Research Articles
2021 (14)
[1] M. A. Conte, F. E. Clark, R. B. Roberts, L. Xu, W. Tao, Q. Zhou, D. Wang, and T. D. Kocher*, “Origin of a Giant Sex Chromosome,” Mol Biol Evol, vol. 38, no. 4, pp. 1554-1569, Apr 13, 2021.
[2] L. He#, X. Long#, J. Qi#, Z. Wang#, Z. Huang, S. Wu, X. Zhang, H. Luo, X. Chen, J. Lin, Q. Yang, S. Huang*, Q. Zhou*, and L. Zheng*, “Genome and gene evolution of seahorse species revealed by the chromosome-level genome of Hippocampus abdominalis,” Mol Ecol Resour, Oct 26, 2021.
[3] J. Li, J. Zhang, J. Liu, Y. Zhou, C. Cai, L. Xu, X. Dai, S. Feng, C. Guo, J. Rao, K. Wei, E. D. Jarvis, Y. Jiang, Z. Zhou, G. Zhang, and Q. Zhou*, “A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals,” Gigascience, vol. 10, no. 1, Jan 6, 2021.
[4] J. Liu#, Z. Wang#, J. Li, L. Xu, J. Liu, S. Feng, C. Guo, S. Chen, Z. Ren, J. Rao, K. Wei, Y. Chen, E. D. Jarvis, G. Zhang, and Q. Zhou*, “A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes,” Genome Res, vol. 31, no. 3, pp. 497-511, Mar, 2021.
[5] V. Peona*, M. P. K. Blom, L. Xu, R. Burri, S. Sullivan, I. Bunikis, I. Liachko, T. Haryoko, K. A. Jonsson, Q. Zhou, M. Irestedt, and A. Suh*, “Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird-of-paradise,” Mol Ecol Resour, vol. 21, no. 1, pp. 263-286, Jan, 2021.
[6] V. Peona*, O. M. Palacios-Gimenez, J. Blommaert, J. Liu, T. Haryoko, K. A. Jonsson, M. Irestedt, Q. Zhou, P. Jern, and A. Suh, “The avian W chromosome is a refugium for endogenous retroviruses with likely effects on female-biased mutational load and genetic incompatibilities,” Philos Trans R Soc Lond B Biol Sci, vol. 376, no. 1833, pp. 20200186, Sep 13, 2021.
[7] M. Stock*, L. Kratochvil*, H. Kuhl, M. Rovatsos, B. J. Evans, A. Suh, N. Valenzuela, F. Veyrunes, Q. Zhou, T. Gamble, B. Capel, M. Schartl, and Y. Guiguen, “A brief review of vertebrate sex evolution with a pledge for integrative research: towards 'sexomics',” Philos Trans R Soc Lond B Biol Sci, vol. 376, no. 1832, pp. 20200426, Aug 30, 2021.
[8] Q. Su, H. He, and Q. Zhou*, “On the Origin and Evolution of Drosophila New Genes during Spermatogenesis,” Genes (Basel), vol. 12, no. 11, pp. 1796, Nov 15, 2021.
[9] W. Tao#, L. Xu#*, L. Zhao, Z. Zhu, X. Wu, Q. Min, D. Wang*, and Q. Zhou*, “High‐quality chromosome‐level genomes of two tilapia species reveal their evolution of repeat sequences and sex chromosomes,” Mol Ecol Resour, vol. 21, no. 2, pp. 543-560, 2021.
[10] Z. Wang, G. Chen, G. Zhang*, and Q. Zhou*, “Dynamic evolution of transposable elements, demographic history, and gene content of paleognathous birds,” Zool Res, vol. 42, no. 1, pp. 51-61, Jan 18, 2021.
[11] Z. Wang, J. Zhang, X. Xu, C. Witt, Y. Deng, G. Chenc, G. Meng, S. Feng, L. Xu, T. Szekely, G. Zhang*, and Q. Zhou*, “Phylogeny and Sex Chromosome Evolution of Palaeognathae,” J Genet Genomics, 2021.
