Research Articles
2021
Valentina Peona*; Mozes P K Blom; Luohao Xu; Reto Burri; Shawn Sullivan; Ignas Bunikis; Ivan Liachko; Tri Haryoko; Knud A Jønsson; Zhou Qi; Martin Irestedt; Alexander Suh*, Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird-of-paradise, Mol Ecol Resour ., 2021, 21(1): 263-286.
Li Jing; Zhang Jilin; Liu Jing; Zhou Yang; Cai Cheng; Xu Luohao; Dai Xuelei; Feng Shaohong; Guo Chunxue; Rao Jinpeng; Wei Kai; Erich D Jarvis; Jiang Yu; Zhou Zhengkui; Zhang Guojie; Zhou Qi*, A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals, Gigascience, 2021, 10(1): 142.
Liu Jing #; Wang Zongji #; Xu Luohao; Liu Jiaqi; Shaohong Feng; Chunxue Guo; Shengchan Chen; Zhanjun Ren; Jinpeng Rao; Kai Wei; Yuezhou Chen; Erich Jarvis; Zhang Guojie ; Zhou Qi*, A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes, Genome Research, 2021, 31(1): gr. 271569.120.
Zhou Y, Shearwin-Whyatt L, Li J, Song Z, Hayakawa T, Stevens D, Fenelon JC, Peel E, Cheng Y, Pajpach F, Bradley N, Suzuki H, Nikaido M, Damas J, Daish T, Perry T, Zhu Z, Geng Y, Rhie A, Sims Y, Wood J, Haase B, Mountcastle J, Fedrigo O, Li Q, Yang H, Wang J, Johnston SD, Phillippy AM, Howe K, Jarvis ED, Ryder OA, Kaessmann H, Donnelly P, Korlach J, Lewin HA, Graves J, Belov K, Renfree MB, Grutzner F*, Zhou Qi*, Zhang G*. 2021. Platypus and echidna genomes reveal mammalian biology and evolution. Nature
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2020
Wang Zong-Ji; Chen Guang-Ji; Zhou Qi*; Zhang Guo-Jie*, Dynamic evolution of transposable elements, demographic history, and gene content of paleognathous birds., Zoological Research, 2020, 42(1): 51-61.
Matthew A Conte; Frances E Clark; Reade B Roberts; Luohao Xu; Wenjing Tao; Zhou Qi; Deshou Wang; Thomas D Kocher*, Origin of a giant sex chromosome, 2020, 319.
Feng, S., Stiller, J., Deng, Y., Armstrong, J., Fang, Q., Reeve, A. H., Xie, D., Chen, G., Guo, C., Faircloth, B. C., Petersen, B., Wang, Z., Zhou, Qi., Diekhans, M., Chen, W., Andreu-Sanchez, S., Margaryan, A., Howard, J. T., Parent, C., Pacheco, G., Sinding, M. S., Puetz, L., Cavill, E., Ribeiro, A. M., Eckhart, L., Fjeldsa, J., Hosner, P. A., Brumfield, R. T., Christidis, L., Bertelsen, M. F., Sicheritz-Ponten, T., Tietze, D. T., Robertson, B. C., Song, G., Borgia, G., Claramunt, S., Lovette, I. J., Cowen, S. J., Njoroge, P., Dumbacher, J. P., Ryder, O. A., Fuchs, J., Bunce, M., Burt, D. W., Cracraft, J., Meng, G., Hackett, S. J., Ryan, P. G., Jonsson, K. A., Jamieson, I. G., Da, F. R., Braun, E. L., Houde, P., Mirarab, S., Suh, A., Hansson, B., Ponnikas, S., Sigeman, H., Stervander, M., Frandsen, P. B., van der Zwan, H., van der Sluis, R., Visser, C., Balakrishnan, C. N., Clark, A. G., Fitzpatrick, J. W., Bowman, R., Chen, N., Cloutier, A., Sackton, T. B., Edwards, S. V., Foote, D. J., Shakya, S. B., Sheldon, F. H., Vignal, A., Soares, A., Shapiro, B., Gonzalez-Solis, J., Ferrer-Obiol, J., Rozas, J., Riutort, M., Tigano, A., Friesen, V., Dalen, L., Urrutia, A. O., Szekely, T., Liu, Y., Campana, M. G., Corvelo, A., Fleischer, R. C., Rutherford, K. M., Gemmell, N. J., Dussex, N., Mouritsen, H., Thiele, N., Delmore, K., Liedvogel, M., Franke, A., Hoeppner, M. P., and Krone, O., et al., 2020, Dense sampling of bird diversity increases power of comparative genomics: Nature, v. 587, p. 252-257.
