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姓　　名： 张秀军
职　　称： 青年研究员
职 务： 博士生导师；PI
电 话/传 真： 027-87700844/027-87700877
电子邮件： zhangxj@wbgcas.cn
所属课题组： 植物生物信息学学科组

简要履历：

2019.1- 至今 中国科学院武汉植物园 研究员、博士研究生导师、课题组长
2016.9-2018.12 中国科学院武汉植物园 副研究员、课题组长
2014.4-2016.8 新加坡南洋理工大学/新加坡基因组研究所 博士后
2013.9-2014.3 美国加州大学洛杉矶分校 博士后
2013.6-2013.8 中国科学院上海生命科学研究院 博士后
2011.5-2013.5 法国昂热大学 （联合培养）博士
2009.9-2013.6 上海大学 生物信息学与系统生物学，博士
2006.8-2009.8 信阳师范学院 数学与统计学院，讲师
2003.9-2006.7 桂林电子科技大学 数学与计算科学学院，硕士
1999.9-2003.7 鲁东大学 数学与统计科学学院，学士

研究领域：

生物信息学、植物基因组学、计算生物学、系统生物学

社会任职：

International Society for Computational Biology，Member
International Conference on Computational Systems Biology，PC Member

获奖及荣誉：

中国科学院武汉分院优秀研究生指导教师
中法“蔡元培”交流合作奖学金
桂林电子科技大学优秀毕业生
鲁东大学优秀教学实习生

代表论著：

  1. Xu J, Zhang A, Liu F, Chen L, Zhang X*. 2023. CIForm as a Transformer-based model for cell type annotation of large-scale single-cell RNA-seq data. Briefings in Bioinformatics, Doi:10.1093/bib/bbad195.
  2. Xu J, Zhang A, Liu F, Zhang X*. 2023. STGRNS: an interpretable transformer-based method for inferring gene regulatory networks from single-cell transcriptomic data. Bioinformatics, 39(4):btad165.
  3. Jiang X, Liu K, Peng H, Fang J, Zhang A, Han Y*, Zhang X*. 2023. Comparative network analysis reveals the dynamics of organic acid diversity during fruit ripening in peach (Prunus persica L. Batsch). BMC Plant Biology, 23(1):1-14.
  4. Zhang A, Fang J, Zhang X*. 2023. Diversity of RNA editing in chloroplast transcripts across three main plant clades. Plant Systematics and Evolution, 309(2):12.
  5. Sun Y, Zhang A, Zhang X, Landis JB, Zhang H, Zhang X, Sun H*, Wang H*. 2023. Insights into the differentiation and adaptation within Circaeasteraceae from Circaeaster agrestis genome sequencing and resequencing. iScience, 26(3):106159.
  6. Zhang A, Xiong Y, Fang J, Liu K, Peng H, Zhang X*. 2022. Genome-wide identification and expression analysis of peach multiple organellar RNA editing factors reveals the roles of RNA editing in plant immunity. BMC Plant Biology, 22(1):1-15.
  7. Jiang X, Zhang X*. 2022. RSNET: inferring gene regulatory networks by a redundancy silencing and network enhancement technique. BMC Bioinformatics, 23(1):1-18.
  8. Wang T, Peng H, Cao Y, Xu J, Xiong Y, Liu K, Fang J, Liu F, Zhang A, Zhang X*. 2022. Dynamic network biomarker analysis reveals the critical phase transition of fruit ripening in grapevine. Genes, 13(10):1851.
  9. Liu K, Zhang X*. 2022. PiTLiD: Identification of plant disease from leaf images based on convolutional neural network. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 20(2):1278-1288.
  10. Zhang A, Xiong Y, Fang J, Jiang X, Wang T, Liu K, Peng H, Zhang X*. 2022. Diversity and functional evolution of terpene synthases in rosaceae. Plants, 11(6):736.
  11. Fang J, Jiang X, Wang T, Deng Z, Zhang A*, Zhang X*. 2022. Dynamic landscape of mitochondrial Cytidine-to-Uridine RNA editing in tobacco (Nicotiana tabacum) shows its tissue specificity. Plant Cell, Tissue and Organ Culture (PCTOC), 148(2):363-376.
  12. Xiong Y, Fang J, Jiang X, Wang T, Liu K, Peng H, Zhang X*, Zhang A*. 2022. Genome-wide analysis of multiple organellar RNA editing factor (MORF) family in kiwifruit (actinidia chinensis) reveals its roles in chloroplast RNA editing and pathogens stress. Plants, 11(2):146.
  13. Jia Z, Zhang X*. 2022. Accurate determination of causalities in gene regulatory networks by dissecting downstream target genes. Frontiers in Genetics, 13.
  14. Zhu Y, Zhang X, Zhang Y, Lü S, Li C. 2022. Identification of genes involved in celastrol biosynthesis by comparative transcriptome analysis in tripterygium wilfordii. Phyton, 91(2):279.
  15. Wang T, Zhang X*. 2021. Genome-wide dynamic network analysis reveals the potential genes for MeJA-induced growth-to-defense transition. BMC Plant Biology, 21:1-13.
  16. Deng Z, Zhang J, Li J, Zhang X*. 2021. Application of deep learning in plant–microbiota association analysis. Frontiers in Genetics, 12:697090.
  17. Zhang A, Zhou H, Jiang X, Han Y*, Zhang X*. 2021. The draft genome of a flat peach (Prunus persica L. cv.‘124 Pan’) provides insights into its good fruit flavor traits. Plants, 10(3):538.
