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吕雪梅  研究员
适应性进化与进化医学学科组
职  务: 适应性进化与进化医学学科组组长
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电子邮件: xuemeilu@mail.kiz.ac.cn
通讯地址: 云南省昆明市教场东路32号    650223
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  简  历

中科院昆明动物所遗传资源与进化国家重点实验室“适应性进化与进化医学学科组”学科组负责人吕雪梅研究员,博士生导师。主要从事适应性进化的群体基因组学研究,利用基因组、表观组等技术手段,结合大数据和高性能计算,依据进化生物学和群体遗传学理论,解析生物多样性、适应性进化、肿瘤等疾病的发生、发展、演化过程和遗传机制。成果发表于PNASScience AdvancesMolecular Biology and EvolutionGenome ResearchAnnual Review Genetics等国际著名刊物发表论文五十余篇;获得多项专利;承担中科院战略先导专项课题、中科院重点部署、基金委重大研究计划集成和重点项目等项目。

  研究方向

1)物种形成的组学机制:以自然物种为研究对象,用组学的手段,研究种群历史和进化驱动力对物种形成的作用,和适应性表型产生的基因组和表观组机理。2)体细胞的进化:以细胞水平的变异和进化为核心,探究从正常体细胞遗传和表观变异的累积、到细胞适应性改变的形成和进化一系列过程的基本规律;在进化理论框架指导下的临床应用研发,利用新材料、新技术,研究肿瘤治疗的老药新用策略。3)生态进化的种群动态:将细胞进化作为模式体系,理解不同物种在进化过程中突变、竞争、选择压力等对进化的作用,解决在自然种群中难以追踪和分析的生态和进化生物学基本问题。

  承担科研项目

1)   中国科学院重点部署项目,KFZD-SW-220,经典化疗药物治疗肿瘤的新理论构建和创新应用,2019/01-2020/12350万元,在研,参与

2)   中国科学院“西部之光--西部引进人才”项目,2019/01-2021/12200万元,在研,主持

3)   国家自然科学基金面上项目,31771416,肿瘤细胞群体适应性权衡的生态进化机制,2018/01-2021/1260万元,在研,主持

4)   国家自然科学基金-云南联合基金,U1902201,高原湖泊水质变化过程中鲫鱼复合种群体多样性变化及其生态适应性,2020/01-2023/1280.85万(个人经费),在研,项目骨干

5)   第二次青藏高原综合科学考察研究,2019QZKK05010405,青藏高原形成与鼢鼠物种多样性, 2019/10-2024/1275万,在研,子课题负责人

6)   中科院先导B类专项,XDB13040300,在模式系统中研究复杂性状演化和稳定性的网络调控,2014/06-2019/06651.093万,结题,课题负责人

7)   国家自然科学基金重大研究计划集成项目,91531305,肿瘤生长、迁移及其进化驱动力的群体基因组学解析,2016/01-2018/12290万,结题,主持

8)   国家自然科学基金重大研究计划重点支持项目,91131903,细胞群体的适应性进化规律和进化关键基因的识别,2012/01-2015/12350万,结题,主持

  专家类别
研究员,西部之光—西部引进人才
  社会任职
  获奖及荣誉
  代表论著

1.        Jing Luo#, Jing Chai1#, Yanling Wen#, Min Tao#, Guoliang Lin#, Xiaochuan Liu, Li Ren, Zeyu Chen, Shigang Wu, Shengnan Li , Yude Wang, Qinbo Qin, Shi Wang, Yun Gao, Feng Huang, Lu Wang, Cheng Ai, Xiaobo Wang, Lianwei Li, Chengxi Ye, Huimin Yang, Mi Luo, Jie Chen, Hong Hu, Liujiao Yuan, Li Zhong, Jing Wang, Jian Xu, Zhenglin Du, Zhanshan (Sam) Ma, Robert W. Murphy, Axel Meyer, Jianfang Gui, Peng Xu*, Jue Ruan*, Z. Jeffrey Chen*, Shaojun Liu*, Xuemei Lu*, Yaping Zhang*, From asymmetrical to balanced genomic diversification during rediploidization: subgenomic evolution in allotetraploid fish, Science Advances, 2020 (Accepted)

