个人简历

2006-2011年获得东北师范大学植物学博士学位，主要研究方向为植物表观遗传学和基因组学。2010-2011年公派至Iowa State University学习分子进化与生物信息学。2011年加入东北师范大学分子表观遗传学教育部重点实验室。2015-2018年至美国University of Georgia进行博士后研究，主要研究内容包括机器学习在复杂性状和基因组研究中的应用，杂交与多倍化对基因组范围表观遗传与基因表达的影响等。在国际主流学术杂志上发表和参与发表多篇研究论文，包括MBE，Nature，PNAS，Plant Cell，Plant Journal，Plant Physiology等。 2006/9-2011/7，东北师范大学，植物学，博士 2002/9-2006/7，黑龙江大学，生物工程，本科 2010/3-2011/3，Iowa State University，Department of Ecology, Evolution, and Organismal Biology，联合培养博士 2011/7-2014/6，东北师范大学，生命科学学院，讲师 2015/5-2018/12，University of Georgia, 博士后 2014/7-至今，东北师范大学，生命科学学院，副教授 ORCID: https://orcid.org/0000-0002-0986-0993 发表论文： 2021 Emiliano Trucchi#*; Andrea Benazzo#; Martina Lari#; Alice Iob; Stefania Vai; Laura Nanni; Elisa Bellucci; Elena Bitocchi; Francesca Raffini; Chunming Xu; Scott A Jackson; Verónica Lema; Pilar Babot; Nurit Oliszewski; Adolfo Gil; Gustavo Neme; Catalina Teresa Michieli; Monica De Lorenzi; Lucio Calcagnile; David Caramelli;  Bastiaan Star; Hugo de Boer; Sanne Boessenkool#; Roberto Papa#;   Giorgio Bertorelle#* (2021) Ancient genomes reveal early Andean farmers selected common beans while preserving diversity. Nature Plants 7:123–128 Tian‐Jing Wang, Shuangzhan Huang, Ai Zhang, Peng Guo, Yutong Liu, Chunming Xu, Weixuan Cong, Bao Liu, Zheng‐Yi Xu* (2021) JMJ17–WRKY40 and HY5–ABI5 modules regulate the expression of ABA‐responsive genes in Arabidopsis. New Phytologist 230: 567–584 2020 Na Zhao, Qianli Dong, Brian D. Nadon, Xiaoyang Ding, Xutong Wang, Yuzhu Dong, Bao Liu, Scott A. Jackson*, Chunming Xu* (2020) Evolution of homeologous gene expression in polyploid wheat. Genes 11(12), 1401 Na Zhao, Xiaoyang Ding, Taotao Lian, Meng Wang, Yan Tong, Di Liang, Qi An, Siwen Sun, Scott A. Jackson*, Bao Liu and Chunming Xu* (2020) The Effects of Gene Duplication Modes on the Evolution of Regulatory Divergence in Wild and Cultivated Soybean. Frontiers in Genetics 11:601003. doi:10.3389/fgene.2020.601003 Lanjuan Hu, Ning Li*, Zhibin Zhang, Xinchao Meng, Qianli Dong, Chunming Xu, Lei Gong, Bao Liu* (2020) CG hypomethylation leads to complex changes in DNA methylation and transpositional burst of diverse transposable elements in callus cultures of rice. The Plant Journal 101, 188–203 2019 Chunming Xu* and Scott A. Jackson* (2019) Machine learning and complex biological data. Genome Biology 20:76 DOI: 10.1186/s13059-019-1689-0 Zhenling Lv, Wenjie Zhang, Ying Wu, Shuangzhan Huang, Yunxiao Zhou, Ai Zhang, Xin Deng, Chunming Xu, Zhengyi Xu, Lei Gong, Bao Liu* (2019) Extensive allele-level remodeling of histone methylation modification in reciprocal F1 hybrids of rice subspecies. Plant Journal 97, 571–586 Ning Li, Chunming Xu, Ai Zhang, Ruili Lv, Xinchao Meng, Xiuyun Lin, Lei Gong, Jonathan F. Wendel, Bao Liu* (2019) DNA methylation repatterning accompanying hybridization, whole genome doubling and homoeolog exchange in nascent segmental rice allotetraploids. New Phytologist 223: 979–992 2018 Xu C*, Nadon BD, Kim KD, Jackson SA*. (2018) Genetic and epigenetic divergence of duplicate genes in two legume species. Plant Cell Environ. 41:2033-2044 (* Corresponding author) Gao D, Chu Y, Xia H, Xu C, Heyduk K, Abernathy B, Ozias-Akins P, Leebens-Mack JH, Jackson SA. (2018) Horizontal Transfer of Non-LTR Retrotransposons from Arthropods to Flowering Plants. Mol Biol Evol 35:354-364. 2017 Sun Y, Wu Y, Yang CW, Sun S, Lin XY, Liu LX, Xu CM, Wendel JF, Gong L, Liu B. (2017) Segmental allotetraploidy generates extensive homoeologous expression rewiring and phenotypic diversity at the population level in rice. Molecular Ecology 26:5451-5466. 