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J.J. Emerson - Publications

Affiliations: 
Integrative Biology University of California, Berkeley, Berkeley, CA, United States 
 Ecology and Evolutionary Biology University of California, Irvine, Irvine, CA 
Area:
population genetics, genomics, molecular evolution, bioinformatics
Website:
https://ccbs.uci.edu/team/james-jordan-emerson/
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31 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Shukla H, Chakraborty M, Emerson JJ. Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome. Biorxiv : the Preprint Server For Biology. PMID 38915508 DOI: 10.1101/2024.06.11.598575  0.391
2023 Chakraborty M, Lara AG, Dang A, McCulloch KJ, Rainbow D, Carter D, Ngo LT, Solares E, Said I, Corbett-Detig RB, Gilbert LE, Emerson JJ, Briscoe AD. Sex-linked gene traffic underlies the acquisition of sexually dimorphic UV color vision in butterflies. Proceedings of the National Academy of Sciences of the United States of America. 120: e2301411120. PMID 37552755 DOI: 10.1073/pnas.2301411120  0.305
2022 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. Nature Communications. 13: 3479. PMID 35710823 DOI: 10.1038/s41467-022-31112-x  0.418
2022 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. Author Correction: Hidden genomic features of an invasive malaria vector, Anopheles stephensi, revealed by a chromosome-level genome assembly. Bmc Biology. 20: 96. PMID 35501892 DOI: 10.1186/s12915-022-01314-2  0.357
2021 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 Biology. 19: 28. PMID 33568145 DOI: 10.1186/s12915-021-00963-z  0.354
2021 Liao Y, Zhang X, Chakraborty M, Emerson JJ. Topologically associating domains and their role in the evolution of genome structure and function in . Genome Research. PMID 33563719 DOI: 10.1101/gr.266130.120  0.427
2021 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 species complex. Genome Research. PMID 33563718 DOI: 10.1101/gr.263442.120  0.422
2020 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. Molecular Biology and Evolution. PMID 32681796 DOI: 10.1093/Molbev/Msaa185  0.487
2020 Heras J, Chakraborty M, Emerson JJ, German DP. Genomic and biochemical evidence of dietary adaptation in a marine herbivorous fish. Proceedings. Biological Sciences. 287: 20192327. PMID 32070255 DOI: 10.1098/Rspb.2019.2327  0.417
2019 Chakraborty M, Emerson JJ, Macdonald SJ, Long AD. Structural variants exhibit widespread allelic heterogeneity and shape variation in complex traits. Nature Communications. 10: 4872. PMID 31653862 DOI: 10.1038/S41467-019-12884-1  0.495
2019 Emerson JJ. Evolution: A Paradigm Shift in Snake Sex Chromosome Genetics. Current Biology : Cb. 27: R800-R803. PMID 28829965 DOI: 10.1016/J.Cub.2017.06.079  0.481
2018 Zhang X, Emerson JJ. Inferring Compensatory Evolution of cis- and trans-Regulatory Variation. Trends in Genetics : Tig. PMID 30503570 DOI: 10.1016/J.Tig.2018.11.003  0.31
2018 Solares EA, Chakraborty M, Miller DE, Kalsow S, Hall K, Perera AG, Emerson JJ, Hawley RS. Rapid Low-Cost Assembly of the Reference Genome Using Low-Coverage, Long-Read Sequencing. G3 (Bethesda, Md.). PMID 30018084 DOI: 10.1534/G3.118.200162  0.454
2017 Chakraborty M, VanKuren NW, Zhao R, Zhang X, Kalsow S, Emerson JJ. Hidden genetic variation shapes the structure of functional elements in Drosophila. Nature Genetics. PMID 29255259 DOI: 10.1038/S41588-017-0010-Y  0.711