2.        Qingyun Liu#, Jianhao Wei#, Yawei Li#, Mei Wang, Jun Su, Yonghui Lu, Mariana G. López, Xueqin Qian, Zhaoqin Zhu, Haiying Wang, Mingyun Gan, Qi Jiang, Yun-Xin Fu, Howard E.Takiff, I?aki Comas, Feng Li*, Xuemei Lu*, Sarah M. Fortune* and Qian Gao*, Mycobacterium tuberculosis clinical isolates carry mutational signatures of host immune environments, Science Advances, 2020 (Accepted)

3.        Yali Hou# , Furong Qi#, Xue Bai#, Tong Ren, Xu Shen, Qin Chu, Xiquan Zhang* and Xuemei Lu*, Genome-wide analysis reveals molecular convergence underlying domestication in 7 bird and mammals, BMC Genomics, 2020. 21(1): p. 204

4.        Yuezheng Zhang#, Yawei Li#, Tao Li#, Xu Shen#, Tianqi Zhu, Yong Tao, Xueying Li, Di Wang, Qin Ma, Zheng Hu, Jialin Liu, Jue Ruan, Jun Cai, Hurng-Yi Wang*, Xuemei Lu*, Genetic load and potential mutational meltdown in cancer cell populations, Molecular Biology and Evolution, 2019, 36(3): 541-552

5.        Ying Xiang, Kai Yan, Qian Zheng, Haiqiang Ke, Jie Cheng, Wenjun Xiong, Xin Shi, Lei Wei, Min Zhao, Fei Yang, Ping Wang, Xing Lu, Li Fu, Xuemei Lu*, and Feng Li*. Histone demethylase KDM4B promotes DNA damage by activating long interspersed nuclear element-1 (LINE-1). Cancer Research. 2019, 79(1):86-98

6.        Liduo Yin#, Yanting Luo#, Xiguang Xu, Shiyu Wen, Xiaowei Wu, Xuemei Lu*, and Hehuang Xie*, Virtual methylome dissection facilitated by single-cell analyses, Epigenetics Chromatin, 2019. 12(1): p. 66.

7.        Juan Li#, Lan Jiang#, Chung-I Wu, Xuemei Lu*, Shu Fang*, Chau-Ti Ting*, Small Segmental Duplications in Drosophila-High Rate of Emergence and Elimination, Genome Biology and Evolution, 2019, 11(2): 486-496

8.        Sixue Liu#, Zuyu Yang#, Guanghao Li#, Chunyan Li, Yanting Luo, Qiang Gong, Xin Wu, Tao Li, Zhiqian Zhang, Baocai Xing, Xiaolan Xu*, Xuemei Lu*. Multi-omics analysis in primary cell cultures reveal the genomic basis of phenotypic diversity within tumor. Genomics, Proteomics & Bioinformatics 2019 (In press)

9.        Furong Qi, Airong Yang, Sadaf Ambreen, Xue Bai, Yali Hou*, Xuemei Lu*. Birth and death of Mx genes and the presence/absence of genes regulating Mx transcription are correlated with the diversity of anti-pathogenicity in vertebrate species. Molecular Genetics and Genomics. 2019, 294(1):121-133

10.    Xue Bai#; Zhenzhen Liu#; Xiaojian Shao; Di Wang; Encheng Dong; Yan Wang; Chung-I Wu; Yunfei Yuan; Xuemei Lu*; Chunyan Li*, The heterogeneity of plasma miRNA profiles in hepatocellular carcinoma patients and the exploration of diagnostic circulating miRNAs for hepatocellular carcinoma, Plos One, 2019, 14(2):e0211581

11.    Yanting Luo#, Jianlin He#, Xiguang Xu, Ming-an Sun, Xiaowei Wu, Xuemei Lu*, Hehuang Xie.* Integrative single-cell omics analyses reveal epigenetic heterogeneity in mouse embryonic stem cells. PLoS Computational Biology 2018, 14(3): e1006034