2016 Wu Y, Sun Y, Wang X, Lin X, Sun S, Shen K, Wang J, Jiang T, Zhong S, Xu C*, Liu B* (2016) Transcriptome shock in an interspecific F1 triploid hybrid of Oryza revealed by RNA sequencing. J Integr Plant Biol 58:150-164. (* Corresponding author) Wang XT, Hu LJ, Wang XF, Li N, Xu CM, Gong L, Liu B. (2016) DNA Methylation Affects Gene Alternative Splicing in Plants: An Example from Rice. Molecular Plant 9:305-307. 2015 Ou XF, Zhuang TT, Yin WC, Miao YL, Wang B, Zhang YH, Lin XY, Xu CM, von Wettstein D, Rustgi S, Liu B. (2015) DNA Methylation Changes Induced in Rice by Exposure to High Concentrations of the Nitric Oxide Modulator, Sodium Nitroprusside. Plant Molecular Biology Reporter 33:1428-1440. Li N, Chen YR, Ding Z, Li P, Wu Y, Zhang A, Yu S, Giovannoni JJ, Fei Z, Zhang W, Xiang, J. Z. Xu, C.* Liu, B. Zhong, S.* (2015) Nonuniform gene expression pattern detected along the longitudinal axis in the matured rice leaf. Sci Rep 5:8015. (* Corresponding author) 2014 Hu, L.J.†, Li, N†, Xu C.†, Zhong, S.L.†, Lin, X.Y., Yang, J.J., Zhou, T.Q., Yuliang, A.Z., Wu,Y., Chen, Y.R., Cao, X.F., Zemach, A., Rustgi, S., von Wettstein, D., and Liu, B. (2014). Mutation of a major CG methylase in rice causes genome-wide hypomethylation, dysregulated genome expression, and seedling lethality. Proc Natl Acad Sci U S A 111(29): p. 10642-10647. († Equal contributors) Xu, C†, Bai, Y.†, Lin, X., Zhao, N., Hu, L.J., Gong, Z, Wendel, J.F., and Liu, B. (2014). Genome-wide disruption of gene expression in allopolyploids but not hybrids of rice subspecies. Mol. Biol. Evol. 31(5):1066–1076. († Equal contributors) Zhang, H., Zhu, B., Qi, B., Gou, X., Dong, Y., Xu, C., Zhang, B., Huang, W., Liu, C., Wang, X., Yang, C., Zhou, H., Kashkush, K., Feldman, M., Wendel, F.J. and Liu, B. (2014). Evolution of the BBAA Component of Bread Wheat during Its History at the Allohexaploid Level. The Plant Cell 26(7): p. 2761-2776. Zhang, D., Wang, Z., Wang, N., Gao, Y., Liu, Y., Wu, Y., Bai, Y., Zhang, Z., Lin, X., Dong, Y., Ou, X., Xu, C.*, Liu, B.* (2014). Tissue Culture-Induced Heritable Genomic Variation in Rice, and Their Phenotypic Implications. PLoS One 7;9(5):e96879 (* Corresponding author) 2013 Zhang, H., Bian, Y., Gou, X., Dong, Y., Rustgi, S., Zhang, B., Xu, C., Li, N., Qi, B., Han, F., von Wettstein, D., and Liu, B. (2013). Intrinsic karyotype stability and gene copy number variations may have laid the foundation for tetraploid wheat formation. Proc Natl Acad Sci U S A 110, 19466-19471. Zhang, H., Bian, Y., Gou, X., Zhu, B., Xu, C., Qi, B., Li, N., Rustgi, S., Zhou, H., Han, F., Jiang, J., von Wettstein, D., and Liu, B. (2013). Persistent whole-chromosome aneuploidy is generally associated with nascent allohexaploid wheat. Proc Natl Acad Sci U S A 110, 3447-3452. Wang, Z., Zhang, D., Bai, Y., Zhang, Y., Liu, Y., Wu, Y., Lin, X., Wen, J., Xu, C., Li, L., and Liu, B. (2013). Genomewide variation in an introgression line of rice-Zizania revealed by whole-genome re-sequencing. Plos One 8, e74479. Wang, X., Wu, R., Lin, X., Bai, Y., Song, C., Yu, X., Xu, C., Zhao, N., Dong, Y., and Liu, B. (2013). Tissue culture-induced genetic and epigenetic alterations in rice pure-lines, F1 hybrids and polyploids. BMC Plant Biology 13. 