崔鵬課題組

Cui peng Lab

　　課題組長(zhǎng)

　　崔鵬,，研究員，博士生導(dǎo)師，Genomics, Proteomics & Bioinformatics雜志編委成員,。主要從事植物基因組學(xué)和生物信息學(xué)領(lǐng)域的研究工作,，發(fā)表過的文章累計(jì)引用次數(shù)700余次,。其中以第一作者及通訊作者身份發(fā)表過SCI論文近26篇,，包括在領(lǐng)域內(nèi)著名期刊Nature Communications、the Plant cell,、Genome biology,、Molecular plant等發(fā)表的文章。

　　

　　工作經(jīng)歷

　　2016.5-至今        中國(guó)農(nóng)科院農(nóng)業(yè)基因組研究所      研究員                         

　　2012.4-2016.4    沙特阿卜杜拉國(guó)王科技大學(xué)         研究科學(xué)家                     

　　2011.4-2012.3    美國(guó)威斯康辛醫(yī)學(xué)院癌癥中心      博士后                         

　　2010.2-2011.3    沙特阿卜杜拉國(guó)王科技大學(xué)         研究科學(xué)家                     

　　2009.8-2010.1    中科院北京基因組研究所             研究助理    

　　

　　教育經(jīng)歷

　　中國(guó)科學(xué)院北京基因組研究所          博士學(xué)位           2004.9-2009.7

　　沈陽(yáng)化工大學(xué)                                  學(xué)士學(xué)位           2000.9-2004.7

　　

　　團(tuán)隊(duì)研究方向

　　量化性植物基因組注釋框架開發(fā),，并以油料相關(guān)作物基因組為主要應(yīng)用方向,。課題組目前致力于植物組學(xué)分析工具的研發(fā)，主要涉及基于機(jī)器學(xué)習(xí)的植物基因組重頭注釋,、公共數(shù)據(jù)的清洗及整合,、注釋流程的優(yōu)化、數(shù)據(jù)庫(kù)構(gòu)建等,。此外,，我們開展油料相關(guān)作物的基因組研究（包括包括油桐樹、蓖麻,、芝麻,、向日葵等），涉及基因組參考序列構(gòu)建及群體重測(cè)序等內(nèi)容,，挖掘農(nóng)藝或物種遺傳特征標(biāo)記,，為分子育種提供理論基礎(chǔ)。課題組濕實(shí)驗(yàn)平臺(tái)的主要方向?yàn)槎喾N微量或單細(xì)胞NGS文庫(kù)的構(gòu)建及優(yōu)化,。

　　

　　研究進(jìn)展

　　重要進(jìn)展一：首次完成染色體水平的瑞香科沉香屬沉香木基因組圖譜繪制,。

　　重要進(jìn)展二：405份蓖麻基因組重測(cè)序，利用全基因組關(guān)聯(lián)分析和群體遺傳分析，找到蓖麻馴化過程中的受選擇區(qū)域,，與性狀相關(guān)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　

　?。?）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.

　　

　　崔鵬課題組更新于2021年2月