张秀军
发布日期：2025-06-06一、个人基本情况
姓名：张秀军
性别：男
职称/职务：教授（科研型）
学位/学历：博士/研究生
硕/博生导师：硕导/博导
所在系： 统计学系
研究方向：生物统计学、计算系统生物学、人工智能与大数据分析等
电子邮箱：zhangxiujun＠whut.edu.cn
个人网页：https://orcid.org/0000-0001-8041-0592
二、教育背景与工作经历
（1）教育背景：
2009.09－2013.07 上海大学，信息学与系统生物学，博士
2011.05－2013.04 法国昂热大学，计算机科学学院，（联合培养）博士
（2）工作经历：
2025.05－至今， 必赢线路检测3003，必赢3003no1线路检测中心，教授，博士生导师
2016.08－2025.04，中国科学院武汉植物园，中科院百人计划研究员，课题组长，博士生导师
2014.05－2016.07，新加坡南洋理工大学/新加坡基因组研究所，博士后
2013.09－2014.05，美国加州大学洛杉矶分校，博士后
三、教学研究
承担《生物统计学》、《生物信息学实践》、《高等数学》等课程。曾获中国科学院优秀指导教师，指导研究生获“中国科学院武汉分院院长特别奖”、“中国科学院院长奖”等。
四、科学研究
（1）科研项目：
1. 湖北省重点研发计划项目：红花多组学数据分析与人工智能育种研究（2023-2025，负责人）
2. 国家自然科学基金面上项目：基于低温胁迫应答基因网络建模的基因挖掘方法研究（2022-2025，负责人）
3. 湖北省重点研发计划项目：基于物联网和作物模型的数字化育种系统研发（2021-2023，子课题负责人）
4. 国家科技创新特区项目：复杂系统状态转变的动态因果逻辑模型及生物系统应用（2020-2021，负责人）
5. 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，负责人）
6. 国家科技创新特区163计划项目：新型因果逻辑模型及基于因果关系的预测（2017-2019，负责人）
7. 中国科学院“百人计划”人才项目：基于大数据处理的生物信息学平台开发（2016-2021，负责人）
8. 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模型和方法研究（2015-2017，负责人）
9. 中国博士后基金特别资助项目：基因调控网络预测的降噪去冗余模型和方法研究（2015-2016，负责人）
10. 中国博士后基金面上项目：基因基因表达数据的基因调控网络预测方法研究（2014-2015，负责人）
（2）学术论文：
（代表性论文）
[1] Jing Xu, De-Shuang Huang, Xiujun Zhang*. scmFormer Integrates Large-Scale Single-Cell Proteomics and Transcriptomics Data by Multi-Task Transformer. Advanced Science,11(19):230783, 2024.
[2] Jing Xu, Aidi Zhang, Fang Liu, Liang Chen*, Xiujun Zhang*. 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, 2023.
[3] Jing Xu, Aidi Zhang, Fang Liu, Xiujun Zhang*. STGRNS: an interpretable transformer-based method for inferring gene regulatory networks from single-cell transcriptomic data. Bioinformatics, 39(4), btad165, 2023.
[4] Kangchen, Liu, Xiujun Zhang*. PiTLiD: Identification of plant disease from leaf images based on convolutional neural network. IEEE/ACM Transactions on Computational Biology and Bioinformatics, DOI:10.1109/TCBB.2022.3195291, 2023.
[5] Juan Zhao, Yiwei Zhou, Xiujun Zhang, Luonan Chen*. Part mutual information for quantifying direct associations in networks. Proc. Natl. Acad. Sci. USA, 113(18): 5130-5135, 2016.
[6] Xiujun Zhang Juan Zhao, Jin-Kao Hao, Xing-Ming Zhao*, and Luonan Chen*. Conditional mutual inclusive information enables accurate quantification of associations in gene regulatory networks. Nucleic Acids Research. 43 (5): e31, 2015.
[7] Xiujun Zhang, Keqin Liu, Zhi-Ping Liu, Béatrice Duval, Jean-Michel Richer, Xing-Ming Zhao*, Jin-Kao Hao* and Luonan Chen*. NARROMI: a noise and redundancy reduction technique improves accuracy of gene regulatory network inference. Bioinformatics, 29(1), 106-113, 2013.
[8] Xiujun Zhang, Xing-Ming Zhao, Kun He, Le Lu, Yongwei Cao, Jingdong Liu, Jin-Kao Hao, Zhi-Ping Liu*, Luonan Chen*. Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information. Bioinformatics, 28(1), 98- 104, 2012.
（其他论文）
[1] Kangchen Liu; Li Li*; Xiujun Zhang*. Fast and Accurate Identification of Kiwifruit Diseases Using a Lightweight Convolutional Neural Network Architecture, IEEE Access, vol. 13, pp. 84826-84843, 2025.