[12] Y. Yin, H. Fan, B. Zhou, Y. Hu, G. Fan, J. Wang, F. Zhou, W. Nie, C. Zhang, L. Liu, Z. Zhong, W. Zhu, G. Liu, Z. Lin, C. Liu, J. Zhou, G. Huang, Z. Li, J. Yu, Y. Zhang, Y. Yang, B. Zhuo, B. Zhang, J. Chang, H. Qian, Y. Peng, X. Chen, L. Chen, Z. Li, Q. Zhou*, W. Wang*, and F. Wei*, “Molecular mechanisms and topological consequences of drastic chromosomal rearrangements of muntjac deer,” Nat Commun, vol. 12, no. 1, pp. 6858, Nov 25, 2021.
[13] Q. Zhou*, “Y chromosome evolution spurs behavioural diversity in male fish,” Nat Ecol Evol, vol. 5, no. 7, pp. 892-893, Jul, 2021.
[14] Y. Zhou, L. Shearwin-Whyatt, J. Li, Z. Song, T. Hayakawa, D. Stevens, J. C. Fenelon, E. Peel, Y. Cheng, F. Pajpach, N. Bradley, H. Suzuki, M. Nikaido, J. Damas, T. Daish, T. Perry, Z. Zhu, Y. Geng, A. Rhie, Y. Sims, J. Wood, B. Haase, J. Mountcastle, O. Fedrigo, Q. Li, H. Yang, J. Wang, S. D. Johnston, A. M. Phillippy, K. Howe, E. D. Jarvis, O. A. Ryder, H. Kaessmann, P. Donnelly, J. Korlach, H. A. Lewin, J. Graves, K. Belov, M. B. Renfree, F. Grutzner*, Q. Zhou*, and G. Zhang*, “Platypus and echidna genomes reveal mammalian biology and evolution,” Nature, vol. 592, no. 7856, pp. 756-762, Apr, 2021.
2020 (4)
[1] S. Feng, J. Stiller, Y. Deng, J. Armstrong, Q. Fang, A. H. Reeve, D. Xie, G. Chen, C. Guo, B. C. Faircloth, B. Petersen, Z. Wang, Q. Zhou, M. Diekhans, W. Chen, S. Andreu-Sanchez, A. Margaryan, J. T. Howard, C. Parent, G. Pacheco, M. S. Sinding, L. Puetz, E. Cavill, A. M. Ribeiro, L. Eckhart, J. Fjeldsa, P. A. Hosner, R. T. Brumfield, L. Christidis, M. F. Bertelsen, T. Sicheritz-Ponten, D. T. Tietze, B. C. Robertson, G. Song, G. Borgia, S. Claramunt, I. J. Lovette, S. J. Cowen, P. Njoroge, J. P. Dumbacher, O. A. Ryder, J. Fuchs, M. Bunce, D. W. Burt, J. Cracraft, G. Meng, S. J. Hackett, P. G. Ryan, K. A. Jonsson, I. G. Jamieson, R. R. da Fonseca, E. L. Braun, P. Houde, S. Mirarab, A. Suh, B. Hansson, S. Ponnikas, H. Sigeman, M. Stervander, P. B. Frandsen, H. van der Zwan, R. van der Sluis, C. Visser, C. N. Balakrishnan, A. G. Clark, J. W. Fitzpatrick, R. Bowman, N. Chen, A. Cloutier, T. B. Sackton, S. V. Edwards, D. J. Foote, S. B. Shakya, F. H. Sheldon, A. Vignal, A. E. R. Soares, B. Shapiro, J. Gonzalez-Solis, J. Ferrer-Obiol, J. Rozas, M. Riutort, A. Tigano, V. Friesen, L. Dalen, A. O. Urrutia, T. Szekely, Y. Liu, M. G. Campana, A. Corvelo, R. C. Fleischer, K. M. Rutherford, N. J. Gemmell, N. Dussex, H. Mouritsen, N. Thiele, K. Delmore, M. Liedvogel, A. Franke, M. P. Hoeppner, O. Krone, A. M. Fudickar, B. Mila, E. D. Ketterson, A. E. Fidler, G. Friis, A. M. Parody-Merino, P. F. Battley, M. P. Cox, N. C. B. Lima, F. Prosdocimi, T. L. Parchman, B. A. Schlinger, B. A. Loiselle, J. G. Blake, H. C. Lim, L. B. Day, M. J. Fuxjager, M. W. Baldwin, M. J. Braun, M. Wirthlin, R. B. Dikow, T. B. Ryder, G. Camenisch, L. F. Keller, J. M. DaCosta, M. E. Hauber, M. I. M. Louder, C. C. Witt, J. A. McGuire, J. Mudge, L. C. Megna, M. D. Carling, B. Wang, S. A. Taylor, G. Del-Rio, A. Aleixo, A. T. R. Vasconcelos, C. V. Mello, J. T. Weir, D. Haussler, Q. Li, H. Yang, J. Wang, F. Lei, C. Rahbek, M. T. P. Gilbert, G. R. Graves, E. D. Jarvis, B. Paten*, and G. Zhang*, “Dense sampling of bird diversity increases power of comparative genomics,” Nature, vol. 587, no. 7833, pp. 252-257, Nov, 2020.
