生物信息学、植物基因组学

   

071001-植物学
086000-生物与医药
0812J3-生物信息学

生物信息学
植物基因组学
计算生物学

2011-04--2013-04   [法国] 昂热大学   （联合培养）博士
2009-09--2013-06   上海大学   博士

   

2016-08~现在, 中国科学院武汉植物园, 研究员，博士生导师
2014-05~2016-08,[新加坡]南洋理工大学、新加坡基因组研究所, 博士后
2013-08~2014-04,[美国]加州大学洛杉矶分校, 博士后

2022-12-31-今,BMC Plant Biology, 编委
2022-05-31-今,Frontiers in Genetics, 编委
2021-12-31-今,Agronomy, 客座编辑

植物基因组学与系统进化

   

论文发表

1.        Jing Xu, De-Shuang Huang, Xiujun Zhang*, scmFormer Integrates Large-Scale Single-Cell Proteomics and Transcriptomics Data by Multi-Task Transformer, Advanced Science, March 14, 2024.  https://doi.org/10.1002/advs.202307835

2.        Xuemei Lu, Xiaofen Yu, ... , Xiujun Zhang (As a Co-author),...,et al. Genome assembly of autotetraploid Actinidia arguta highlights adaptive evolution and dissects important economic traits. Plant Communications, 100856, March 1, 2024. https://pubmed.ncbi.nlm.nih.gov/38431772/

3.        Zhang, Aidi, Yuhong Xiong, Fang Liu, and Xiujun Zhang*. 2023.  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, no. 18: 13700. https://doi.org/10.3390/ijms241813700

4.        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, Volume 24, Issue 4, July 2023, bbad195, https://doi.org/10.1093/bib/bbad195

5.        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, 2023;, elad040, https://doi.org/10.1093/bfgp/elad040

6.        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, Volume 39, Issue 4, April 2023, btad165, https://doi.org/10.1093/bioinformatics/btad165

7.        Yanxia Sun, Aidi Zhang, Jacob B Landis, 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, 2023; uhad180, https://doi.org/10.1093/hr/uhad180

8.        Xu J, Zhang A, Liu F, Chen L, Zhang X*. CIForm as a Transformer-based model for cell type annotation of large-scale single-cell RNA-seq data. Briefings in Bioinformatics 2023, 24(4): bbad195.

9.        Xu J, Zhang A, Liu F, Zhang X*. STGRNS: an interpretable transformer-based method for inferring gene regulatory networks from single-cell transcriptomic data. Bioinformatics 2023, 39(4):btad165.

10.    Jiang X, Liu K, Peng H, Fang J, Zhang A, Han Y*, Zhang X*. Comparative network analysis reveals the dynamics of organic acid diversity during fruit ripening in peach (Prunus persica L. Batsch). BMC Plant Biology 2023, 23(1):1-14.

11.    Peng H#, Xu J#, Liu K, Liu F, Zhang A, Zhang X*. EIEPCF: accurate inference of functional gene regulatory networks by eliminating indirect effects from confounding factors, Briefings in Functional Genomics 2023.   

12.    Zhang A, Fang J, Zhang X*. Diversity of RNA editing in chloroplast transcripts across three main plant clades. Plant Systematics and Evolution 2023, 309(2):12.

13.    Sun Y, Zhang A, Zhang X, Landis JB, Zhang H, Zhang X, Sun H*, Wang H*. Insights into the differentiation and adaptation within Circaeasteraceae from Circaeaster agrestis genome sequencing and resequencing. iScience 2023, 26(3):106159.

14.    Zhang A, Xiong Y, Fang J, Liu K, Peng H, Zhang X*. 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 2022, 22(1):1-15.

15.    Jiang X, Zhang X*. RSNET: inferring gene regulatory networks by a redundancy silencing and network enhancement technique. BMC Bioinformatics 2022, 23(1):1-18.

16.    Wang T, Peng H, Cao Y, Xu J, Xiong Y, Liu K, Fang J, Liu F, Zhang A, Zhang X*. Dynamic network biomarker analysis reveals the critical phase transition of fruit ripening in grapevine. Genes 2022, 13(10):1851.

17.    Liu K, Zhang X*. PiTLiD: Identification of plant disease from leaf images based on convolutional neural network. IEEE/ACM Transactions on Computational Biology and Bioinformatics 2022, 20(2):1278-1288.

18.    Zhang A, Xiong Y, Fang J, Jiang X, Wang T, Liu K, Peng H, Zhang X*. Diversity and functional evolution of terpene synthases in rosaceae. Plants 2022, 11(6):736.

19.    Fang J, Jiang X, Wang T, Deng Z, Zhang A*, Zhang X*. Dynamic landscape of mitochondrial Cytidine-to-Uridine RNA editing in tobacco (Nicotiana tabacum) shows its tissue specificity. Plant Cell, Tissue and Organ Culture (PCTOC) 2022, 148(2):363-376.

20.    Xiong Y, Fang J, Jiang X, Wang T, Liu K, Peng H, Zhang X*, Zhang A*. 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 2022, 11(2):146.

21.    Jia Z, Zhang X*. Accurate determination of causalities in gene regulatory networks by dissecting downstream target genes. Frontiers in Genetics 2022, 13.

22.    Zhu Y, Zhang X, Zhang Y, Lü S, Li C. Identification of genes involved in celastrol biosynthesis by comparative transcriptome analysis in tripterygium wilfordii. Phyton 2022, 91(2):279.

