林学中心团队 (Research)
林木生物信息学(Plant Bioinformatics)

主任(PI): 顾连峰 (Lianfeng Gu, PhD)

 

团队成员(Members)张航晓(Hangxiao Zhang,PhD),王永生(Yongsheng Wang),高宇帮(Yubang Gao),吴伟煌(Weihuang Wu),王汇源(Huiyuan Wang),王慧慧(Huihui Wang),赵良真(Liangzhen Zhao)

PI简介(PI Introduction)

顾连峰,教授,博士生导师。2012年获得中国科学院生物信息学博士学位,2015年从美国加州大学河滨分校访学回国,受聘为福建农林大学林学中心全职教授。2016年入选福建省C类引进高层次人才,2017年获福建农林大学“金山学者”荣誉称号。以福建农林大学为依托单位主持2015年国家自然科学基金面上项目“自毒胁迫下杉木可变剪接与microRNA相互调控网络研究”,主持2016年国家重点专项“林木次生生长的分子调控和环境胁迫机制”子课题。在PNAS、Cell Research、Nature genetics等权威期刊上发表相关文章20篇。目前主要从事生物信息学和林木遗传改良相关研究。

实验室网址: www.bioinfor.org

电子邮箱:lfgu@fafu.edu.cn
       研究领域 (Research focus):
开发生物信息学分析方法解析来自高通量技术所产生的大批量数据,从基因组,转录组和蛋白质组这些组学数据中挖掘生物学规律。结合二代高通量测序与蛋白组学 数据利用生物信息学开展重要农林业物种(毛竹、杉树、水稻和玉米)的基因表达调控网络研究。深入开展模式植物转录后调控网络之间的相互调节研究,为提高农 林业物种的产量提供理论依据。

Developing bioinformatics methods and computational tools to analyze large-scale datasets from high throughput technologies to understand the massive amounts of information at system level including genome, transcriptome and proteome.  Application of next-generation sequencing technologies, proteomics, and bioinformatics on crop species, including bamboo, China fir, rice and maize, to infer gene regulatory networks by integrating omics data.  Investigation of the interplay between different post-transcriptional regulation mechanisms to provide theoretical basis for improving production of important crop species.

发表文章(Publications):

2017
      Taotao Wang , Huiyuan Wang, Dawei Cai, Yubang Gao, Hangxiao Zhang,Yongsheng Wang , Chentao Lin , Liuyin Ma , Lianfeng Gu .(2017) Comprehensive profiling of rhizome-associated alternative splicing  and  alternative polyadenylation in moso bamboo (Phyllostachys edulis) The Plant Journal doi: 10.1111/tpj.13597.

2016

Wang Q,Zuo Z C,Wang X,Gu L F, Yoshizumi T,Yang,Z H,Liu Q,Liu W,Han Y J,Liu B, Wohlschlegel J A, Matsui M, Oka Y and Lin C.(2016) Photoactivation and inactivation mechanisms of Arabidopsis cryptochrome2 Science 354:343-347.

Li C, Gu L, Gao L, Chen C, Wei C, Qiu Q, Chien C, Wang S, Jiang L, Chen C, Yang S, Nguyen V, Snyder M, Burlingame A, Kohalmi S, Huang S, Cao X, Wang Z, Wu K, Chen X, Cui Y. (2016) Concerted genomic targeting of histone H3 lysine 27 demethylase REF6 and chromatin-remodeling ATPase BRM in Arabidopsis Nature genetics 48(6):687-693.
      Wu, Z, Zhu D, Lin X, Miao L, Gu L, Deng X, Yang Q, Sun K, Zhu D, Cao X, TSUGE T, Dean C, Aoyama T, Gu H, Qu L. (2016)  RNA-binding proteins At RZ-1B and At RZ-1C play a critical role in regulation of pre-mRNA splicing and gene expression during Arabidopsis development The Plant Cell 28(1):55-73.
      Yan H, Zhang H, Wang Q, Jian H, Qiu X, Baudino S, Just J, Raymond O, Gu L, Jihua W, Bendahmane M and Tang K. (2016) The Rosa chinensis cv. Viridiflora phyllody phenotype is associated with misexpression of flower organ identity genes Front Plant Sci (12)7:996. doi: 10.3389/fpls.
      Li S, Zhang G, Zhang X, Yuan J, Deng C, Gu L, Gao W.( 2016) DPTEdb, an integrative database of transposable elements in dioecious plants Database 5(12) baw078 doi:10.1093/database/baw078.
     Cui X, Lu F, Qiu Q, Zhou B, Gu L, Zhang S, Kang Y, Cui X, Ma X, Yao Q, Ma J, Zhang X, Cao X. (2016) REF6 recognizes a specific DNA sequence to demethylate H3K27me3 and regulate organ boundary formation in Arabidopsis Nature genetics 48(6):694-699.
     Deng X, Lu T, Wang L, Gu L, Sun J, Kong X, Liu C, Cao X. (2016) Recruitment of the NineTeen Complex to the activated spliceosome requires AtPRMT5 PNAS 113(19):5447-5452.
     Zhang S, Xu M, Qiu Z, Wang K, Du Y, Gu L, Cui X.(2016) Spatiotemporal transcriptome provides insights into early fruit development of Solanum lycopersicum Sci Rep 18;6, 23173; doi: 10.1038/srep23173.

