Faculty and Staff

LU Xuemei
E-mail:luxm@big.ac.cn

Group leader

Dr. LU Xuemei is a professor of Beijing Institute of Genomics, Chinese Academy of Sciences. Dr. LU started scientific career since 1997 when she received her Master degree from the South China Agricultural University. After 3-years professional training at the State Key Laboratory of Molecular Genetics and Evolution, in the Kunming Institute of Zoology in CAS, Dr. LU received her Ph.D. degree in Molecular Evolution in 2001. Dr. LU continued her postdoctoral research in the Center for Reproduction of Endangered Species, Zoological Society of San Diego from 2001 to 2002; and in the Department of Ecology and Evolution in the University of Chicago from 2003 to 2005. She was recruited to be an Associate Professor by School of Life Science, Sun Yet-Sen University in 2006 and promoted to Professor in Beijing Institute of Genomics in 2009. Dr. LU’s lab is currently focusing on genomic variations and evolution of complex traits and cancers.

 

Introduction

Dr. LU’s lab focuses on evolutionary genomics of complex traits and cancer in human and animal model systems using genomic and population genetic approaches. Our current research interests are in addressing 1) the evolutionary process and diversity within and between cellular populations/tumors, 2) evolution of complex traits and artificial selection in animals, and 3) evolution of gene regulatory in cells and polyploidy animal species by analyzing genomic, epigenomic and transcriptional variations.

Phenotypic evolution is driven by mutation, drift, migration and natural selection. Genetic variation is the basis of phenotypic changes, which affects the phenotypes by altering the regulation of gene expression. Adaptation can happen at various levels, population, organism, or cellular. Based on the identification of genomic variations, we are focusing on understanding the genomic basis and evolution of gene regulation in order to bridge the genotypic variations and phenotypic changes at various levels. Our previous transcriptional analysis sheds light on understanding the genetic basis of gene-gene interaction during speciation and the evolution of evolvability of miRNA regulation in biodiversity. We also work on the evolution of the population of cancerous cells (adaptation at cellular level) with carrying out large-scale sequencing. Cells from within a tumor and from the adjacent normal tissues may be treated as human individuals sampled from all over the world. We are testing the action of selection both within and between tumors by comparing the observations with the null model, in which all clones have the same neutral growth rate. Regardless of whether and how selection influences the genetic diversity, a large amount of neutral diversity, possibly orders of magnitude higher than the "adaptive" diversity, is expected to exist. If the mutations are involved in cellular properties that are selectively advantageous to tumor cell motility, migration, proliferation or drug resistance, they may increase the fitness variation and the likelihood of selective expansion of different subclones within a tumor. The phenotypic changes can mostly be represented by transcriptome profiles. In addition, epigenetic changes can be crucial in cellular but not organismal evolution. Therefore, the selectivity of the genetic and epigenetic divergence within a tumor for cellular fitness, which results in phenotypic variations, will to be examined.

 

Selected Publications(# :co-first author; *: corresponding author)

1.Shaoping Ling#, Zheng Hu#, Zuyu Yang#, Yang, Fang#, Yawei Li, Pei Lin, Ke Chen, Lili Dong, Lihua Cao, Yong Tao, Lingtong Hao, Qingjian Chen, Qiang Gong, Dafei Wu, Wenjie Li, Wenming Zhao, Xiuyun Tian, Chunyi Hao*,Eric A. Hungate, Daniel V. T. Catenacci, Richard R. Hudson, Wen-Hsiung Li*, Xuemei Lu*, Chung-I Wu*, Extremely high genetic diversity in a single tumor points to prevalence of non-Darwinian cell evolution,Proceedings of the National Academy of Sciences of the United States of America, 2015, 112(47):E6496-E6505

2.Guojing Liu#, Rui Zhang#, Jin Xu, Chung-I Wu* and Xuemei Lu*. Functional conservation of both CDS- and 3’UTR- located miRNA binding sites between species. Molecular biology and evolution, 2015, 32(3): 623-628

