Yuwen Liu 课题组

Yuwen Liu课题组

　　Yuwen Liu  Lab

　　

　　课题组长

　　Yuwen Liu，研究员、博士生导师。2006年于清华大学本科毕业，2014年在芝加哥大学取得博士学位。Yuwen Liu研究员在基因组和表观遗传学领域有着十多年的科学研究经历，长期专注于开发新的实验和计算方法，研究转录调控中的增强子定位和功能，以及非编码区 DNA 变异如何通过影响增强子功能而影响生物性状。截至2020年初，Yuwen Liu研究员共发表 11 篇 SCI 论文，Google Scholar总引用次数超过 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 等高水平杂志上共发表文章5 篇（累积影响因子 57.206），以共同作者在 Nature Genetics, Nature Communications 等高水平期刊发表 6 篇文章。引进农科院后，获得国家自然科学青年科学基金以及深圳科创委面上项目各 1 项。

 

　　工作经历

　　2019.1至今                 中国农业科学院深圳农业基因组研究所            研究员               

　　2014.8 - 2018.7          芝加哥大学                                                    博士后         

　　

　　教育经历

　　2006.9 - 2014.6            芝加哥大学                 博士               

　　2002.9 - 2006.6            清华大学                    学士                

　　

　　研究方向

　　1）建立起完整的猪骨骼肌不同发育阶段的非编码区功能基因组注释；

　　2）在群体层面研究DNA变异如何通过影响转录调控的不同元件来影响猪的产肉性状，继而在全基因组层面解析产肉性状的遗传机理；

　　3）开发新的实验方法找寻影响复杂性状的非编码区调控原件；

　　4）开发新计算方法，提高全基因组选育的准确性，包括结合功能基因组注释进行性状预测和跨群体的性状预测；

　　5）开发基于新生突变寻找复杂性状效应基因的新算法。

 

 

　　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课题组更新于2020年7月