12.    Wen Ye, Shaoping Ling, RanYi Liu, ZhiZhong Pan, Gaoyuan Wang, Shijuan Gao, Jiangxue Wu, Lihua Cao, Lili Dong, Yingchang Li, Yi Zhou, Wuying Du, Xiangqi Meng, Jinna Chen, Xinyuan Guan, Yulong He, Changchuan Pan, XF Steven Zheng, Xuemei Lu* , Shuai Chen*, Wenlin Huang*. Exome sequencing reveals the genetic landscape and frequent inactivation of PCDHB3 in Chinese rectal cancers. Journal of Pathology. 2018, 245(2): 222-234

13.    Chunyan Li#, Yali Hou#, Jin Xu#, Aiqun Zhang, Zhenzhen Liu, Furong Qi, Zuyu Yang, Ke Chen, Sixue Liu, Huanwei Huang, Qianfei Wang, Jiahong Dong, Chung-I Wu and Xuemei Lu*, A Direct Test of Selection in Cell Populations Using the Diversity in Gene Expression within Tumors, Molecular Biology and Evolution, 2017, 34(7):1730-1742

14.    Jin Xu#, Xinxin Peng#, Yuxin Chen#, Yuezheng Zhang, Qin Ma, Liang Liang, Ava C. Carter, Xuemei Lu* and Chung-I Wu*, Free-living human cells reconfigure their chromosomes in the evolution 1 back to uni-cellularity, eLife, 2017, 6. pii: e28070

15.    Kaile Wang, Shujuan Lai, Xiaoxu Yang, Tianqi Zhu, Xuemei Lu, Chung-I Wu* and Jue Ruan*. Ultrasensitive and high-efficiency screen of de novo low-frequency mutations by o2n-seq. Nature communications, 2017.8:15335.

16.    You-Yu Lin* , Chia-Hung Hsieh, Jiun-Hong Chen, Xuemei Lu, Jia-Horng Kao, Pei-Jer Chen, Ding-Shinn Chen and Hurng-Yi Wang*. De novo assembly of highly polymorphic metagenomic data using in situ generated reference sequences and a novel BLAST-based assembly pipeline. BMC bioinformatics, 2017.18(1):223.

17.    Zuyu Yang#, Mingming Jia#, Guojing Liu, Huaining Hao, Li Chen, Guanghao Li, Sixue Liu, Yawei Li, Chung-I Wu, Xuemei Lu*, Shengdian Wang*, Genomic sequencing identifies a few mutations driving the independent origin of primary liver tumors in a chronic hepatitis murine model, Plos one, 2017;12(11):e0187551

18.    Chung-I Wu*, Hurng-Yi Wang, Shaoping Ling, Xuemei Lu*, The Ecology and Evolution of Cancer: The Ultra-Microevolutionary Process, Annual Review of Genetics, 2016, 50:347-369

19.    Xu Shen, Xue Bai, Jin Xu, Min Zhou, Haipin Xu, Qinghua Nie, Xuemei Lu*, Xiquan Zhang*, Transcriptome sequencing reveals genetic mechanisms underlying the transition between the laying and brooding phases and gene expression changes associated with divergent reproductive phenotypes in chickens, Molecular Biology Reports, 2016, 43(9):977-989

20.    Guojing Liu#, Rui Zhang#, Jin Xu, Chung-I Wu*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

21.    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

22.    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, Proc Natl Acad Sci U S A, 2015, 112(47):E6496-E6505

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

24.    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):1296-1307

25.    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

26.    Yanting Luo#Xuemei Lu*, Hehuang Xie*, Dynamic Alu Methylation during Normal Development, Aging, and Tumorigenesis, Biomed Research International, 2014(784706)

27.    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

28.    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) :e76390

29.    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

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

31.    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

32.    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

 

  研究团队

工作人员

汤易雨立 助理实验师

 助理实验师

     助理实验师

研究生

殷利夺 2016级博士研究生

陈泽宇 2016级博士研究生

  2017级博士研究生

  2019级博士研究生

Rex Frimpong Anane 2019级博士研究生

魏昀旸 2019级博士研究生

OUEDRAOGO RAOGO BLAISE 2018级博士研究生

陶鑫灵 2018级硕士研究生

魏婉宜 2019级硕士研究生

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