进化生物学中心标注论文

[1] Wanxing Xu#, Jiaojiao Liu#, Xiaoxi Zhang#, Jia Wen, Qidi Feng, Yang Gao, Yuwen Pan, Yan Lu, Asifullah Khan, Shuhua Xu*. Multiple-wave admixture and adaptive evolution of the Pamirian Wakhi people. Molecular Biology and Evolution. 2024. doi: 10.1093/molbev/msae237.

[2] Shuangshuang Cheng#, Zhilin Ning, Yan Lu, Yuhan Du, Xiaonan Yang, Minghui Li, Dilinuer Maimaitiyiming, Shuhua Xu*. DNA methylation and genetic regulation in natural populations of East Asian and mixed Eurasian ancestry. Science Bulletin. 2024. doi: 10.1016/j.scib.2024.10.006.

[3] Yan Lu#*, Fang Luo#, An Zhou, Cun Yi, Hao Chen, Jian Li, Yunhai Guo, Yuxiang Xie, Wei Zhang, Datao Lin, Yaming Yang, Zhongdao Wu, Yi Zhang, Shuhua Xu, Wei Hu*. Whole-genome sequencing of the invasive golden apple snail Pomacea canaliculate from Asia reveals rapid expansion and adaptive evolution. GigaScience. 2024.13: giae064.

[4] Shuangshuang Cheng#, Zhilin Ning#, Ke Huang#, Yuan Yuan, Xinjiang Tan, Yuwen Pan, Rui Zhang, Lei Tian, Yan Lu, Xiaoji Wang, Dongsheng Lu, Yajun Yang, Yaqun Guan, Dolikun Mamatyusupu, Shuhua Xu*. Analysis of sex-biased gene expression in a Eurasian admixed population. Briefings in Bioinformatics. 2024. 25(5):bbae451.

[5] Weibin Liu#, Yan Li, George P. Patrinos, Shuhua Xu, Meow-Keong Thong, Zhengming Chen, Francis P. Crawley, Liming Li, Perihan Elif Ekmekci, Radoje Drmanac, Weiyang Cheong, Robert Benamouzig, Quan Nguyen, Pavel Volchkov, Juergen K. V. Reichardt, Piero Carninci, Partha Majumder*, Xin Jin*, George Church*, Jian Wang* & Xun Xu*. The 1% gift to humanity: The Human Genome Project II. Cell Research. 2024. doi: 10.1038/s41422-024-01026-y.

[6] Hao Chen#, Shuhua Xu*. Population genomics advances in frontier ethnic minorities in China. Science China Life Sciences. 2024. doi: 10.1007/s11427-024-2659-2.

[7] Linda Repetto#, Jiantao Chen#, Zhijian Yang#, Ranran Zhai#, Paul R. H. J. Timmers, Xiao Feng, Ting Li, Yue Yao, Denis Maslov, Anna Timoshchuk, Fengyu Tu, Emma L. Twait, Sebastian May-Wilson, Marisa D. Muckian, Bram P. Prins, Grace Png, Charles Kooperberg, Åsa Johansson, Robert F. Hillary, Eleanor Wheeler, Lu Pan, Yazhou He, Sofia Klasson, Shahzad Ahmad, ... Xia Shen*. The genetic landscape of neuro-related proteins in human plasma. Nature Human Behaviour. 2024. doi: 10.1038/s41562-024-01963-z.

[8] Hong-Xiang Zheng#, Shi Yan, Menghan Zhang, Zhenglong Gu, Jiucun Wang, Li Jin*. MtDNA genomes reveal relaxed purifying selection during human population expansion after the Last Glacial Maximum. Molecular Biology and Evolution. 2024. doi: 10.1093/molbev/msae175.

[9] Siqi Yang#, Jixiang Xing, Dongyang Liu, Yancheng Song, Haoyu Yu, Shuhua Xu*, Yongchun Zuo*. Review and new insights into the catalytic structural domains of the Fe(ll) and 2-Oxoglutarate families. International Journal of Biological Macromolecules. 2024. doi: 10.1016/j.ijbiomac.2024.134798.