[2] J. Liu, M. Ali, and Q. Zhou*, “Establishment and evolution of heterochromatin,” Ann N Y Acad Sci, vol. 1476, no. 1, pp. 59-77, Sep, 2020.
[3] L. Xu*, M. Irestedt, and Q. Zhou, “Sequence Transpositions Restore Genes on the Highly Degenerated W Chromosomes of Songbirds,” Genes (Basel), vol. 11, no. 11, pp. 1267, Oct 28, 2020.
[4] L. Xu, and Q. Zhou*, “The Female-Specific W Chromosomes of Birds Have Conserved Gene Contents but Are Not Feminized,” Genes (Basel), vol. 11, no. 10, Sep 25, 2020.
2019 (3)
[1] R. Wu, X. Xu, and Q. Zhou*, “Evolution of sex determination mechanisms and sex chromosomes,” SCIENTIA SINICA Vitae, vol. 49, no. 4, pp. 403-420, 2019.
[2] L. Xu, G. Auer, V. Peona, A. Suh, Y. Deng, S. Feng, G. Zhang, M. P. K. Blom, L. Christidis, S. Prost, M. Irestedt*, and Q. Zhou*, “Dynamic evolutionary history and gene content of sex chromosomes across diverse songbirds,” Nat Ecol Evol, vol. 3, no. 5, pp. 834-844, May, 2019.
[3] J. Y. Zhang, and Q. Zhou*, “On the Regulatory Evolution of New Genes Throughout Their Life History,” Mol Biol Evol, vol. 36, no. 1, pp. 15-27, Jan 1, 2019.
2018 (2)
[1] J. Q. Lin#, Q. Zhou#, H. Q. Yang, L. M. Fang, K. Y. Tang, L. Sun, Q. H. Wan, and S. G. Fang*, “Molecular mechanism of temperature-dependent sex determination and differentiation in Chinese alligator revealed by developmental transcriptome profiling,” Sci Bull, vol. 63, no. 4, pp. 209-212, Feb 28, 2018.
[2] Z. Wang#, J. Lyu#, F. Wang, C. Miao, Z. Nan, J. Zhang, Y. Xi, Q. Zhou, X. Yang, and W. Ge*, “The histone deacetylase HDAC1 positively regulates Notch signaling during Drosophila wing development,” Biol Open, vol. 7, no. 2, Feb 20, 2018.
2017 (2)
[1] R. Seki#, C. Li#, Q. Fang, S. Hayashi, S. Egawa, J. Hu, L. Xu, H. Pan, M. Kondo, T. Sato, H. Matsubara, N. Kamiyama, K. Kitajima, D. Saito, Y. Liu, M. T. Gilbert, Q. Zhou, X. Xu, T. Shiroishi, N. Irie*, K. Tamura*, and G. Zhang*, “Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features,” Nat Commun, vol. 8, pp. 14229, Feb 6, 2017.
[2] J. Zhang, J. Li, and Q. Zhou*, "Genomic and Transcriptomic Analyses of Avian Sex Chromosomes and Sex-Linked Genes," Avian and Reptilian Developmental Biology, pp. 69-85: Springer, 2017.