[2] Jing Xu, De-Shuang Huang, Xiujun Zhang*. scmFormer Integrates Large-Scale Single-Cell Proteomics and Transcriptomics Data by Multi-Task Transformer. Advanced Science,11(19):230783, 2024.
[3] Huixiang Peng, Jing Xu, Kangchen Liu, Fang Liu, Aidi Zhang, Xiujun Zhang*. EIEPCF: accurate inference of functional gene regulatory networks by eliminating indirect effects from confounding factors, Briefings in Functional Genomics, 23(4): 373–383, 2024.
[4] Yingying Cao, Congxiao Zhang, Fang Liu, Dawei Li, Aidi Zhang, Li Li*, Xiujun Zhang*. Genome-Wide Identification and Expression Analysis of Kiwifruit Leucine-Rich Repeat Receptor-like Proteins Reveal Their Roles in Biotic and Abiotic Stress Responses. International Journal of Molecular Sciences, 25(8): 4497, 2024.
[5] Xuemei Lu, Xiaofen Yu, ... , Xiujun Zhang,...,Yanchang Wang. Genome assembly of autotetraploid Actinidia arguta highlights adaptive evolution and dissects important economic traits. Plant Communications, 100856, March 1, 2024.
[6] Jing Xu, Aidi Zhang, Fang Liu, Liang Chen*, Xiujun Zhang*. 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, 2023.
[7] Jing Xu, Aidi Zhang, Fang Liu, Xiujun Zhang*. STGRNS: an interpretable transformer-based method for inferring gene regulatory networks from single-cell transcriptomic data. Bioinformatics, 39(4), btad165, 2023.
[8] Aidi Zhang, Yuhong Xiong, Fang Liu, Xiujun Zhang*. A Genome-Wide Analysis of the Pentatricopeptide Repeat Protein Gene Family in Two Kiwifruit Species with an Emphasis on the Role of RNA Editing in Pathogen Stress, International Journal of Molecular Sciences, 24:13700, 2023.
[9] Huixiang Peng, Jing Xu, Kangchen Liu, Aidi Zhang, Xiujun Zhang*. EIEPCF: accurate inference of functional gene regulatory networks by eliminating indirect effects from confounding factors, Briefings in Functional Genomics, elad040, 2023.
[10] Xiaohan Jiang, Kangchen Liu, Huixiang Peng, Jing Fang, Aidi Zhang, Yuepeng Han*, Xiujun Zhang*. 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, 2023.
[11] Aidi Zhang, Jing Fang, Xiujun Zhang*. Diversity of RNA editing in chloroplast transcripts across three main plant clades. Plant Systematics and Evolution, 309(2), 12, 2023.
[12] Kangchen, Liu, Xiujun Zhang*. PiTLiD: Identification of plant disease from leaf images based on convolutional neural network. IEEE/ACM Transactions on Computational Biology and Bioinformatics, DOI:10.1109/TCBB.2022.3195291, 2023.
[13] Yanxia Sun, Aidi Zhang, Xu Zhang, Jacob B Landi, Huajie Zhang, Xiujun Zhang, Hang Sun, Hengchang Wang. Insights into the differentiation and adaptation within Circaeasteraceae from Circaeaster agrestis genome sequencing and resequencing, iScience, 26:106159, 2023.
[14] Yanxia Sun, Aidi Zhang, Jacob B Landi, Wei Shi, Xiujun Zhang, Hang Sun, Hengchang Wang. Genome assembly of the snow lotus species Saussurea involucrata provides insights into acacetin and rutin biosynthesis and tolerance to an alpine environment, Horticulture Research, uhad180, 2023.
[15] Aidi Zhang, Yuhong Xiong, Jing Fang, Kangchen Liu, Huixiang Peng, Xiujun Zhang*. 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, 583, 2022.
[16] Yuhong Xiong, Jing Fang, Xiaohan Jiang, Tengfei Wang, Kangchen Liu, Huixiang Peng, Xiujun Zhang*, Aidi Zhang*. 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, 2022.
[17] Aidi Zhang, Yuhong Xiong, Jing Fang, Xiaohan Jiang, Tengfei Wang, Kangchen Liu, Huixiang Peng, Xiujun Zhang*. Diversity and functional evolution of terpene synthases in rosaceae. Plants, 11(6):736, 2022.
[18] Zhigang Jia, Xiujun Zhang*. Accurate determination of causalities in gene regulatory networks by dissecting downstream target genes. Frontiers in Genetics, 13, 3354, 2022.