Xu, Luohao*; Irestedt, Martin; Zhou Qi, Sequence Transpositions Restore Genes on the Highly Degenerated W Chromosomes of Songbirds, Genes, 2020, 11(11): 1267.
Tao, Wenjing; Xu, Luohao*; Zhao, Lin; Zhu, Zexian; Wu, Xin; Min, Qianwen; Wang, Deshou*; Zhou Qi*, High-quality chromosome-level genomes of two tilapia species reveal their evolution of repeat sequences and sex chromosomes, Molecular Ecology Resources, 2020, 21(2): 543-560.
Xu Luohao; Zhou Qi*, The Female-Specific W Chromosomes of Birds Have Conserved Gene Contents but Are Not Feminized, Genes, 2020, 11(10).
Liu Jing; Mujahid Ali;Zhou Qi*, Establishment and evolution of heterochromatin., Annals of the New York Academy of Sciences, 2020.
2019
Xu, Luohao; Auer, Gabriel; Peona, Valentina; Suh, Alexander; Deng, Yuan; Feng, Shaohong; Zhang, Guojie; Blom, Mozes P K; Christidis, Les; Prost, Stefan; Irestedt, Martin*; Zhou,Qi*, Dynamic evolutionary history and gene content of sex chromosomes across diverse songbirds, Nature Ecology & Evolution, 2019, 3(5): 834-844.
Zhang Jiayu; Zhou Qi*, On the Regulatory Evolution of New Genes Throughout Their Life History, Molecular Biology and Evolution, 2019, 36(1): 15-27.
吴芮封; 徐小曼; 周琦*, 性别决定机制和性染色体的演化, 中国科学:生命科学 , 2019, (04): 403-420.
2018
Lin Jian Qing#; Zhou Qi#; Yang Hai Qiong; Fang Li Ming; Tang Ke Yi; Sun Li; Wan Qiu Hong; Fang Sheng Guo*, Molecular mechanism of temperature-dependent sex determination and differentiation in Chinese alligator revealed by developmental transcriptome profiling, Science Bulletin, 2018, 63(4): 209-212.
Lyu Jialan#; Wang Zehua#; Wang Fang; Miao Chen; Nan Zi; Zhang Jiayu; Xi Yongmei; Zhou Qi; Yang Xiaohang; Ge Wanzhong*, The histone deacetylase HDAC1 positively regulates Notch signaling during Drosophila wing development, Biology Open, 2018, 7(2): UNSP bio029637.
2017
Seki, Ryohei#; Li, Cai#; Fang, Qi; Hayashi, Shinichi; Egawa, Shiro; Hu, Jiang; Xu, Luohao; Pan, Hailin; Kondo, Mao; Sato, Tomohiko; Matsubara, Haruka; Kamiyama, Namiko; Kitajima, Keiichi; Saito, Daisuke; Liu, Yang; Gilbert, M Thomas P; Zhou Qi; Xu, Xing; Shiroishi, Toshihiko; Irie, Naoki*; Tamura, Koji*; Zhang, Guojie*, Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features., Nature Communications, 2017, 8: 14229-14229.
Zhang Jilin; Li Jing; Zhou Qi*, Genomic and Transcriptomic Analyses of Avian Sex Chromosomes and Sex-Linked Genes, Avian and Reptilian Developmental Biology, Springer New York, 69-85, 2017.