2012 Paterson, A.H., Wendel, J.F., Gundlach, H., Guo, H., Jenkins, J., Jin, D.C., Llewellyn, D., Showmaker, K.C., Shu, S.Q., Udall, J., Yoo, M.J., Byers, R., Chen, W., Doron-Faigenboim, A., Duke, M.V., Gong, L., Grimwood, J., Grover, C., Grupp, K., Hu, G.J., Lee, T.H., Li, J.P., Lin, L.F., Liu, T., Marler, B.S., Page, J.T., Roberts, A.W., Romanel, E., Sanders, W.S., Szadkowski, E., Tan, X., Tang, H.B., Xu, C., Wang, J.P., Wang, Z.N., Zhang, D., Zhang, L., Ashrafi, H., Bedon, F., Bowers, J.E., Brubaker, C.L., Chee, P.W., Das, S., Gingle, A.R., Haigler, C.H., Harker, D., Hoffmann, L.V., Hovav, R., Jones, D.C., Lemke, C., Mansoor, S., Rahman, M.U., Rainville, L.N., Rambani, A., Reddy, U.K., Rong, J.K., Saranga, Y., Scheffler, B.E., Scheffler, J.A., Stelly, D.M., Triplett, B.A., Van Deynze, A., Vaslin, M.F.S., Waghmare, V.N., Walford, S.A., Wright, R.J., Zaki, E.A., Zhang, T.Z., Dennis, E.S., Mayer, K.F.X., Peterson, D.G., Rokhsar, D.S., Wang, X.Y., and Schmutz, J. (2012). Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres. Nature 492, 423-+. Ou, X., Zhang, Y., Xu, C., Lin, X., Zang, Q., Zhuang, T., Jiang, L., von Wettstein, D., and Liu, B. (2012). Transgenerational Inheritance of Modified DNA Methylation Patterns and Enhanced Tolerance Induced by Heavy Metal Stress in Rice (Oryza sativa L.). PloS One 7. Qi, B., Huang, W., Zhu, B., Zhong, X., Guo, J., Zhao, N., Xu, C., Zhang, H., Pang, J., Han, F., and Liu, B. (2012). Global transgenerational gene expression dynamics in two newly synthesized allohexaploid wheat (Triticum aestivum) lines. BMC Biology 10. Lin, C., Lin, X., Hu, L., Yang, J., Zhou, T., Long, L., Xu, C., Xing, S., Qi, B., Dong, Y., and Liu, B. (2012). Dramatic genotypic difference in, and effect of genetic crossing on, tissue culture-induced mobility of retrotransposon Tos17 in rice. Plant Cell Report 31, 2057-2063. 2011 Li, Y., Xia, Q., Kou, H., Wang, D., Lin, X., Wu, Y., Xu, C., Xing, S., and Liu, B. (2011). Induced Pib Expression and Resistance to Magnaporthe grisea are Compromised by Cytosine Demethylation at Critical Promoter Regions in Rice. Journal of Integrative Plant Biology 53, 814-823. Zhang, M., Xu, C., von Wettstein, D., and Liu, B. (2011). Tissue-Specific Differences in Cytosine Methylation and Their Association with Differential Gene Expression in Sorghum. Plant Physiology 156, 1955-1966. Zhao, N., Xu, L., Zhu, B., Li, M., Zhang, H., Qi, B., Xu, C., Han, F., and Liu, B. (2011). Chromosomal and genome-wide molecular changes associated with initial stages of allohexaploidization in wheat can be transit and incidental. Genome 54, 692-699. 2009 Zhang, M.†, Xu, C.†, Yan, H., Zhao, N., von Wettstein, D., and Liu, B. (2009). Limited tissue culture-induced mutations and linked epigenetic modifications in F-1 hybrids of sorghum pure lines are accompanied by increased transcription of DNA methyltransferases and 5-methylcytosine glycosylases. The Plant Jornal 57, 666-679. († Equal contributors) Ngezahayo, F.†, Xu, C.†, Wang, H., Jiang, L., Pang, J., and Liu, B. (2009). Tissue culture-induced transpositional activity of mPing is correlated with cytosine methylation in rice. BMC Plant Biology 9. († Equal contributors) Wang, H., Chai, Y., Chu, X., Zhao, Y., Wu, Y., Zhao, J., Ngezahayo, F., Xu, C.*, and Liu, B.* (2009). Molecular characterization of a rice mutator-phenotype derived from an incompatible cross-pollination reveals transgenerational mobilization of multiple transposable elements and extensive epigenetic instability. BMC Plant Biology 9. (* Corresponding author) Liu, B., Xu, C., Zhao, N., Qi, B., Kimatu, J.N., Pang, J., and Han, F. (2009). Rapid genomic changes in polyploid wheat and related species: implications for genome evolution and genetic improvement. Journal of Genetics and Genomics 36, 519-528.