[19] Wang, Tengfei, Huixiang Peng, Yingying Cao, Jing Xu, Yuhong Xiong, Kangchen Liu, Jing Fang, Fang Liu, Aidi Zhang, Xiujun Zhang*. Dynamic Network Biomarker Analysis Reveals the Critical Phase Transition of Fruit Ripening in Grapevine. Genes, 13,10: 1851, 2022.
[20] Xiaohan Jiang, Xiujun Zhang*. RSNET: inferring gene regulatory networks by a redundancy silencing and network enhancement technique. BMC Bioinformatics, 23(1): 1-18, 2022.
[21] Jing Fang, Xiaohan Jiang, Tengfei Wang, Zhiyu Deng, Aidi Zhang*, Xiujun Zhang*. 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, 2022.
[22] Yaru Zhu, Xiujun Zhang, Yansheng Zhang, Shiyou Lv*, Changfu Li*. Identification of Genes Involved in Celastrol Biosynthesis by Comparative Transcriptome Analysis in Tripterygium wilfordii. Phyton, 91(2): 279, 2022.
[23] Wang, Tengfei, Xiujun Zhang*. Genome-wide dynamic network analysis reveals the potential genes for MeJA-induced growth-to-defense transition. BMC Plant Biology, 21(1): 1-13, 2021.
[24] Zhiyu Deng, Jinming Zhang, Junya Li, Xiujun Zhang*. Application of deep learning in plant–microbiota association analysis. Frontiers in Genetics, 12, 2021.
[25] Jing Fang, Xiaohan Jiang,Tengfei Wang, Xiujun Zhang*, Aidi Zhang*. Tissue-specificity of RNA editing in plant: Analysis of transcripts from three tobacco (Nicotiana tabacum) varieties. Plant Biotechnology Reports, 15(4): 471-482, 2021.
[26] Aidi Zhang, Hui Zhou, Xiaohan Jiang, Yuepeng Han*, Xiujun Zhang*. 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, 2021.
[27] Hui Zhou, Ruijuan Ma, Lei Gao, Jinyun Zhang, Aidi Zhang, Xiujun Zhang, Fei Ren, Weihan Zhang, Liao Liao, Qiurui Yang, Shengli Xu, Ogutu Collins Otieno, Jianbo Zhao, Mingliang Yu, Quan Jiang, Schuyler S Korban, Yuepeng Han*. A 1.7-Mb chromosomal inversion downstream of a PpOFP1gene is responsible for flat fruit shape in peach. Plant Biotechnology Journal, 19(1): 192-205, 2021.
[28] Beibei Zheng, Li Zhao, Xiaohan Jiang, Sylvia Cherono, Jingjing Liu; Collins Ogutu, Charmaine Ntini, Xiujun Zhang, Yuepeng Han*. Assessment of organic acid accumulation and its related genes in peach. Food Chemistry, 334: 127567, 2021.
[29] Yanxia Sun, Tao Deng, Aidi Zhang, Michael J.Moore, Jacob B. Landis, Nan Lin, Huajie Zhang, Xu Zhang, Jinling Huang, Xiujun Zhang*, Hang Sun*, Hengchang Wang*. Genome sequencing of the endangered Kingdonia uniflora (Circaeasteraceae, Ranunculales) reveals potential mechanisms of evolutionary specialization. iScience, 23(5): 101124, 2020.
[30] Aidi Zhang, Xiaohan Jiang, Fuping Zhang, Tengfei Wang, Xiujun Zhang*. Dynamic response of RNA editing to temperature in grape by RNA deep sequencing. Functional & Integrative Genomics, 20(3): 421-432, 2020.
[31] Fuping Zhang, Xiaoping Liu, Aidi Zhang, Zhonglin Jiang, Luonan Chen*, Xiujun Zhang*. Genome-wide dynamic network analysis reveals a critical transition state of flower development in Arabidopsis. BMC Plant Biology, 19(1), 1-18, 2019.
[32] Xiujun Zhang Juan Zhao, Jin-Kao Hao, Xing-Ming Zhao*, and Luonan Chen*. Conditional mutual inclusive information enables accurate quantification of associations in gene regulatory networks. Nucleic Acids Research. 43 (5): e31, 2015.
[33] Xiujun Zhang, Keqin Liu, Zhi-Ping Liu, Béatrice Duval, Jean-Michel Richer, Xing-Ming Zhao*, Jin-Kao Hao* and Luonan Chen*. NARROMI: a noise and redundancy reduction technique improves accuracy of gene regulatory network inference. Bioinformatics, 29(1), 106-113, 2013.
[34] Xiujun Zhang, Xing-Ming Zhao, Kun He, Le Lu, Yongwei Cao, Jingdong Liu, Jin-Kao Hao, Zhi-Ping Liu*, Luonan Chen*. Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information. Bioinformatics, 28(1), 98- 104, 2012.
