Yuwen Liu課題組

　　Yuwen Liu  Lab

　　

　　課題組長(zhǎng)

　　Yuwen Liu,，研究員,、博士生導(dǎo)師。2006年于清華大學(xué)本科畢業(yè),，2014年在芝加哥大學(xué)取得博士學(xué)位,。Yuwen Liu研究員在基因組和表觀遺傳學(xué)領(lǐng)域有著十多年的科學(xué)研究經(jīng)歷，長(zhǎng)期專注于開發(fā)新的實(shí)驗(yàn)和計(jì)算方法,，研究轉(zhuǎn)錄調(diào)控中的增強(qiáng)子定位和功能,，以及非編碼區(qū) DNA 變異如何通過(guò)影響增強(qiáng)子功能而影響生物性狀。截至2020年初,，Yuwen Liu研究員共發(fā)表 11 篇 SCI 論文,，Google Scholar總引用次數(shù)超過(guò) 670 次，其中以第一作者或并列第一作者在 Bioinformatics, Genome Biology, American Journal of Human Genetics, Journal of the American Chemical Society 等高水平雜志上共發(fā)表文章5 篇（累積影響因子 57.206）,，以共同作者在 Nature Genetics, Nature Communications 等高水平期刊發(fā)表 6 篇文章,。引進(jìn)農(nóng)科院后，獲得國(guó)家自然科學(xué)青年科學(xué)基金以及深圳科創(chuàng)委面上項(xiàng)目各 1 項(xiàng),。

 

　　工作經(jīng)歷

　　2019.1至今                 中國(guó)農(nóng)業(yè)科學(xué)院深圳農(nóng)業(yè)基因組研究所            研究員               

　　2014.8 - 2018.7          芝加哥大學(xué)                                                    博士后         

　　

　　教育經(jīng)歷

　　2006.9 - 2014.6            芝加哥大學(xué)                 博士               

　　2002.9 - 2006.6            清華大學(xué)                    學(xué)士                

　　

　　研究方向

　　1）建立起完整的豬骨骼肌不同發(fā)育階段的非編碼區(qū)功能基因組注釋；

　　2）在群體層面研究DNA變異如何通過(guò)影響轉(zhuǎn)錄調(diào)控的不同元件來(lái)影響豬的產(chǎn)肉性狀,，繼而在全基因組層面解析產(chǎn)肉性狀的遺傳機(jī)理,；

　　3）開發(fā)新的實(shí)驗(yàn)方法找尋影響復(fù)雜性狀的非編碼區(qū)調(diào)控原件；

　　4）開發(fā)新計(jì)算方法,，提高全基因組選育的準(zhǔn)確性,，包括結(jié)合功能基因組注釋進(jìn)行性狀預(yù)測(cè)和跨群體的性狀預(yù)測(cè),；

　　5）開發(fā)基于新生突變尋找復(fù)雜性狀效應(yīng)基因的新算法。

 

 

　　PI

　　Yuwen Liu is a principal investigator and doctoral advisor at AGIS-CAAS. Dr. Liu obtained his bachelor degree in Biology from Tsinghua University in 2006 and his PhD degree at The University of Chicago in 2014. He has been focusing on genomics and epigenomics over a decade, with broad experience in developing novel experimental and computational methods to study enhancer function and how DNA variants affect complex traits and diseases through modulating enhancer activity. As of early 2020, Dr. Liu has published 11 papers with more than 670 citations in prestigious journals, including Nature Genetics, Genome Biology, Bioinformatics, American Journal of Human Genetics, and Journal of the American Chemical Society. He is currently funded by AGIS, National Natural Science Foundation and Shenzhen Science and Innovation Commission.

 

　　Working Experience

　　2019.1 - present             Agricultural Genomics Institute at Shenzhen-CAAS            Principle investigator                                                 

　　2014.8 – 2018.7            The University of Chicago                                                     Postdoctoral Fellow       

　　

　　Education Experience

　　2006.09 - 2014.06        The University of Chicago                           Ph.D                   

　　2002.09 - 2006.06        Tsinghua University                                     Bachelor          

 

　　Research Interest

　　Establish a comprehensive non-coding functional genomic annotation of pig skeletal muscle at different developmental stages. Investigate how DNA mutations affect pig meat-production traits through modulating the activity of cis-regulatory elements of key genes. Develop innovative experimental methods to locate non-coding regulatory elements that affect complex traits. Develop new computational methods to improve the accuracy of genomic selection, from the perspective of integrating functional annotations and of cross-population trait prediction. Develop de novo mutation-based algorithm to identify risk/effector genes for complex diseases and traits.