2016
Gibilisco, Lauren; Zhou, Qi; Mahajan, Shivani; Bachtrog, Doris*, Alternative Splicing within and between Drosophila Species, Sexes, Tissues, and Developmental Stages., PLoS Genetics, 2016, 12(12).
Yin, Wei#; Wang, Zong-Ji#; Li, Qi-Ye; Lian, Jin-Ming; Zhou, Yang; Lu, Bing-Zheng; Jin, Li-Jun; Qiu, Peng-Xin; Zhang, Pei; Zhu, Wen-Bo; Wen, Bo; Huang, Yi-Jun; Lin, Zhi-Long; Qiu, Bi-Tao; Su, Xing-Wen; Yang, Huan-Ming; Zhang, Guo-Jie; Yan, Guang-Mei*; Zhou Qi*, Evolutionary trajectories of snake genes and genomes revealed by comparative analyses of five-pacer viper., Nature Communications, 2016, 7: 13107-13107.
2015
Zhou, Qi; Bachtrog, Doris*, Ancestral Chromatin Configuration Constrains Chromatin Evolution on Differentiating Sex Chromosomes in Drosophila, PLoS Genetics, 2015, 11(6): e1005331.
Zhang, Jilin; Li, Cai; Zhou, Qi; Zhang, Guojie*, Improving the ostrich genome assembly using optical mapping data, GigaScience, 2015, 4: 24.
2014
Wang, Zongji; Zhang, Jilin; Yang, Wei; An, Na; Zhang, Pei; Zhang, Guojie*; Zhou, Qi*, Temporal genomic evolution of bird sex chromosomes, Bmc Evolutionary Biology, 2014, 14: 250.
Zhou, Qi#*; Zhang, Jilin#; Bachtrog, Doris#; An, Na; Huang, Quanfei; Jarvis, Erich D.; Gilbert, M. Thomas P.; Zhang, Guojie*, Complex evolutionary trajectories of sex chromosomes across bird taxa, Science, 2014, 346(6215): 1332.
Jarvis, E.D.#*, Mirarab, S.#, Aberer, A.J., Li, B., Houde, P., Li, C., Ho, S.Y., Faircloth, B.C., Nabholz, B., Howard, J.T., Suh, A., Weber, C.C., Da, F.R., Li, J., Zhang, F., Li, H., Zhou, L., Narula, N., Liu, L., Ganapathy, G., Boussau, B., Bayzid, M.S., Zavidovych, V., Subramanian, S., Gabaldon, T., Capella-Gutierrez, S., Huerta-Cepas, J., Rekepalli, B., Munch, K., Schierup, M., Lindow, B., Warren, W.C., Ray, D., Green, R.E., Bruford, M.W., Zhan, X., Dixon, A., Li, S., Li, N., Huang, Y., Derryberry, E.P., Bertelsen, M.F., Sheldon, F.H., Brumfield, R.T., Mello, C.V., Lovell, P.V., Wirthlin, M., Schneider, M.P., Prosdocimi, F., Samaniego, J.A., Vargas, V.A., Alfaro-Nunez, A., Campos, P.F., Petersen, B., Sicheritz-Ponten, T., Pas, A., Bailey, T., Scofield, P., Bunce, M., Lambert, D.M., Zhou, Q., Perelman, P., Driskell, A.C., Shapiro, B., Xiong, Z., Zeng, Y., Liu, S., Li, Z., Liu, B., Wu, K., Xiao, J., Yinqi, X., Zheng, Q., Zhang, Y., Yang, H., Wang, J., Smeds, L., Rheindt, F.E., Braun, M., Fjeldsa, J., Orlando, L., Barker, F.K., Jonsson, K.A., Johnson, W., Koepfli, K.P., O'Brien, S., Haussler, D., Ryder, O.A., Rahbek, C., Willerslev, E., Graves, G.R., Glenn, T.C., McCormack, J., Burt, D., Ellegren, H., Alstrom, P., Edwards, S.V., Stamatakis, A., Mindell, D.P., Cracraft, J., Braun, E.L., Warnow, T., Jun, W., Gilbert, M.T., & Zhang, G. 2014. Whole-genome analyses resolve early branches in the tree of life of modern birds. SCIENCE, 346(6215)