[10] Jia Wen#, Jiaojiao Liu#, Qidi Feng#, Yan Lu, Kai Yuan, Xiaoxi Zhang, Chao Zhang, Yang Gao, Xiaoji Wang, Dolikun Mamatyusupu, Shuhua Xu*. Ancestral origins and post-admixture adaptive evolution of highland Tajiks. National Science Review. 2024. doi:10.1093/nsr/nwae284.

[11] Shufen Zheng#, Philip S Tsao*, Cuiping Pan*. Abdominal aortic aneurysm and cardiometabolic traits share strong genetic susceptibility to lipid metabolism and inflammation. Nature Communications. 2024.15(1):5652.

[12] Xixian Ma#, Yan Lu#*, Shuhua Xu*. Adaptive Evolution of Two Distinct Adaptive Haplotypes of Neanderthal Origin at the Immunoglobulin Heavy-chain Locus in East Asian and European Populations. Molecular Biology and Evolution. 2024.41(7):msae147.

[13] Chang Lei#, Jiaojiao Liu#, Rui Zhang, Yuwen Pan, Yan Lu, Yang Gao, Xixian Ma, Yajun Yang, Yaqun Guan, Dolikun Mamatyusupu, Shuhua Xu*. Ancestral Origins and Admixture History of Kazakhs. Molecular Biology and Evolution. 2024.41(7):msae144.

[14] Sihan Chen#, Die Tang#, Lian Deng*, Shuhua Xu*. Asian-European differentiation of schizophrenia-associated genes driven by admixture and natural selection. iScience. 2024. 27(5):109560.

[15] Chengkun Yang#, Xiaoxi Zhang#, Shi Yan, Sizhe Yang, Baihui Wu, Fengshuo You, Yue Cui, Ni Xie, Zhiyi Wang, Li Jin*, Shuhua Xu*, Menghan Zhang*. Large-scale lexical and genetic alignment supports a hybrid model of Han Chinese demic and cultural diffusions. Nature Human Behaviour. 2024. doi: 10.1038/s41562-024-01886-9.

[16] Xiaomeng Cheng#, Guanghui Jiang#, Xiaolan Zhou, Jing Wang, Zhaozhao Zhao, Jiayu Zhang, Ting Ni*. The landscape and clinical relevance of intronic polyadenylation in human cancers. J Genet Genomics. 2024. doi: 10.1016/j.jgg.2024.04.014.

[17] Yi Huang#, Anyongqi Wang#, Wenjiang Zhou, Baoguo Li, Linshan Zhang, Agata M. Rudolf, Zengguang Jin, Catherine Hambly, Guanlin Wang*, and John R. Speakman*. Maternal dietary fat during lactation shapes single nucleus transcriptomic profile of postnatal offspring hypothalamus in a sexually dimorphic manner in mice. Nature Communications. 2024. 15(1):2382.

[18] Yang Gao#, Xiaoxi Zhang#, Hao Chen, Yan Lu, Sen Ma, Yajun Yang, Menghan Zhang, Shuhua Xu*. Reconstructing the ancestral gene pool to uncover the origins and genetic links of Hmong-Mien speakers. BMC Biology. 2024. 22(59):1518.

[19] Shi Zhang#, Rui Zhang#, Kai Yuan#, Lu Yang, Chang Liu, Yuting Liu, Xumin Ni*, Shuhua Xu*. Reconstructing complex admixture history using a hierarchical model. Briefings In Bioinformatics. 2024. 25(2):bbad540.

[20] Yuxin Tao#, Yuancheng Wei#, Jiaqi Ge#, Yan Pan#, Wenmin Wang, Qianqi Bi, Pengfei Sheng, Changzhong Fu, Wuyun Pan, Li Jin, HongXiang Zheng*, Menghan Zhang*. Phylogenetic evidence reveals early KraDai divergence and dispersal in the late Holocene. Nature Communications. 2023. 14:6924.

[21] Zeshan Lin#, Yan Lu#, Guoliang Yu#, Huajing Teng#, Bao Wang, Yajun Yang, Qinglan Li, Zhongsheng Sun, Shuhua Xu*, Wen Wang*, Peng Tian*. Genome-wide DNA methylation landscape of four Chinese populations and epigenetic variation linked to Tibetan high-altitude adaptation. SCIENCE CHINA Life Sciences. 2023. 66(10):2354-2369.

