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
12.Wen Ye, Shaoping Ling, Ran‐Yi Liu, Zhi‐Zhong 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