Introduction

　　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.