Selected Publications:

Zhou, Y., Shearwin-Whyatt, L., Li, J., Song, Z., Hayakawa, T., Stevens, D., Fenelon, J. C., 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, S. D., Phillippy, A. M., Howe, K., Jarvis, E. D., Ryder, O. A., Kaessmann, H., Donnelly, P., Korlach, J., Lewin, H. A., Graves, J., Belov, K., Renfree, M. B., Grutzner, F., Zhou, Q., & Zhang, G. (2021). Platypus and echidna genomes reveal mammalian biology and evolution. Nature. doi:10.1038/s41586-020-03039-0

Wang, Z.-J., Chen, G.-J., Zhang, G.-J., & Zhou, Q. (2021). Dynamic evolution of transposable elements, demographic history, and gene content of paleognathous birds. Zoological research, 42(1), 51.

Tao, W., Xu, L., Zhao, L., Zhu, Z., Wu, X., Min, Q., Wang, D., & Zhou, Q. (2021). High‐quality chromosome‐level genomes of two tilapia species reveal their evolution of repeat sequences and sex chromosomes. Molecular Ecology Resources, 21(2), 543-560.

Peona, V., Blom, M. P., Xu, L., Burri, R., Sullivan, S., Bunikis, I., Liachko, I., Haryoko, T., Jønsson, K. A., & Zhou, Q. (2021). Identifying the causes and consequences of assembly gaps using a multiplatform genome assembly of a bird‐of‐paradise. Molecular Ecology Resources, 21(1), 263-286.

Liu, J., Wang, Z., Li, J., Xu, L., Liu, J., Feng, S., Guo, C., Chen, S., Ren, Z., & Rao, J. (2021). A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes. Genome Research, gr. 271569.271120.

Li, J., Zhang, J., Liu, J., Zhou, Y., Cai, C., Xu, L., Dai, X., Feng, S., Guo, C., & Rao, J. (2021). A new duck genome reveals conserved and convergently evolved chromosome architectures of birds and mammals. GigaScience, 10(1), giaa142.

Xu, L., & Zhou, Q. (2020). The Female-Specific W Chromosomes of Birds Have Conserved Gene Contents but Are Not Feminized. Genes, 11(10), 1126.

Xu, L., Irestedt, M., & Zhou, Q. (2020). Sequence Transpositions Restore Genes on the Highly Degenerated W Chromosomes of Songbirds. Genes, 11(11), 1267.

Liu, J., Ali, M., & Zhou, Q. (2020). Establishment and evolution of heterochromatin. Annals of the New York Academy of Sciences, 1476(1), 59.

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, Q., 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 Fonseca, R. 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. E. R., 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., Krone, O., Fudickar, A. M., Mila, B., Ketterson, E. D., Fidler, A. E., Friis, G., Parody-Merino, A. M., Battley, P. F., Cox, M. P., Lima, N. C. B., Prosdocimi, F., Parchman, T. L., Schlinger, B. A., Loiselle, B. A., Blake, J. G., Lim, H. C., Day, L. B., Fuxjager, M. J., Baldwin, M. W., Braun, M. J., Wirthlin, M., Dikow, R. B., Ryder, T. B., Camenisch, G., Keller, L. F., DaCosta, J. M., Hauber, M. E., Louder, M. I. M., Witt, C. C., McGuire, J. A., Mudge, J., Megna, L. C., Carling, M. D., Wang, B., Taylor, S. A., Del-Rio, G., Aleixo, A., Vasconcelos, A. T. R., Mello, C. V., Weir, J. T., Haussler, D., Li, Q., Yang, H., Wang, J., Lei, F., Rahbek, C., Gilbert, M. T. P., Graves, G. R., Jarvis, E. D., Paten, B., & Zhang, G. (2020). Dense sampling of bird diversity increases power of comparative genomics. Nature, 587(7833), 252-257. doi:10.1038/s41586-020-2873-9

Conte, M. A., Clark, F. E., Roberts, R. B., Xu, L., Tao, W., Zhou, Q., Wang, D., & Kocher, T. D. (2020). Origin of a giant sex chromosome. Molecular Biology and Evolution.

Zhang, J.-Y., & Zhou, Q. (2019). On the regulatory evolution of new genes throughout their life history. Molecular Biology and Evolution, 36(1), 15-27.

Xu, L., Auer, G., Peona, V., Suh, A., Deng, Y., Feng, S., Zhang, G., Blom, M. P., Christidis, L., & Prost, S. (2019). Dynamic evolutionary history and gene content of sex chromosomes across diverse songbirds. Nature ecology & evolution, 3(5), 834-844.

WU, R., XU, X., & ZHOU, Q. (2019). Evolution of sex determination mechanisms and sex chromosomes. SCIENTIA SINICA Vitae, 49(4), 403-420.

Wang, Z., Lyu, J., Wang, F., Miao, C., Nan, Z., Zhang, J., Xi, Y., Zhou, Q., Yang, X., & Ge, W. (2018). The histone deacetylase HDAC1 positively regulates Notch signaling during Drosophila wing development. Biology open, 7(2).

Lin, J.-Q., Zhou, Q., Yang, H.-Q., Fang, L.-M., Tang, K.-Y., Sun, L., Wan, Q.-H., & Fang, S.-G. (2018). Molecular mechanism of temperature-dependent sex determination and differentiation in Chinese alligator revealed by developmental transcriptome profiling. Sci Bull, 63(4), 209-212.

Zhang, J., Li, J., & Zhou, Q. (2017). Genomic and Transcriptomic Analyses of Avian Sex Chromosomes and Sex-Linked Genes. In Avian and Reptilian Developmental Biology (pp. 69-85): Springer.

Seki, R., Li, C., Fang, Q., Hayashi, S., Egawa, S., Hu, J., Xu, L., Pan, H., Kondo, M., & Sato, T. (2017). Functional roles of Aves class-specific cis-regulatory elements on macroevolution of bird-specific features. Nature communications, 8(1), 1-14.

Yin, W., Wang, Z.-j., Li, Q.-y., Lian, J.-m., Zhou, Y., Lu, B.-z., Jin, L.-j., Qiu, P.-x., Zhang, P., & Zhu, W.-b. (2016). Evolutionary trajectories of snake genes and genomes revealed by comparative analyses of five-pacer viper. Nature communications, 7(1), 1-11.

Gibilisco, L., Zhou, Q., Mahajan, S., & Bachtrog, D. (2016). Alternative splicing within and between Drosophila species, sexes, tissues, and developmental stages. PLoS genetics, 12(12), e1006464.