[22] Chentao Yang#, Yang Zhou#, Yanni Song#, Dongya Wu#, Yan Zeng#, Lei Nie, Panhong Liu, Shilong Zhang, Guangji Chen, Jinjin Xu, Hongling Zhou, Long Zhou, Xiaobo Qian, Chenlu Liu, Shangjin Tan, Chengran Zhou, Wei Dai, Mengyang Xu, Yanwei Qi, Xiaobo Wang, Lidong Guo, Guangyi Fan, Aijun Wang, Yuan Deng, Yong Zhang, Jiazheng Jin, Yunqiu He, Chunxue Guo, Guoji Guo, Qing Zhou, Xun Xu, Huanming Yang, Jian Wang, Shuhua Xu, Yafei Mao, Xin Jin, Jue Ruan* & Guojie Zhang*. The complete and fully-phased diploid genome of a male Han Chinese. Cell Research. 2023. 33(10):745-761.

[23] Yaoxi He#*, Yongbo Guo#, Wangshan Zheng#, Tian Yue#, Hui Zhang#, Bin Wang#, Zhanying Feng, Ouzhuluobu, Chaoying Cui, Kai Liu, Bin Zhou, Xuerui Zeng, Liya Li, Tianyun Wang, Yong Wang, Chao Zhang, Shuhua Xu, Xuebin Qi*, Bing Su*. Polygenic adaptation leads to a higher reproductive fitness of native Tibetans at high altitude. Current Biology. 2023. 33(19):4037-4051.e5.

[24] Xueling Ge#, Yan Lu#, Shuanghui Chen#, Yang Gao, Lifeng Ma, Lijun Liu, Jiaojiao Liu, Xixian Ma, Longli Kang*, Shuhua Xu*. Genetic origins and adaptive evolution of the Deng people on the Tibetan Plateau. Molecular Biology and Evolution. 2023. 40(10):msad205.

[25] Zeshuai Wang#, Zhisheng Wu#, Hao Wang#, Ruoqing Feng#, Guanlin Wang#*, Muxi Li#, Shuang-Yin Wang#, Xiaoyan Chen, Yiyi Su, Jun Wang, Weiwen Zhang, Yuzhou Bao, Zhenwei Lan, Zhuo Song, Yiheng Wang, Xianyang Luo, Lingyu Zhao, Anli Hou, Shuye Tian, Hongliang Gao, Wenbin Miao, Yingyu Liu, Huilin Wang, Cui Yin, Zhi-Liang Ji, Mingqian Feng, Hongkun Liu, Lianghui Diao, Ido Amit, Yun Chen, Yong Zeng, Florent Ginhoux*, Xueqing Wu*, Yuanfang Zhu*, Hanjie Li*. An immune cell atlas reveals the dynamics of human macrophage specification during prenatal development. Cell. 2023. 186(20):4454-4471.e19. doi: 10.1016/j.cell.2023.08.019.

[26] Weixu Wang#, Xiaolan Zhou#, Jing Wang#, Jun Yao, Haimei Wen, Yi Wang, Mingwan Sun, Chao Zhang, Wei Tao, Jiahua Zou, Ting Ni*. Approximate estimation of cell-type resolution transcriptome in bulk tissue through matrix completion. Brief Bioinform. 2023. 24(5):bbad273.

[27] Qi Liu, Bo Xie, Yang Gao, Shuhua Xu* and Yan Lu*. A protocol for applying low-coverage whole-genome sequencing data in structural variation studies. STAR Protocols. 2023. 4(3):102433.

[28] Bo Wang, Ningxin Dang, Xiaofei Yang*, Shuhua Xu*, Kai Ye*. The human pangenome reference: the beginning of a new era for genomics. Science Bulletin. 2023. 68(14):1484-1487

[29] Baihui Wu, Hanzhi Zhang, Menghan Zhang*, Phylogenetic insight into the origin of tones. Proceedings of the Royal Society B: Biological Sciences. 2023. 290: 20230606.

[30] Yang Gao#, Xiaofei Yang#, Hao Chen#, Xinjiang Tan#, Zhaoqing Yang#, Lian Deng#, Baonan Wang, Shuang Kong, Songyang Li, Yuhang Cui, Chang Lei, Yimin Wang, Yuwen Pan, Sen Ma, Hao Sun, Xiaohan Zhao, Yingbing Shi, Ziyi Yang, Dongdong Wu, Shaoyuan Wu, Xingming Zhao, Binyin Shi, Li Jin, Zhibin Hu, Chinese Pangenome Consortium (CPC), Yan Lu*, Jiayou Chu*, Kai Ye*, Shuhua Xu*. A Pangenome Reference of 36 Chinese populations. Nature. 2023. 19(7968):112-121.