  18. Fang J, Jiang X, Wang T, Zhang X*, Zhang A*. 2021. Tissue-specificity of RNA editing in plant: analysis of transcripts from three tobacco (Nicotiana tabacum) varieties. Plant Biotechnology Reports, 15:471-482.
  19. Zheng B, Zhao L, Jiang X, Cherono S, Liu J, Ogutu C, Ntini C, Zhang X, Han Y. 2021. Assessment of organic acid accumulation and its related genes in peach. Food Chemistry, 334:127567.
  20. Zhou H, Ma R, Gao L, Zhang J, Zhang A, Zhang X, Ren F, Zhang W, Liao L, Yang Q. 2021. A 1.7‐Mb chromosomal inversion downstream of a PpOFP1 gene is responsible for flat fruit shape in peach. Plant Biotechnology Journal, 19(1):192-205.
  21. Sun Y, Deng T, Zhang A, Moore MJ, Landis JB, Lin N, Zhang H, Zhang X*, Sun H, Wang H. 2020. Genome sequencing of the endangered Kingdonia uniflora (Circaeasteraceae, Ranunculales) reveals potential mechanisms of evolutionary specialization. iScience, 23(5):101124.
  22. Zhang A, Jiang X, Zhang F, Wang T, Zhang X*. 2020. Dynamic response of RNA editing to temperature in grape by RNA deep sequencing. Functional & integrative genomics, 20:421-432.
  23. Zhang F, Liu X, Zhang A, Jiang Z, Chen L*, Zhang X*. 2019. Genome-wide dynamic network analysis reveals a critical transition state of flower development in Arabidopsis. BMC Plant Biology, 19(1):1-18.
  24. Shanmugam R, Zhang F, Srinivasan H, Charles Richard JL, Liu KI, Zhang X, Woo CWA, Chua ZHM, Buschdorf JP, Meaney MJ. 2018. SRSF9 selectively represses ADAR2-mediated editing of brain-specific sites in primates. Nucleic Acids Research, 46(14):7379-7395.
  25. Zhao J, Zhou Y, Zhang X, Chen L. 2016. Part mutual information for quantifying direct associations in networks. Proceedings of the National Academy of Sciences, 113(18):5130-5135.
  26. Liu KI, Ramli MNB, Woo CWA, Wang Y, Zhao T, Zhang X, Yim GRD, Chong BY, Gowher A, Chua MZH. 2016. A chemical-inducible CRISPR–Cas9 system for rapid control of genome editing. Nature Chemical Biology, 12(11):980-987.
  27. Zheng G, Xu Y, Zhang X, Liu Z-P, Wang Z, Chen L, Zhu X-G. 2016. CMIP: a software package capable of reconstructing genome-wide regulatory networks using gene expression data. BMC Bioinformatics, 17:137-144.
  28. Aghdam R, Ganjali M, Zhang X, Eslahchi C. 2015. CN: a consensus algorithm for inferring gene regulatory networks using the SORDER algorithm and conditional mutual information test. Molecular BioSystems, 11(3):942-949.
  29. Zhang X, Zhao J, Hao J-K, Zhao X-M, Chen L. 2015. Conditional mutual inclusive information enables accurate quantification of associations in gene regulatory networks. Nucleic Acids Research, 43(5):e31-e31.
  30. Zhang X, Liu K, Liu Z-P, Duval B, Richer J-M, Zhao X-M, Hao J-K, Chen L. 2013. NARROMI: a noise and redundancy reduction technique improves accuracy of gene regulatory network inference. Bioinformatics, 29(1):106-113.
  31. Zhang X, Zhao X-M, He K, Lu L, Cao Y, Liu J, Hao J-K, Liu Z-P, Chen L. 2012. Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information. Bioinformatics, 28(1):98-104.
  32. Zhang X. 2013. Evolution algorithm based transcription regulatory network construction. Encyclopedia of Systems Biology, 693-695.
  33. Li A, Xu A, Zhang X. 2006. Research overview of parallel algorithms for tridiagonal systems, Popular Science, 2(5).
  34. Tang J, Dong L, Zhang X. 2009. A new class of memory gradient methods with Wolfe line search. Journal of Shandong University, 44(7):34-37.
  35. Jiang L, Xu A, Zhang X, Li A. 2005. The research of the existence of double limit. Journal of Anhui University of Science and Technology, 25(4):3.
  36. Li A, Zhang X, Xu A. 2007. An AGE method for solving diffusion-convection equation. Guangxi Science, 14(2):124-127.
  37. Zhang X, Xu A. 2006. Global convergence properties of a new class of nonlinear conjugate gradient methods. Guangxi Science, 12(4): 282-287.
  38. Zhang X, Xu A, Li A, Jiang L. 2005. Modified conjugate gradient method with global convergence property. Journal of Guilin University of Electronic Technology, 25(6): 64-67.
  39. Zhang X, Jia Z. 2009. Global convergence of a class of conjugate gradient algorithms containing a parameter with weak Wolfe line search. Journal of Huaihua University, 28(5): 24-27.
  40. Zhang X, Xu X, Zheng L. 2009. A hybrid conjugate gradient method for unconstrained optimization. Journal of Xinyang Normal University, 22(2): 175 -178.