Zhang, G.#*, Li, C.#, Li, Q., Li, B., Larkin, D. M., Lee, C., Storz, J. F., Antunes, A., Greenwold, M. J., Meredith, R. W., Odeen, A., Cui, J., Zhou, Q., Xu, L., Pan, H., Wang, Z., Jin, L., Zhang, P., Hu, H., Yang, W., Hu, J., Xiao, J., Yang, Z., Liu, Y., Xie, Q., Yu, H., Lian, J., Wen, P., Zhang, F., Li, H., Zeng, Y., Xiong, Z., Liu, S., Zhou, L., Huang, Z., An, N., Wang, J., Zheng, Q., Xiong, Y., Wang, G., Wang, B., Wang, J., Fan, Y., Da Fonseca, R. R., Alfaro-Nunez, A., Schubert, M., Orlando, L., Mourier, T., Howard, J. T., Ganapathy, G., Pfenning, A., Whitney, O., Rivas, M. V., Hara, E., Smith, J., Farre, M., Narayan, J., Slavov, G., Romanov, M. N., Borges, R., Machado, J. P., Khan, I., Springer, M. S., Gatesy, J., Hoffmann, F. G., Opazo, J. C., Hastad, O., Sawyer, R. H., Kim, H., Kim, K. W., Kim, H. J., Cho, S., Li, N., Huang, Y., Bruford, M. W., Zhan, X., Dixon, A., Bertelsen, M. F., Derryberry, E., Warren, W., Wilson, R. K., Li, S., Ray, D. A., Green, R. E., O'Brien, S. J., Griffin, D., Johnson, W. E., Haussler, D., Ryder, O. A., Willerslev, E., Graves, G. R., Alstrom, P., Fjeldsa, J., Mindell, D. P., Edwards, S. V., Braun, E. L., Rahbek, C., Burt, D. W., Houde, P., and Zhang, Y., et al., 2014, Comparative genomics reveals insights into avian genome evolution and adaptation: Science, v. 346, p. 1311-1320.
Lott, Susan E*; Villalta, Jacqueline E; Zhou, Qi; Bachtrog, Doris; Eisen, Michael B, Sex-specific embryonic gene expression in species with newly evolved sex chromosomes., PLoS Genetics, 2014, 10(2).
2013
Zhou, Qi; Ellison, Christopher E; Kaiser, Vera B; Alekseyenko, Artyom A; Gorchakov, Andrey A; Bachtrog, Doris*, The epigenome of evolving Drosophila neo-sex chromosomes: dosage compensation and heterochromatin formation., PLoS Biol, 2013, 11(11).
Alekseyenko, Artyom A.#; Ellison, Christopher E.#; Gorchakov, Andrey A.#; Zhou, Qi; Kaiser, Vera B.; Toda, Nick; Walton, Zaak; Peng, Shouyong; Park, Peter J.; Bachtrog, Doris*; Kuroda, Mitzi I.*, Conservation and de novo acquisition of dosage compensation on newly evolved sex chromosomes in Drosophila, Genes & Development, 2013, 27(8): 853-858.
2012
Zhou, Qi; Bachtrog, Doris*, Sex-Specific Adaptation Drives Early Sex Chromosome Evolution in Drosophila, Science, 2012, 337(6092): 341-345.
Zhan, Zubing; Ding, Yun; Zhao, Ruopin; Zhang, Yue; Yu, Haijing; Zhou, Qi; Yang, Shuang; Xiang, Hui*; Wang, Wen*, Rapid Functional Divergence of a Newly Evolved Polyubiquitin Gene in Drosophila and Its Role in the Trade-off between Male Fecundity and Lifespan, Molecular Biology and Evolution, 2012, 29(5): 1407-1416.