[31] Hui Qiao, Jingze Tan, Shaoqing Wen, Menghan Zhang*, Shuhua Xu*, Li Jin*. De Novo Dissecting the Three Dimensional Facial Morphology of 2379 Han Chinese Individuals. Phenomic. 2023. doi:10.1007/s43657-023-00109-x.

[32] Qi Liu#, Ke Yang#, Bo Xie, Yang Gao, Shuhua Xu* and Yan Lu*. Mapping structural variations in Haemaphysalis longicornis and Rhipicephalus microplus reveals vector-pathogen adaptation. iScience. 2023. 26(4):106398.

[33] Zhilin Ning#, Xinjiang Tan#, Yuan Yuan#, Ke Huang, Yuwen Pan,Lei Tian, Yan Lu, Xiaoji Wang, Ruicheng Qi, Dongsheng Lu, Yajun Yang, Yaqun Guan, Dolikun Mamatyusupu and Shuhua Xu*. Expression profiles of east–west highly differentiated genes in Uyghur genomes. National Science Review. 2023. 10(4):nwad077.

[34] Juntao Hu* and Rowan D. H. Barrett. The role of plastic and evolved DNA methylation in parallel adaptation of threespine stickleback (Gasterosteus aculeatus). Molecular Ecology. 2023. 32(7):1581-1591.

[35] Hongru Wang#, Melinda A. Yang#, Shargan Wangdue, Hongliang Lu#, Honghai Chen, Linhui Li, Guanghui Dong, Tinley Tsring, Haibing Yuan, Wei He, Manyu Ding, Xiaohong Wu, Shuai Li, Norbu Tashi, Tsho Yang, Feng Yang, Yan Tong, Zujun Chen, Yuanhong He, Peng Cao, Qingyan Dai, Feng Liu, Xiaotian Feng, Tianyi Wang, Ruowei Yang, Wanjing Ping, Zhaoxia Zhang, Yang Gao, Ming Zhang, Xiaoji Wang, Chao Zhang, Kai Yuan, Albert Min-Shan Ko, Mark Aldenderfer, Xing Gao, Shuhua Xu, Qiaomei Fu*. Human genetic history on the Tibetan Plateau in the past 5100 years. Science Advances. 2023. 9(11):eadd5582.

[36] Yuwen Pan#, Jia Wen#, Zhilin Ning#, Yuan Yuan, Xubing Liu, Yajun Yang, Yaqun Guan, Yan Lu*, Dolikun Mamatyusupu, Shuhua Xu*. Comparative genomic and transcriptomic analyses reveal the impacts of genetic admixture in Kazaks, Uyghurs, and Huis. Molecular Biology and Evolution. 2023. 40(3):msad054.

[37] Yan Zhao#, Juntao Hu#, Jijiao Wu and Zhihong Li*. ChIP-seq profiling of H3K4me3 and H3K27me3 in an invasive insect, Bactrocera dorsalis. Frontiers in Genetics. 2023. 14:1108104.

[38] Tong Wu, Shuhua Xu*. Understanding the contemporary high obesity rate from an evolutionary genetic perspective. Hereditas. 2023. 160(1):5.

[39] Yimin Wang#, Yunchao Ling#, Jiao Gong#, Xiaohan Zhao, Hanwen Zhou, Bo Xie, Haiyi Lou, Xinhao Zhuang, Li Jin, The Han100K Initiative, Shaohua Fan*, Guoqing Zhang* and Shuhua Xu*. PGG.SV: a whole-genome-sequencing-based structural variant resource and data analysis platform. Nucleic Acids Research. 2023. 51(D1):D1109-D1116.

[40] Xiaohan Zhao#, Sen Ma#, Baonan Wang#, Xuetong Jiang, The Han100K Initiative and Shuhua Xu*. PGG.MHC: toward understanding the diversity of major histocompatibility complexes in human populations. Nucleic Acids Research. 2023. 51(D1):D1102-D1108.