2017 Long M, Emerson JJ. Meiotic Sex Chromosome Inactivation: Compensation by Gene Traffic. Current Biology : Cb. 27: R659-R661. PMID 28697367 DOI: 10.1016/J.Cub.2017.05.077  0.634
2016 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 Research. PMID 27458204 DOI: 10.1093/Nar/Gkw654  0.407
2014 Groot AT, Schöfl G, Inglis O, Donnerhacke S, Classen A, Schmalz A, Santangelo RG, Emerson J, Gould F, Schal C, Heckel DG. Within-population variability in a moth sex pheromone blend: genetic basis and behavioural consequences. Proceedings. Biological Sciences / the Royal Society. 281: 20133054. PMID 24500170 DOI: 10.1098/Rspb.2013.3054  0.364
2013 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 Biology. 11: e1001643. PMID 24015111 DOI: 10.1371/Journal.Pbio.1001643  0.685
2013 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. Molecular Biology and Evolution. 30: 2121-33. PMID 23793114 DOI: 10.1093/Molbev/Mst114  0.569
2013 Groot AT, Staudacher H, Barthel A, Inglis O, Schöfl G, Santangelo RG, Gebauer-Jung S, Vogel H, Emerson J, Schal C, Heckel DG, Gould F. One quantitative trait locus for intra- and interspecific variation in a sex pheromone. Molecular Ecology. 22: 1065-80. PMID 23294019 DOI: 10.1111/Mec.12171  0.336
2012 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 Genetics. 8: e1003080. PMID 23284287 DOI: 10.1371/Journal.Pgen.1003080  0.635
2011 Cardoso-Moreira M, Emerson JJ, Clark AG, Long M. Drosophila duplication hotspots are associated with late-replicating regions of the genome. Plos Genetics. 7: e1002340. PMID 22072977 DOI: 10.1371/Journal.Pgen.1002340  0.675
2011 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. Proceedings of the National Academy of Sciences of the United States of America. 108: 18009-13. PMID 22025696 DOI: 10.1073/Pnas.1115675108  0.546
2010 Emerson JJ, Li WH. The genetic basis of evolutionary change in gene expression levels. Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences. 365: 2581-90. PMID 20643748 DOI: 10.1098/Rstb.2010.0005  0.603
2010 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 Research. 20: 826-36. PMID 20445163 DOI: 10.1101/Gr.101576.109  0.585
2008 Emerson JJ, Cardoso-Moreira M, Borevitz JO, Long M. Natural selection shapes genome-wide patterns of copy-number polymorphism in Drosophila melanogaster. Science (New York, N.Y.). 320: 1629-31. PMID 18535209 DOI: 10.1126/Science.1158078  0.647
2005 Cowan AT, Bowman GR, Edwards KF, Emerson JJ, Turkewitz AP. Genetic, genomic, and functional analysis of the granule lattice proteins in Tetrahymena secretory granules. Molecular Biology of the Cell. 16: 4046-60. PMID 15958493 DOI: 10.1091/Mbc.E05-01-0028  0.344
2005 Chen Y, Emerson JJ, Martin TM. Evolutionary genomics: codon volatility does not detect selection. Nature. 433: E6-7; discussion E7-. PMID 15662371 DOI: 10.1038/Nature03223  0.483
2004 Betrán E, Emerson JJ, Kaessmann H, Long M. Sex chromosomes and male functions: where do new genes go? Cell Cycle (Georgetown, Tex.). 3: 873-5. PMID 15190200 DOI: 10.4161/Cc.3.7.960  0.728
2004 Wang W, Thornton K, Emerson JJ, Long M. Nucleotide variation and recombination along the fourth chromosome in Drosophila simulans. Genetics. 166: 1783-94. PMID 15126398 DOI: 10.1534/Genetics.166.4.1783  0.716
2004 Emerson JJ, Kaessmann H, Betrán E, Long M. Extensive gene traffic on the mammalian X chromosome. Science (New York, N.Y.). 303: 537-40. PMID 14739461 DOI: 10.1126/Science.1090042  0.734
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