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崔鹏课题组

崔鹏课题组

Cui peng Lab

  课题组长

  崔鹏,研究员,博士生导师。广东省青年拔尖人才,中国农业科学院青年英才,深圳市海外高层次人才, Genomics, Proteomics & Bioinformatics杂志编委成员。主要从事植物基因组学和生物信息学领域的研究工作,发表过的文章累计引用次数700余次。其中以第一作者及通讯作者身份发表过SCI论文近26篇,包括在领域内著名期刊Nature Communications、the Plant cell、Genome biology、Molecular plant等发表的文章。

  

  工作经历

  2016.5-至今        中国农科院农业基因组研究所      研究员                         

  2012.4-2016.4    沙特阿卜杜拉国王科技大学         研究科学家                     

  2011.4-2012.3    美国威斯康辛医学院癌症中心      博士后                         

  2010.2-2011.3    沙特阿卜杜拉国王科技大学         研究科学家                     

  2009.8-2010.1    中科院北京基因组研究所             研究助理    

  

  教育经历

  中国科学院北京基因组研究所          博士学位           2004.9-2009.7

  沈阳化工大学                                  学士学位           2000.9-2004.7

  

  团队研究方向

  量化性植物基因组注释框架开发,并以油料相关作物基因组为主要应用方向。课题组目前致力于植物组学分析工具的研发,主要涉及基于机器学习的植物基因组重头注释、公共数据的清洗及整合、注释流程的优化、数据库构建等。此外,我们开展油料相关作物的基因组研究(包括包括油桐树、蓖麻、芝麻、向日葵等),涉及基因组参考序列构建及群体重测序等内容,挖掘农艺或物种遗传特征标记,为分子育种提供理论基础。课题组湿实验平台的主要方向为多种微量或单细胞NGS文库的构建及优化。

  

  研究进展

  重要进展一:首次完成染色体水平的瑞香科沉香属沉香木基因组图谱绘制。

  重要进展二:405份蓖麻基因组重测序,利用全基因组关联分析和群体遗传分析,找到蓖麻驯化过程中的受选择区域,与性状相关基因。

  

  

  PI

  Cui Peng, Professor. Recognized as Top Young Talents of Guangdong Province, Young talent of the Chinese Academy of Agricultural Sciences, Overseas High-Caliber Personnel, the member of editorial board of the journal Genomics, Proteomics & Bioinformatics. He is mainly engaged in the field of plant genomics and bioinformatics. He has already published 26 papers at the international journals including Nature Communications, Plant cell, Genome biology, Molecular Plant etc., as the first or corresponding author. The publication has been cited more than 700 times.

  

  Working Experience

  2016.05–Present    Agricultural Genomics Institute at Shenzhen-CAAS         Professor 

  2012.04-2016.04   King Abdullah University of Science and Technology, KSA  Research Scientist

  2011.04-2012.03  Medical college of Wisconsin, USA   Postdoctoral Fellow

  2010.02-2011.03   King Abdullah University of Science and Technology, KSA  Research Scientist

  2009.08-2010.01  Beijing Institute of Genomics, CAS  Researcher Fellow

  

  Education

  2004.9-2009.7    Beijing Institute of Genomics, CAS                         Ph.D                        

  2000.9-2004.7    Shenyang University of Chemical Technology        Bachelor 

  

  Research Interest

  Research direction is quantitative annotation framework for plant genome, with oil-related crop genome project as the main application. The research team is currently developing new bioinformatic tools for genome analysis, focusing on machine learning-based annotation of plant genomes, cleaning and integration of public data, optimization of annotation pipeline, and database construction. In addition, the team is studying on several genome researches for oil crops(including tung tree, castor, sesame, etc.), involving the reference sequence construction and population studies. We expect to dig the genetic basic for agronomic and species  characteristics to provide information for molecular breeding. The wet platform in out lab focuses on the construction and optimization of a variety of micro-scale DNA or single-cell NGS libraries.

 

  Major Achievements

  (1)Genome sequence of the agarwood tree Aquilaria sinensis (Lour.) Spreng: the first chromosome-level draft genome in the Thymelaeceae family 

  (2)Whole genome resequencing of 405 Ricinus communis reveals trait-associated gene and genome region under selection during domestication through population genetics analysis and GWAS.

 

  Selected Publication 

  1. Ding X, Mei W, Lin Q, Wang H, Wang J, Peng S, Li H, Zhu J, Li W, Wang P, Chen H, Dong W, Guo D, Cai C, Huang S, Cui P, Dai H. Genome sequence of the agarwood tree Aquilaria sinensis (Lour.) Spreng: the first chromosome-level draft genome in the Thymelaeceae family. Gigascience . 2020 Mar 1;9(3)

        2. Fan W, Lu J, 2.Pan C, Tan M, Lin Q, Liu W, Li D, Wang L, Hu L, Wang L, Chen C, Wu A, Yu X, Ruan J, Yu J, Hu S, Yan X, Lü S, Cui P. Sequencing of Chinese castor lines reveals genetic signatures of selection and yield-associated loci. Nature Communications . 2019 Jul 31;10(1):3418.

  3.Cui P, Lin Q, Fang D, Zhang L, Li R, Cheng J, et al. Tung Tree (Vernicia fordii, Hemsl.) Genome and Transcriptome Sequencing Reveals Co-Ordinate Up-Regulation of Fatty Acid beta-Oxidation and Triacylglycerol Biosynthesis Pathways During Eleostearic Acid Accumulation in Seeds. Plant Cell Physiology . 2018;59(10):1990-2003.

  4. Wu Z#, Fang D#, Yang R#, Gao F, An X, Zhuo X, Li Y, Yi C, Zhang T, Liang C, Cui P*, Cheng Z*, et al. De novo genome assembly of Oryza granulata reveals rapid genome expansion and adaptive evolution. Communications Biology 2018;1.

  5. Cui P, Chen T, Ding F, Ali S, Xiong L. The protein phosphatase FRY2 interacts with eIF4AIII and UPF3 and is essential for nonsense-mediated mRNA decay in Arabidopsis, The Plant Cell 2016, 28(3):770-85.

  6. Cui P, Xiong L. Environmental Stress and Pre-mRNA Splicing. Molecular Plant 2015, p1302–1303.

  7. Cui P, Zhang S, Ding F, Ali S, Xiong L: Dynamic regulation of genome-wide pre-mRNA splicing and stress tolerance by the Sm-like protein LSm5 in Arabidopsis. Genome Biology 2014, 15:R1.

  

  崔鹏课题组更新于2021年2月

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