2016 (2)
[1] L. Gibilisco, Q. Zhou, S. Mahajan, and D. Bachtrog*, “Alternative Splicing within and between Drosophila Species, Sexes, Tissues, and Developmental Stages,” PLoS Genet, vol. 12, no. 12, pp. e1006464, Dec, 2016.
[2] W. Yin#, Z. Wang#, Q. Y. Li, J. M. Lian, Y. Zhou, B. Z. Lu, L. J. Jin, P. X. Qiu, P. Zhang, W. B. Zhu, B. Wen, Y. J. Huang, Z. L. Lin, B. T. Qiu, X. W. Su, H. M. Yang, G. J. Zhang, G. M. Yan*, and Q. Zhou*, “Evolutionary trajectories of snake genes and genomes revealed by comparative analyses of five-pacer viper,” Nat Commun, vol. 7, pp. 13107, Oct 6, 2016.
2015 (2)
[1] J. Zhang, C. Li, Q. Zhou, and G. Zhang*, “Improving the ostrich genome assembly using optical mapping data,” Gigascience, vol. 4, pp. 24, 2015.
[2] Q. Zhou, and D. Bachtrog*, “Ancestral Chromatin Configuration Constrains Chromatin Evolution on Differentiating Sex Chromosomes in Drosophila,” PLoS Genet, vol. 11, no. 6, pp. e1005331, Jun, 2015.
2014 (5)
[1] E. D. Jarvis#*, S. Mirarab#, A. J. Aberer, B. Li, P. Houde, C. Li, S. Y. Ho, B. C. Faircloth, B. Nabholz, J. T. Howard, A. Suh, C. C. Weber, R. R. da Fonseca, J. Li, F. Zhang, H. Li, L. Zhou, N. Narula, L. Liu, G. Ganapathy, B. Boussau, M. S. Bayzid, V. Zavidovych, S. Subramanian, T. Gabaldon, S. Capella-Gutierrez, J. Huerta-Cepas, B. Rekepalli, K. Munch, M. Schierup, B. Lindow, W. C. Warren, D. Ray, R. E. Green, M. W. Bruford, X. Zhan, A. Dixon, S. Li, N. Li, Y. Huang, E. P. Derryberry, M. F. Bertelsen, F. H. Sheldon, R. T. Brumfield, C. V. Mello, P. V. Lovell, M. Wirthlin, M. P. Schneider, F. Prosdocimi, J. A. Samaniego, A. M. Vargas Velazquez, A. Alfaro-Nunez, P. F. Campos, B. Petersen, T. Sicheritz-Ponten, A. Pas, T. Bailey, P. Scofield, M. Bunce, D. M. Lambert, Q. Zhou, P. Perelman, A. C. Driskell, B. Shapiro, Z. Xiong, Y. Zeng, S. Liu, Z. Li, B. Liu, K. Wu, J. Xiao, X. Yinqi, Q. Zheng, Y. Zhang, H. Yang, J. Wang, L. Smeds, F. E. Rheindt, M. Braun, J. Fjeldsa, L. Orlando, F. K. Barker, K. A. Jonsson, W. Johnson, K. P. Koepfli, S. O'Brien, D. Haussler, O. A. Ryder, C. Rahbek, E. Willerslev, G. R. Graves, T. C. Glenn, J. McCormack, D. Burt, H. Ellegren, P. Alstrom, S. V. Edwards, A. Stamatakis, D. P. Mindell, J. Cracraft, E. L. Braun, T. Warnow*, W. Jun*, M. T. Gilbert*, and G. Zhang*, “Whole-genome analyses resolve early branches in the tree of life of modern birds,” Science, vol. 346, no. 6215, pp. 1320-31, Dec 12, 2014.
[2] S. E. Lott*, J. E. Villalta, Q. Zhou, D. Bachtrog, and M. B. Eisen, “Sex-specific embryonic gene expression in species with newly evolved sex chromosomes,” PLoS Genet, vol. 10, no. 2, pp. e1004159, Feb, 2014.
[3] Z. Wang, J. Zhang, W. Yang, N. An, P. Zhang, G. Zhang*, and Q. Zhou*, “Temporal genomic evolution of bird sex chromosomes,” BMC Evol Biol, vol. 14, no. 1, pp. 250, Dec 12, 2014.