2015

Zhang Y, Gu, L, Hou, Y, Wang L, Deng, X, Hang, R, Chen, D, Zhang, X, Zhang, Y, Liu, C, and Cao, X. (2015) Integrative genome-wide analysis reveals HLP1, a novel RNA-binding protein, regulates plant flowering by targeted alternative polyadenylation Cell Research 25(7):864-876.

2014
      Zhou H, Zhou M, Yang Y, Li J, Zhu L, Jiang D, Dong J, Liu Q, Gu L, Zhou L., Cao X, Zhuang C. (2014) RNAase Zs1 processes UBL40 mRNA and controls thermo-sensitive genic male sterility in rice NATURE COMMUNICATIONS doi:10.1038/ncomms5884.
      Wei L, Gu L, Song X, Cui X, Lu Z, Zhou M, Wang L, Hu F, Zhai J, Meyer B, Cao X. (2014) Dicer-like 3 produces transposable element-associated 24-nt siRNAs that control agricultural traits in rice Proc Natl Acad Sci U S A 111: 3877-3882.
      Wu B, Suo F, Lei, W and Gu, L.(2014) Comprehensive Analysis of Alternative Splicing in Digitalis purpurea by Strand-Specific RNA-Seq PLoS One 9, e106001.

Before 2014
      Cui X, Jin P., Cui X, Gu L, Lu Z, Xue Y, Wei L, Qi J, Song X, Luo M, Gynheung An, Cao X. (2013) Control of Transposon Activity by a Histone H3K4 Demethylase in Rice Proc Natl Acad Sci U S A 110(5):1953-1958.
      Wang L, Song X, Gu L, Li X, Cao S, Chu C, Cui X, Chen X, and Cao X. (2013) NOT2 proteins promote polymerase II-dependent transcription and interact with multiple MicroRNA biogenesis factors in Arabidopsis Plant Cell 25: 715-727.
      Zhang L, Cheng Z, Qin R, Qiu Y, Wang J, Cui X, Gu L, Zhang X, Guo X, Wang D, Jiang L, Wu C, Wang H, Cao X, Wan J. (2012) Identification and Characterization of an Epi-1 allele of OsFIE1 Reveals a Regulatory Linkage between two Epigenetic Marks in Rice Plant Cell 24: 4407-4421.
      Deng X, Gu L, Liu C, Lu T, Lu F, Lu Z, Cui P, Pei Y, Wang B, Hu S, and Cao X. (2010) Arginine methylation mediated by the Arabidopsis homolog of PRMT5 is essential for proper pre-mRNA splicing Proc Natl Acad Sci U S A 107: 19114-19119.
      Zhou M, Gu L, Li P, Song X, Wei L, Chen Z. and Cao X. (2010) Degradome sequencing reveals endogenous small RNA targets in rice (Oryza sativa L. ssp. indica) Front. Biol 5: 67–90.
      Gu,L and Guo,R.(2007) Genome-wide detection and analysis of alternative splicing for nucleotide binding site-leucine-rich repeats sequences in rice J Genet Genomics 34: 247-257.