3.Yong Tao#, Zheng Hu#, Shaoping Ling#, Shiou-Hwie Yeh, Weiwei Zhai, Ke Chen, Chunyan Li, Yu Wang, Kaile Wang, Hurng-Yi Wang, Eric A Hungate, Kenan Onel, Jiang Liu, Changqing Zeng, Richard R Hudson, Pei-Jer Chen, Xuemei Lu*, Chung-I Wu* Further genetic diversification in multiple tumors and an evolutionary perspective on therapeutics. 2015, bioRxiv doi: http://dx.doi.org/10.1101/025429

4.Chunyan Li#, Zhenzhen Liu#, Fang Yang#, Wensheng Liu,Di Wang, Encheng Dong, Yu Wang, Chung-I Wu, Xuemei Lu*, siRNAs with decreased off-target effect facilitate the identification of essential genes in cancer cells, Oncotarget, 2015,6(25):21603-21613

5.Lei Zhao#, Ming-an Sun#, Zejuan Li#, Xue Bai, Miao Yu, Min Wang, Liji Liang, Xiaojian Shao, Stephen Arnovitz, Qianfei Wang, Chuan He, Xuemei Lu*, Jianjun Chen*, Hehuang Xie*. The dynamics of DNA methylation fidelity during mouse embryonic stem cell self-renewal and differentiation. Genome research. 2014; 24(8):1296-307

6.Xiaojian Shao, Cuiyun Zhang, Ming-an Sun, Xuemei Lu*, Hehuang Xie*. Deciphering the heterogeneity in DNA methylation patterns during stem cell differentiation and reprogramming. BMC genomics. 2014;(18): 978-987

7.Yanting Luo, Xuemei Lu*, Hehuang Xie*. Dynamic methylation during normal development, aging, and tumorigenesis. BioMed research international. 2014:784706

8.Jue Ruan#, Lan Jiang#, Zechen Chong#, Qiang Gong#, Heng Li, Chunyan Li, Yong Tao, Caihong Zheng, Weiwei Zhai, David Turissini, Charles H Cannon, Xuemei Lu*, Chung-I Wu*. Pseudo-sanger sequencing: Massively parallel production of long and near error-free reads using ngs technology. BMC genomics. 2013; 14(1): 711-719

9.Yali Hou#, Yachun Wang#, Xuemei Lu#, Xu Zhang, Qian Zhao, Rory J. Todhunter*, Zhiwu Zhang*. Monitoring hip and elbow dysplasia achieved modest genetic improvement of 74 dog breeds over 40 years in USA. PloS one. 2013;8(10)

10.Yong Tao#, Jue Ruan#, Shiou-Hwei Yeh#, Xuemei Lu#, Yu Wang#, Weiwei Zhai#, Jun Cai#, Shaoping Ling, Qiang Gong, Zechen Chong, Zhengzhong Qu, Qianqian Li, Jiang Liu, Jin Yang, Caihong Zheng, Changqing Zeng, Hurng-Yi Wang, Jing Zhang, Sheng-Han Wang, Lingtong Hao, Lili Dong, Wenjie Li, Min Sun, Wei Zou, Caixia Yu, Chaohua Li, Guojing Liu, Lan Jiang, Jin Xu, Huanwei Huang, Chunyan Li, Shuangli Mi, Bing Zhang, Baoxian Chen, Wenming Zhao, Songnian Hu, Shi-Mei Zhuang, Yang Shen, Suhua Shi, Christopher Brown, Kevin P.White, Ding-Shinn Chen*, Pei-Jer Chen, Chung-I Wu*. Rapid growth of a hepatocellular carcinoma and the driving mutations revealed by cell-population genetic analysis of whole-genome data. Proc Natl Acad Sci U S A. 2011;108:12042-12047

11.Xuemei Lu, Chung-I Wu*. Sex, sex chromosomes and gene expression. BMC biology. 2011;9:30-32

12.Xuemei Lu#, Joshua A. Shapiro#, Chau-Ti Ting, Yan Li, Chunyan Li, Jin Xu, Huanwei Huang, Ya-Jen Cheng, Anthony J. Greenberg, Shou-Hsien Li, Mao-Lien Wu, Yang Shen, Chung-I Wu*. Genome-wide misexpression of x-linked versus autosomal genes associated with hybrid male sterility. Genome research. 2010, 20(8): 1097-1102

