huang CJ, Lu HH, Lu MY, Wu SH, Li WH. Natural selection on cis and trans regulation in yeasts. Genome Res. 2010 Jun;20(6):826-36. doi: 10.1101/gr.101576.109. Epub 2010 May 5. PubMed PMID: 20445163; PubMed Central PMCID: PMC2877579.

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Emerson JJ, Cardoso-Moreira M, Borevitz JO, Long M. Natural selection shapes genome-wide patterns of copy-number polymorphism in Drosophila melanogaster. Science. 2008 Jun 20;320(5883):1629-31. doi: 10.1126/science.1158078. Epub 2008 Jun 5. PubMed PMID: 18535209.

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Fan C, Emerson JJ, Long M. The origin of new genes. In: Pagel M, Pomiankowski A, editors. Evolutionary Genomics and Proteomics Sunderland, Massachusetts: Sinauer Associates, Inc.; 2007. 27-44p.

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Cowan AT, Bowman GR, Edwards KF, Emerson JJ, Turkewitz AP. Genetic, genomic, and functional analysis of the granule lattice proteins in Tetrahymena secretory granules. Mol Biol Cell. 2005 Sep;16(9):4046-60. doi: 10.1091/mbc.e05-01-0028. Epub 2005 Jun 15. PubMed PMID: 15958493; PubMed Central PMCID: PMC1196318.

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Chen Y, Emerson JJ, Martin TM. Evolutionary genomics: codon volatility does not detect selection. Nature. 2005 Jan 20;433(7023):E6-7; discussion E7-8. doi: 10.1038/nature03223. PubMed PMID: 15662371.

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Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature. 2004 Dec 9;432(7018):695-716. doi: 10.1038/nature03154. PubMed PMID: 15592404.

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Betrán E, Emerson JJ, Kaessmann H, Long M. Sex chromosomes and male functions: where do new genes go?. Cell Cycle. 2004 Jul;3(7):873-5. Epub 2004 Jul 5. Review. PubMed PMID: 15190200.

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Wang W, Thornton K, Emerson JJ, Long M. Nucleotide variation and recombination along the fourth chromosome in Drosophila simulans. Genetics. 2004 Apr;166(4):1783-94. doi: 10.1534/genetics.166.4.1783. PubMed PMID: 15126398; PubMed Central PMCID: PMC1470817.

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Emerson JJ, Kaessmann H, Betrán E, Long M. Extensive gene traffic on the mammalian X chromosome. Science. 2004 Jan 23;303(5657):537-40. doi: 10.1126/science.1090042. PubMed PMID: 14739461.

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Strassmann JE, Queller DC, Emerson JJ, Stagi M, Servo R, Turillazzi S. Comparing the costs and benefits of grouping with non-relatives in the social amoeba Dictyostelium discoideum (Amoebazoa) and the social wasp Polistes dominulus (Hymenoptera Vespidae). Redia - Giornale di Zoologia. 2004; LXXXVII:145-148.

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Bergelson J, Dwyer G, Emerson JJ. Models and data on plant-enemy coevolution. Annu Rev Genet. 2001;35:469-99. doi: 10.1146/annurev.genet.35.102401.090954. Review. PubMed PMID: 11700291.