承担科研项目情况：

1. 国家自然科学基金面上项目：基于低温胁迫应答基因调控网络建模的植物抗寒基因挖掘方法研究（2021-2024，主持）
3. 中国科学院重点实验室重点方向培育项目：资源植物重要性状形成的机理解析（2019-2020，主持）
4. 中国科学院项目：核心植物园功能领域与特色学科 （2019-2021，子课题负责人）
5. 国家自然科学基金青年项目：基于高通量数据的基因调控网络构建模型和方法研究（2015-2017，主持）
6. 中国博士后科学基金特别资助项目：基因调控网络预测的降噪去冗余模型和方法研究（2015-2016，主持）
7. 中国博士后科学基金面上项目：基因基因表达数据的基因调控网络预测方法研究（2014-2015，主持）
8. 武汉市科学技术局项目：作物表型组学研究神农设施关键技术研发（2019-2021，参与）
9. 国家自然科学基金重大研究计划项目：心血管斑块易损性识别的光声成像及分子标志物筛选的新方法与新技术研究（2016-2020，参与）
10. 国家自然科学基金重大研究计划项目：肝脏炎癌恶性转化关键节点的动态网络标志物模型及临床应用研究（2016-2020，参与）
11. 国家自然科学基金重大研究计划项目：基于多层次分子网络的药物重新定位预测方法研究（2012-2014，参与）