Zhou, Qi#; Huang, Quan-fei#; Zhu, Hong-mei*; Zhao, Li; Zhang, Guo-jie; Roy, Scott W.; Vicoso, Beatriz; Xuan, Zhao-lin; Ruan, Jue; Zhang, Yue; Zhao, Ruo-ping; Ye, Chen; Zhang, Xiu-qing; Wang, Jun*; Wang, Wen*; Bachtrog, Doris*, Deciphering neo-sex and B chromosome evolution by the draft genome of Drosophila albomicans, BMC Genomics, 2012, 13: 109.
Zhou, Qi; Bachtrog, Doris*, Chromosome-Wide Gene Silencing Initiates Y Degeneration in Drosophila, Current Biology, 2012, 22(6): 522-525.
Assis, Raquel*; Zhou, Qi; Bachtrog, Doris, Sex-Biased Transcriptome Evolution in Drosophila, Genome Biology and Evolution, 2012, 4(11): 1189-1200.
Ding, Yun#; Zhou, Qi#; Wang, Wen*, Origins of New Genes and Evolution of Their Novel Functions, Annual Review of Ecology Evolution and Systematics, 2012, 43: 345-363.
2011
Kaiser, Vera B.*; Zhou, Qi; Bachtrog, Doris, Nonrandom Gene Loss from the Drosophila miranda Neo-Y Chromosome, Genome Biology and Evolution, 2011, 3: 1329-1337.
2010
Ding, Yun#; Zhao, Li#; Yang, Shuang; Jiang, Yu; Chen, Yuan; Zhao, Ruoping; Zhang, Yue; Zhang, Guojie; Dong, Yang; Yu, Haijing; Zhou, Qi; Wang, Wen*, A Young Drosophila Duplicate Gene Plays Essential Roles in Spermatogenesis by Regulating Several Y- Linked Male Fertility Genes, PLoS Genetics, 2010, 6(12): e1001255.
2008
Zhou, Qi; Wang, Wen*, On the origin and evolution of new genes-a genomic and experimental perspective, Journal of Genetics and Genomics, 2008, 35(11): 639-648.
Yang, Shuang#; Arguello, J. Roman#; Li, Xin; Ding, Yun; Zhou, Qi; Chen, Ying; Zhang, Yue; Zhao, Ruoping; Brunet, Frederic; Peng, Lixin; Long, Manyuan*; Wang, Wen*, Repetitive element-mediated recombination as a mechanism for new gene origination in Drosophila, PLoS Genetics, 2008, 4(1): e3.
Zhou, Qi#; Wang, Jun#; Huang, Ling#; Nie, Wenhui; Wang, Jinhuan; Liu, Yan; Zhao, Xiangyi; Yang, Fengtang*; Wang, Wen*, Neo-Sex chromosomes in the black muntjac recapitulate incipient evolution of mammalian sex chromosomes, Genome Biology, 2008, 9(6): R98.
2006
Zhou, Qi#; Huang, Ling#; Zhang, Jianguo#; Zhao, Xiangyi; Zhang, Qingpeng; Song, Fei; Chi, Jianxiang; Yang, Fengtang*; Wang, Wen*, Comparative genomic analysis links karyotypic evolution with genomic evolution in the Indian Muntjac (Muntiacus muntjak vaginalis), Chromosoma, 2006, 115(6): 427-436.
Yu, Haijing*; Jiang, Huifeng; Zhou, Qi; Yang, Jufen; Cun, Yina; Su, Bing; Xiao, Chunjie; Wang, Wen, Origination and evolution of a human-specific transmembrane protein gene, c1orf37-dup., Human Molecular Genetics, 2006, 15(11): 1870-1875.
2004
周琦; 王文*, DNA水平自然选择作用的检测, 动物学研究, 2004, (01): 73-80.