13.Yan Li#, Liqing Zhang#, Dexiang Zhang, Xiquan Zhang, Xuemei Lu*. Faster evolution of z-linked duplicate genes in chicken. Journal of genetics and genomics. 2010; 37(10): 695-702

14.Shaojun Liu#*, Jing Luo#, Jing Chai#, Li Ren#, Yi Zhou#, Feng Huang#,Xiaochuan Liu, Yubao Chen, Chun Zhang, Min Tao, Bin Lu, Wei Zhou, Guoliang Lin, Chao Mai, Shuo Yuan, Jun Wang, Tao Li, Qinbo Qin, Hao Feng, Kaikun Luo, Jun Xiao, Huan Zhong, Rurong Zhao, Wei Duan, Zhenyan Song, Yanqin Wang, Jing Wang, Li Zhong, Lu Wang, Zhaoli Ding, Zhenglin Du, Xuemei Lu, Yun Gao, Robert W. Murphy, Yun Liu, Axel Meyer*, and Yaping Zhang*, Genomic incompatibilities in the diploid and tetraploid offspring of the goldfish × common carp cross, Proc Natl Acad Sci, 2016, 2;113(5): 1327-1332

15.Kaile Wang#, Qin Ma#, Lan Jiang, Shujuan Lai, Xuemei Lu, Yali Hou*,, Chung-I Wu*, Jue Ruan*, Ultra-precise detection of mutations bydroplet-based amplification of circularized DNA, BMC Genomics. 2016,17:214

16.Kaile Wang#, Xiaolu Ma#, Xue Zhang, Dafei Wu, Chenyi Sun, Yazhou Sun, Xuemei Lu, Chung-I Wu*, Caixia Guo*, Jue Ruan*. Using ultra-sensitive next generation sequencing to dissect DNA damage-induced mutagenesis. Sci Rep. 2016,6:25310

17.Han-Hsuan Chou#, Wer-Hung Chien#, Li-Ling Wu, Chi-Hung Cheng, Chen-Han Chung, Jau-Haw Horng, Yen-Hsuan Ni, Hong-Tai Tseng, Dafei Wu, Xuemei Lu, Hurng-Yi Wang*, Pei-Jer Chen, and Ding-Shinn Chen*. “Age-related immune clearance of hepatitis B virusinfection requires the establishment of gut microbiota.” Proc Natl Acad Sci U S A, 2015,112(7): 2175-2180

18.You-Yu Lin, Chieh Liu, Wei-Hung Chien, Li-Ling Wu, Yong Tao, Dafei Wu, Xuemei Lu, Chia-Hung HsieH, Pei-Jer Chen, Hurng-Yi Wang*, Jia-Horng Kao*, Ding-Shinn Chen. New insights into the evolutionary rate of hepatitis B virus at different biological scales. Journal of Virology, 2015,1128(10): 3114-3131

19.Xiaogang Cui#, Yali Hou#, Shaohua Yang, Yan Xie, Shengli Zhang, Yuan Zhang, Qin Zhang, Xuemei Lu, George E Liu, Dongxiao Sun*. Transcriptional profiling of mammary gland in holstein cows with extremely different milk protein and fat percentage using rna sequencing. BMC genomics. 2014;15:226

20.Zechen Chong#,Weiwei Zhai#,Chunyan Li,Min Gao,Qiang Gong,Jue Ruan,Juan Li,Lan Jiang,Xuemei Lu,EricHungate,Chung-I Wu*. The evolution of small insertions and deletions in the coding genes of drosophila melanogaster. Molecular biology and evolution. 2013;30:2699-2708

21.Qiang Gong, Yong Tao, Jianrong Yang, Jun Cai, Yunfei Yuan, Jue Ruan, Jin Yang, Huiliang Liu, Wanghua Li, Xuemei Lu, Shimei Zhuang, Sanming Wang, Chung-I Wu*. Identification of medium-sized genomic deletions with low coverage, mate-paired restricted tags. BMC genomics. 2013;14:51-55