[4] G. Zhang#*, C. Li#, Q. Li, B. Li, D. M. Larkin, C. Lee, J. F. Storz, A. Antunes, M. J. Greenwold, R. W. Meredith, A. Odeen, J. Cui, Q. Zhou, L. Xu, H. Pan, Z. Wang, L. Jin, P. Zhang, H. Hu, W. Yang, J. Hu, J. Xiao, Z. Yang, Y. Liu, Q. Xie, H. Yu, J. Lian, P. Wen, F. Zhang, H. Li, Y. Zeng, Z. Xiong, S. Liu, L. Zhou, Z. Huang, N. An, J. Wang, Q. Zheng, Y. Xiong, G. Wang, B. Wang, J. Wang, Y. Fan, R. R. da Fonseca, A. Alfaro-Nunez, M. Schubert, L. Orlando, T. Mourier, J. T. Howard, G. Ganapathy, A. Pfenning, O. Whitney, M. V. Rivas, E. Hara, J. Smith, M. Farre, J. Narayan, G. Slavov, M. N. Romanov, R. Borges, J. P. Machado, I. Khan, M. S. Springer, J. Gatesy, F. G. Hoffmann, J. C. Opazo, O. Hastad, R. H. Sawyer, H. Kim, K. W. Kim, H. J. Kim, S. Cho, N. Li, Y. Huang, M. W. Bruford, X. Zhan, A. Dixon, M. F. Bertelsen, E. Derryberry, W. Warren, R. K. Wilson, S. Li, D. A. Ray, R. E. Green, S. J. O'Brien, D. Griffin, W. E. Johnson, D. Haussler, O. A. Ryder, E. Willerslev, G. R. Graves, P. Alstrom, J. Fjeldsa, D. P. Mindell, S. V. Edwards, E. L. Braun, C. Rahbek, D. W. Burt, P. Houde, Y. Zhang, H. Yang, J. Wang, C. Avian Genome, E. D. Jarvis*, M. T. Gilbert*, and J. Wang*, “Comparative genomics reveals insights into avian genome evolution and adaptation,” Science, vol. 346, no. 6215, pp. 1311-20, Dec 12, 2014.
[5] Q. Zhou#*, J. Zhang#, D. Bachtrog#, N. An, Q. Huang, E. D. Jarvis, M. T. Gilbert, and G. Zhang*, “Complex evolutionary trajectories of sex chromosomes across bird taxa,” Science, vol. 346, no. 6215, pp. 1246338, Dec 12, 2014.
2013 (2)
[1] A. A. Alekseyenko#, C. E. Ellison#, A. A. Gorchakov#, Q. Zhou, V. B. Kaiser, N. Toda, Z. Walton, S. Peng, P. J. Park, D. Bachtrog*, and M. I. Kuroda*, “Conservation and de novo acquisition of dosage compensation on newly evolved sex chromosomes in Drosophila,” Genes Dev, vol. 27, no. 8, pp. 853-8, Apr 15, 2013.
[2] Q. Zhou, C. E. Ellison, V. B. Kaiser, A. A. Alekseyenko, A. A. Gorchakov, and D. Bachtrog*, “The epigenome of evolving Drosophila neo-sex chromosomes: dosage compensation and heterochromatin formation,” PLoS Biol, vol. 11, no. 11, pp. e1001711, Nov, 2013.
2012 (7)
[1] R. Assis*, Q. Zhou, and D. Bachtrog, “Sex-biased transcriptome evolution in Drosophila,” Genome Biol Evol, vol. 4, no. 11, pp. 1189-200, 2012.
[2] Y. Ding#, Q. Zhou#, and W. Wang*, “Origins of New Genes and Evolution of Their Novel Functions,” Annual Review of Ecology, Evolution, and Systematics, Vol 43, vol. 43, no. 1, pp. 345-363, 2012.
[3] Q. Long#, Q. Zhou#, L. Ji#, J. Wu, W. Wang, and J. Xie*, “Mycobacterium smegmatis genomic characteristics associated with its saprophyte lifestyle,” J Cell Biochem, vol. 113, no. 10, pp. 3051-5, Oct, 2012.