[41] Xixian Ma, Shuhua Xu*. Archaic introgression contributed to the pre-agriculture adaptation of vitamin B1 metabolism in East Asia. iScience. 2022. 25(12):105614.

[42] Hao Chen#, Rong Lin#, Yan Lu, Rui Zhang, Yang Gao, Yungang He*, Shuhua Xu*. Tracing Bai-Yue ancestry in aboriginal Li people on Hainan Island. Molecular Biology and Evolution. 2022. 39(10):msac210.

[43] Rui Zhang#, Xumin Ni#, Kai Yuan#, Yuwen Pan, Shuhua Xu*. MultiWaverX: modeling latent sex-biased admixture history. Briefings in Bioinformatics. 2022. 23(5):bbac179.

[44] Yuwen Pan, Panhong Liu, Fang Wang, Peng Wu, Fanjun Cheng, Xin Jin, Shuhua Xu*. Lineage-specific positive selection on ACE2 contributes to the genetic susceptibility of COVID-19. National Science Review. 2022. 9(9):nwac118.

[45] Zhaoqing Yang#, Hao Chen#, Yan Lu, Yang Gao, Hao Sun, Jiucun Wang, Li Jin, Jiayou Chu*, Shuhua Xu*. Genetic evidence of tri-genealogy hypothesis on the origin of ethnic minorities in Yunnan. BMC Biology. 2022. 20:166.

[46] Yangchun Gao, Yiyong Chen, Shiguo Li, Xuena Huang, Juntao Hu*, Dan G. Bock, Hugh J. Maclsaac and Aibin Zhan*. Complementary genomic and epigenomic adaptation to environmental heterogeneity. Molecular Ecology. 2022. 31(13):3598-3612.

[47] Lian Deng, Bo Xie, Yimin Wang, Xiaoxi Zhang, Shuhua Xu*. A protocol for applying a population-specific reference genome assembly to population genetics and medical studies. STAR Protocols. 2022. 3(2):101440.

[48] Rui Zhang, Kai Yuan and Shuhua Xu*. Detecting archaic introgression and modeling multiple-wave admixture with ArchaicSeeker 2.0. STAR Protocols. 2022. 3:101314.

[49] Haiyi Lou#*, Yang Gao#, Bo Xie#, Yimin Wang#, Haikuan Zhang, Miao Shi, Sen Ma, Xiaoxi Zhang, Chang Liu, Shuhua Xu*. Haplotype-resolved de novo assembly of a Tujia genome suggests the necessity for high-quality population-specific genome references. Cell Systems. 2022. 13(4):321-333.

[50] Haiyi Lou#*, Bo Xie#, Yimin Wang#, Yang Gao, Shuhua Xu*. Improved NGS variant calling tool for the PRSS1–PRSS2 locus. Gut. 2022. 72(1):210-212.

[51] Lian Deng#, Yuwen Pan#, Yinan Wang, Hao Chen, Kai Yuan, Sihan Chen, Dongsheng Lu, Yan Lu, Siti Shuhada Mokhtar, Thuhairah Abdul Rahman, Boon-Peng Hoh, Shuhua Xu*. Genetic connections and convergent evolution of tropical indigenous peoples in Asia. Molecular Biology and Evolution. 2022. 39(2):msab361.

[52] Boon-Peng Hoh*, Lian Deng, Shuhua Xu. The Peopling and Migration History of the Natives in Peninsular Malaysia and Borneo: A Glimpse on the Studies Over the Past 100 years. Frontiers in genetics. 2022. 13:767018-767018.

[53] Mingyue Cheng#, Xueling Ge#, Chaofang Zhong, Ruiqing Fu, Kang Ning*, Shuhua Xu*. Micro-co-evolution of Host Genetics with Gut Microbiome in Three Chinese Ethnic Groups. Journal of Genetics and Genomics. 2021. 48(11):972-983.

[54] Kai Yuan#, Xumin Ni#, Chang Liu#, Yuwen Pan#, Lian Deng#, Rui Zhang#, Yang Gao, Xueling Ge, Jiaojiao Liu, Xixian Ma, Haiyi Lou, Taoyang Wu and Shuhua Xu*. Refining models of archaic–modern human admixture in Eurasia with ArchaicSeeker 2.0. Nature Communications. 2021. 12:6232.