[35] Rosa Aghdama, Mojtaba Ganjalia, Xiujun Zhang* and Changiz Eslahchi*. CN: A Consensus Algorithm for Inferring Gene Regulatory Networks Using SORDER Algorithm and Conditional Mutual Information Test. Molecular Biosystems, 11(3):942-9, 2015.
[36] Yanxia Sun, Aidi Zhang, Xu Zhang, Jacob Landis, Huajie Zhang, Xiujun Zhang, Hengchang Wang. Insights into the differentiation and adaptation within Circaeasteraceae from Circaeaster agrestis genome sequencing and resequencing. iScience, 26(3), 106159, 2023.
[37] Raghuvaran Shanmugam, Fan Zhang, Harini Srinivasan, John Lalith Charles Richard, Kaiwen I Liu, Xiujun Zhang, Cheok Wei A Woo, Zi Hao M Chua, Jan Paul Buschdorf, Michael J Meaney, Meng How Tan*. SRSF9 selectively represses ADAR2-mediated editing of brain-specific sites in primates. Nucleic Acids Research, 46(14), 7379-7395, 2018.
[38] Juan Zhao, Yiwei Zhou, Xiujun Zhang, Luonan Chen*. Part mutual information for quantifying direct associations in networks. Proc. Natl. Acad. Sci. USA, 113(18): 5130-5135, 2016.
[39] Kaiwen Liu, Muhammad Ramli, Cheok Woo, Yuanming Wang, Tianyun Zhao, Xiujun Zhang, Guo Rong Daniel Yim, Bao Yi Chong, Ali Gowher, Mervyn Chua, Jonathan Jung, Jia Lee, Meng How Tan*. A chemical-inducible CRISPR-Cas9 system for rapid control of genome editing. Nature Chemical Biology, 12, 980–987, 2016.
[40] Guangyong Zheng, Yaochen Xu, Xiujun Zhang, Zhi-Ping Liu, Zhuo Wang, Luonan Chen*, Xin-Guang Zhu*. CMIP: a software package capable of reconstructing genome-wide regulatory networks using gene expression data. BMC Bioinformatics, 17(17): 137-144, 2016.
[41] Xiujun Zhang. Boolean Network,Position Weight Matrices. Encyclopedia of Systems Biology, Springer, 2013.
[42] Xiujun Zhang. Binding Affinity, Graphical Model. Encyclopedia of Systems Biology, Springer, 2013.
[43] Xiujun Zhang. Evolution algorithm based transcription regulatory network construction. Encyclopedia of Systems Biology, Springer, 2013.
[44] Jingyong Tang, Li Dong, Xiujun Zhang. A new class of memory gradient methods with Wolfe line search. Journal of Shandong University, 44(7):34-37, 2009.
[45] Xiujun Zhang, Xin Xu, Lili Zheng. A hybrid conjugate gradient method for unconstrained optimization. Journal of Xinyang Normal University,22(2): 175 -178, 2009.
[46] Xiujun Zhang, Zhigang Jia. 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, 2009.
[47] Li Ankun, Xu Annong, Zhang Xiujun. Research overview of parallel algorithms for tridiagonal systems, Popular Science, 2(5) , 2006.
[48] Tang Jingyong, Dong Li, Zhang Xiujun. A new class of memory gradient methods with Wolfe line search. Journal of Shandong University, 44(7):34-37, 2009.
[49] Jiang Lihua, Xu Annong, Zhang Xiujun, Li Annong. The research of the existence of double limit. Journal of Anhui University of Science and Technology, 25(4):3, 2005.
[50] Li Ankun, Zhang Xiujun, Xu Annong. An AGE method for solving diffusion-convection equation. Guangxi Science, 14(2):124-127, 2005.
[51] Xiujun Zhang, Annong Xu. Global convergence properties of a new class of nonlinear conjugate gradient methods. Guangxi Sciences, 12(4): 282-287, 2006.
[52] Xiujun Zhang, Annong Xu, Ankun Li, Lihua Jiang. Modified conjugate gradient method with global convergence property. Journal of Guilin University of Electronic Technology, 25(6): 64-67, 2005.
（3）学术兼职：
担任BMC Plant Biology, Frontiers in Genetics, Crop Breeding Genetics and Genomics, International Journal of Molecular Sciences等期刊编委或客座编辑。
（4）招生信息：
招收统招硕士生、博士生4-5人/年, 同时接收科研培训本科生2-3人/年。欢迎有志于开展生物统计学、人工智能、大数据分析等多学科交叉研究的同学加入研究组！同时接收博士后和研究助理，开展智能生物统计学团队的建设。有意者请邮件联系！zhangxiujun@whut.edu.cn