[4] Z. Zhan, Y. Ding, R. Zhao, Y. Zhang, H. Yu, Q. Zhou, S. Yang, H. Xiang*, and W. Wang*, “Rapid functional divergence of a newly evolved polyubiquitin gene in Drosophila and its role in the trade-off between male fecundity and lifespan,” Mol Biol Evol, vol. 29, no. 5, pp. 1407-16, May, 2012.
[5] Q. Zhou, and D. Bachtrog*, “Chromosome-wide gene silencing initiates Y degeneration in Drosophila,” Curr Biol, vol. 22, no. 6, pp. 522-5, Mar 20, 2012.
[6] Q. Zhou, and D. Bachtrog*, “Sex-specific adaptation drives early sex chromosome evolution in Drosophila,” Science, vol. 337, no. 6092, pp. 341-5, Jul 20, 2012.
[7] Q. Zhou#, H. Zhu#, Q. Huang*, L. Zhao, G. Zhang, S. Roy, B. Vicoso, Z. Xuan, J. Ruan, Y. Zhang, R. Zhao, C. Ye, X. Zhang, J. Wang, W. Wang*, and D. Bachtrog*, “Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans,” BMC Genomics, vol. 13, no. 1, pp. 109, Mar 22, 2012.
2011 (1)
[1] V. B. Kaiser*, Q. Zhou, and D. Bachtrog, “Nonrandom gene loss from the Drosophila miranda neo-Y chromosome,” Genome Biol Evol, vol. 3, pp. 1329-37, 2011.
2010 (1)
[1] Y. Ding#, L. Zhao#, S. Yang, Y. Jiang, Y. Chen, R. Zhao, Y. Zhang, G. Zhang, Y. Dong, H. Yu, Q. Zhou, and W. Wang*, “A young Drosophila duplicate gene plays essential roles in spermatogenesis by regulating several Y-linked male fertility genes,” PLoS Genet, vol. 6, no. 12, pp. e1001255, Dec 23, 2010.
2008 (4)
[1] S. Yang#, J. R. Arguello#, X. Li, Y. Ding, Q. Zhou, Y. Chen, Y. Zhang, R. Zhao, F. Brunet, L. Peng, M. Long*, and W. Wang*, “Repetitive element-mediated recombination as a mechanism for new gene origination in Drosophila,” PLoS Genet, vol. 4, no. 1, pp. e3, Jan, 2008.
[2] Q. Zhou#, J. Wang#, L. Huang#, W. Nie, J. Wang, Y. Liu, X. Zhao, F. Yang*, and W. Wang*, “Neo-sex chromosomes in the black muntjac recapitulate incipient evolution of mammalian sex chromosomes,” Genome Biol, vol. 9, no. 6, pp. R98, 2008.
[3] Q. Zhou, and W. Wang*, “On the origin and evolution of new genes--a genomic and experimental perspective,” J Genet Genomics, vol. 35, no. 11, pp. 639-48, Nov, 2008.
[4] Q. Zhou#, G. Zhang#, Y. Zhang#, S. Xu, R. Zhao, Z. Zhan, X. Li, Y. Ding, S. Yang, and W. Wang*, “On the origin of new genes in Drosophila,” Genome Res, vol. 18, no. 9, pp. 1446-55, Sep, 2008.
2006 (2)
[1] H. Yu*, H. Jiang, Q. Zhou, J. Yang, Y. Cun, B. Su, C. Xiao*, and W. Wang*, “Origination and evolution of a human-specific transmembrane protein gene, c1orf37-dup,” Hum Mol Genet, vol. 15, no. 11, pp. 1870-5, Jun 1, 2006.
[2] Q. Zhou#, L. Huang#, J. Zhang#, X. Zhao, Q. Zhang, F. Song, J. Chi, F. Yang, and W. Wang, “Comparative genomic analysis links karyotypic evolution with genomic evolution in the Indian muntjac (Muntiacus muntjak vaginalis),” Chromosoma, vol. 115, no. 6, pp. 427-36, Dec, 2006.
2004 (1)
[1] Q. Zhou, and W. Wang*, “Detecting natural selection at the DNA level,” 2004.