23.    Wang T, Zhang X*. Genome-wide dynamic network analysis reveals the potential genes for MeJA-induced growth-to-defense transition. BMC Plant Biology 2021, 21:1-13.

24.    Deng Z, Zhang J, Li J, Zhang X*. Application of deep learning in plant–microbiota association analysis. Frontiers in Genetics 2021, 12:697090.

25.    Zhang A, Zhou H, Jiang X, Han Y*, Zhang X*. The draft genome of a flat peach (Prunus persica L. cv.‘124 Pan’) provides insights into its good fruit flavor traits. Plants 2021, 10(3):538.

26.    Fang J, Jiang X, Wang T, Zhang X*, Zhang A*. Tissue-specificity of RNA editing in plant: analysis of transcripts from three tobacco (Nicotiana tabacum) varieties. Plant Biotechnology Reports 2021, 15:471-482.

27.    Zhang F, Liu X, Zhang A, Jiang Z, Chen L*, Zhang X*. Genome-wide dynamic network analysis reveals a critical transition state of flower development in Arabidopsis. BMC Plant Biology 2019, 19(1):1-18.

28.    Zheng B, Zhao L, Jiang X, Cherono S, Liu J, Ogutu C, Ntini C, Zhang X, Han Y. Assessment of organic acid accumulation and its related genes in peach. Food Chemistry 2021, 334:127567.

29.    Zhou H, Ma R, Gao L, Zhang J, Zhang A, Zhang X, Ren F, Zhang W, Liao L, Yang Q. A 1.7‐Mb chromosomal inversion downstream of a PpOFP1 gene is responsible for flat fruit shape in peach. Plant Biotechnology Journal 2021, 19(1):192-205.

30.    Sun Y, Deng T, Zhang A, Moore MJ, Landis JB, Lin N, Zhang H, Zhang X*, Sun H*, Wang H*. Genome sequencing of the endangered Kingdonia uniflora (Circaeasteraceae, Ranunculales) reveals potential mechanisms of evolutionary specialization. iScience 2020, 23(5):101124.

31.    Zhang A, Jiang X, Zhang F, Wang T, Zhang X*. Dynamic response of RNA editing to temperature in grape by RNA deep sequencing. Functional & integrative genomics 2020, 20:421-432.

32.    Zhang F, Liu X, Zhang A, Jiang Z, Chen L*, Zhang X*. Genome-wide dynamic network analysis reveals a critical transition state of flower development in Arabidopsis. BMC Plant Biology 2019, 19(1):1-18.

33.    Shanmugam R, Zhang F, Srinivasan H, Charles Richard JL, Liu KI, Zhang X, Woo CWA, Chua ZHM, Buschdorf JP, Meaney MJ. SRSF9 selectively represses ADAR2-mediated editing of brain-specific sites in primates. Nucleic Acids Research 2018, 46(14):7379-7395.

34.    Zhao J, Zhou Y, Zhang X, Chen L. Part mutual information for quantifying direct associations in networks. Proceedings of the National Academy of Sciences 2016, 113(18):5130-5135.

35.    Liu KI, Ramli MNB, Woo CWA, Wang Y, Zhao T, Zhang X, Yim GRD, Chong BY, Gowher A, Chua MZH. A chemical-inducible CRISPR–Cas9 system for rapid control of genome editing. Nature Chemical Biology 2016, 12(11):980-987.

36.    Zheng G, Xu Y, Zhang X, Liu Z-P, Wang Z, Chen L, Zhu X-G. CMIP: a software package capable of reconstructing genome-wide regulatory networks using gene expression data. BMC Bioinformatics 2016, 17:137-144.

37.    Aghdam R, Ganjali M, Zhang X, Eslahchi C. CN: a consensus algorithm for inferring gene regulatory networks using the SORDER algorithm and conditional mutual information test. Molecular BioSystems 2015, 11(3):942-949.

38.    Zhang X, Zhao J, Hao J-K, Zhao X-M, Chen L. Conditional mutual inclusive information enables accurate quantification of associations in gene regulatory networks. Nucleic Acids Research 2015, 43(5):e31-e31.

39.    Zhang X, Liu K, Liu Z-P, Duval B, Richer J-M, Zhao X-M, Hao J-K, Chen L. NARROMI: a noise and redundancy reduction technique improves accuracy of gene regulatory network inference. Bioinformatics 2013, 29(1):106-113.

40.    Zhang X, Zhao X-M, He K, Lu L, Cao Y, Liu J, Hao J-K, Liu Z-P, Chen L. Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information. Bioinformatics 2012, 28(1):98-104.

   

已指导学生

张富萍  硕士研究生  071001-植物学  

赵苗苗  硕士研究生  085238-生物工程  

邓智予  硕士研究生  085238-生物工程  

蒋小涵  博士研究生  071001-植物学  

王腾飞  博士研究生  071001-植物学  

方静  博士研究生  071001-植物学  

彭慧香  硕士研究生  071001-植物学  

熊玉洪  硕士研究生  071001-植物学  

现指导学生

刘康晨  博士研究生  071001-植物学  

曹莹莹  硕士研究生  071001-植物学  

徐菁  硕士研究生  086000-生物与医药  

丁世龙  硕士研究生  086000-生物与医药  

李星诺  博士研究生  071001-植物学  

马浩然  硕士研究生  086000-生物与医药