22.Guodong Wang#, Weiwei Zhai#, HechuangYang, Ruoxi Fan, Xue Cao, Li Zhong, Lu Wang, Fei Liu, Hong Wu, Luguang Cheng, Andrei D. Poyarkov, Nikolai A. Poyarkov JR, Shu-sheng Tang, Wenming Zhao, Yun Gao, Xuemei Lu, David M. Irwin, Peter Savolainen, Chung-I Wu*, Yaping Zhang*. The genomics of selection in dogs and the parallel evolution between dogs and humans. Nature communications. 2013;4:1860-1864

23.Jin Xu#,Rui Zhang#,Yang Shen,Guojing Liu,Xuemei Lu,Chung-I Wu*. The evolution of evolvability in microrna target sites in vertebrates. Genome research. 2013;23:1810-1816

24.Ziwen He#, Weiwei Zhai#, Haijun Wen#, Tian Tang, Yu Wang, Xuemei Lu, Anthony J. Greenberg, Richard R. Hudson, Chung-I Wu*, Suhua Shi*. Two evolutionary histories in the genome of rice: The roles of domestication genes. PLoS genetics. 2011; 7(6): 1-3

25.Renchao Zhou#, Shaoping Ling#, Wenming Zhao#, Naoki Osada, Sufang Chen, Meng Zhang, Ziwen He, Hua Bao, Cairong Zhong, Bing Zhang, Xuemei Lu, David Turissini, Norman C. Duke, Jian Lu*, Suhua Shi*, Chung-I Wu*. Population genetics in nonmodel organisms: Ii. Natural selection in marginal habitats revealed by deep sequencing on dual platforms. Molecular biology and evolution. 2011; 28(10): 2833-2842

26.Hua Bao, Yuanyan Xiong, Hui Guo, Renchao Zhou, Xuemei Lu, Zhen Yang, Yang Zhong, Suhua Shi*, MapNext:a software tool for spliced and unspliced alignments and SNP detection of short sequence reads,BMC Genomics 2009, 10(Suppl 3):S13,2009,10(Suppl 3):S13-1-S13-6

27.Hua Bao, Hui Guo, Jinwei Wang, Renchao Zhou, Xuemei Lu, Suhua Shi*, MapView: visualization of short reads alignment on a desktop computer,Bioinformatics, 2009, 25 (12):1554-1555

 

Patents

1.Method and device for matching character strings. CN102929900A. Shaoping Ling, Xuemei Lu.

2.Composition for treating cancers and use thereof. CN102895672A. Chunyan Li, Fang Yang, Wensheng Liu, Yu Wang, Xuemei Lu, Chung-I Wu

3.Construction method of Small RNA-Seq library for screening early diagnosis targets of tumor. CN102586892A. Chunyan Li , Encheng Dong, Zhenzhen Liu, Xuemei Lu, Chung-I Wu

4.Trace DNA-based next-generation sequencing library construction method. CN103938277A. Zuyu Yang, Kaile Wang, Dafei Wu, Xuemei Lu, Chung-I Wu

 

Research Grant Support

The Strategic Priority Research Program of the Chinese Academy of Sciences,

Major Research Project of Nature Science Foundation of China (NSFC),

National High-tech R&D Program (863 Program),

Hundred Talents Program of the CAS,

National Basic Research Program of China (973 Program)(Yali Hou),

CAS Youth Innovation Promotion Association(Yali Hou),

The Youth Foundation of National Natural Science (Yali Hou)

 

Group Members

Staff:

HOU Yali, PhD, Associate Professor

BAI Xue, Research Associate

LIU Zhenzhen, Research Assistant

Graduate Students:

PhD Candidate:

LI Tao (2013);

LI Yawei (2014);

LUO Yanting (2014);

QI Furong (2015);

Sadaf Ambreen(2015)

YIN Liduo (2016)

Master Candidate:

ZHAO Binbin (2014);

FENG Jing(2015)

DOU Yanliang(2016)

HU Zhenyu(2016)

YAN Kai(2016)