 

　　Selected Publication

　　1)  Liu Y#, Zhou J, White K P*. RNA-seq differential expression studies: more sequence or more replication?. Bioinformatics, 2013, 30(3): 301-304.

　　2)  Liu Y#, Yu S#, Dhiman V K#, Tonya Brunetti, Heather Eckart*, Kevin P White*. Functional assessment of human enhancer activities using whole-genome STARR-sequencing. Genome biology, 2017, 18(1): 219.

　　3)  Song Liu#, Yuwen Liu#, Qin Zhang, Jiayu Wu, Junbo Liang, Shan Yu, Gong-Hong Wei, Kevin P White*, Xiaoyue Wang*. Systematic identification of regulatory variants associated with cancer risk. Genome biology, 2017, 18(1): 194.

　　4)  Lulu Hu#,，Yuwen Liu#,， Shengtong Han#，Lei Yang#,，Xiaolong Cui,，Yawei Gao，Qing Dai,，Xingyu Lu,，Xiaochen Kou，Yanhong Zhao,，Wenhui Sheng,，Shaorong Gao，Xin He*,，Chuan He*. Jump-seq: Genome-Wide Capture and Amplification of 5Hydroxymethylcytosine Sites. Journal of the American Chemical Society, 2019.

　　5)  Yuwen Liu#, Yanyu Liang, A Ercument Cicek, Zhongshan Li, Jinchen Li, Rebecca A Muhle, Martina Krenzer, Yue Mei, Yan Wang, Nicholas Knoblauch, Jean Morrison, Siming Zhao, Yi Jiang, Evan Geller, Iuliana Ionita-Laza, Jinyu Wu, Kun Xia, James P Noonan, Zhong Sheng Sun*, Xin He*. A statistical framework for mapping risk genes from de novo mutations in whole-genome-sequencing studies. The American Journal of Human Genetics, 2018, 102(6): 1031-1047.

　　6)  Donna M Werling#, Harrison Brand, Joon-Yong An, Matthew R Stone, Lingxue Zhu, Joseph T Glessner, Ryan L Collins, Shan Dong, Ryan M Layer, Eirene Markenscoff-Papadimitriou, Andrew Farrell, Grace B Schwartz, Harold Z Wang, Benjamin B Currall, Xuefang Zhao, Jeanselle Dea, Clif Duhn, Carolyn A Erdman, Michael C Gilson, Rachita Yadav, Robert E Handsaker, Seva Kashin, Lambertus Klei, Jeffrey D Mandell, Tomasz J Nowakowski, Yuwen Liu, Sirisha Pochareddy, Louw Smith, Michael F Walker, Matthew J Waterman, Xin He, Arnold R Kriegstein, John L Rubenstein, Nenad Sestan, Steven A McCarroll, Benjamin M Neale, Hilary Coon, A Jeremy Willsey, Joseph D Buxbaum, Mark J Daly, Matthew W State, Aaron R Quinlan, Gabor T Marth, Kathryn Roeder, Bernie Devlin*, Michael E Talkowski*, Stephan J Sanders*. An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder. Nature genetics, 2018, 50(5): 727.

　　7)  Siming Zhao#, Jun Liu, Pranav Nanga, Yuwen Liu, A. Ercument Cicek, Nicholas Knoblauch, Chuan He, Matthew Stephens*,，Xin He*. Detailed modeling of positive selection improves detection of cancer driver genes. Nature communications, 2019, 10(1): 3399.

　　8)  Xinxin Ke#, Alesia Walker, Sven-Bastiaan Haange, Ilias Lagkouvardos, Yuwen Liu, Philippe Schmitt-Kopplin, Martinvon Bergen, Nico Jehmlich, Xin He, Thomas Clavel, Peter C.K. Cheung*. Synbiotic-driven improvement of metabolic disturbances is associated with changes in the gut microbiome in diet-induced obese mice. Molecular metabolism, 2019, 22: 96-109.

　　9)  Yingzheng Wang#, Mingjun Liu, Jiyang Zhang, Yuwen Liu, Megan Kopp, Weiwei Zheng, Shuo Xiao*. Multidrug resistance protein 1 deficiency promotes doxorubicin-induced ovarian toxicity in female mice. Toxicological Sciences, 2018, 163(1): 279-292.

 

Yuwen Liu課題組更新于2020年7月