进化生物学中心标注论文

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. Journal of Genetics and Genomics. 2024. ISSN 1673-8527

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.

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, Shuhua Xu*. Expression profiles of East-West highly differentiated genes in Uyghur genomes. National Science Review. 2023. 10:nwad077.

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.

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. doi:10.1007/s11427-022-2284-8.

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.

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

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.

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.

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.

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

Xiaohan Zhao#, Sen Ma#, Baonan Wang#, Xuetong Jiang, Shuhua Xu*. PGG.MHC: Toward understanding the diversity of major histocompatibility complexes in human populations. Nucleic Acids Research. 2022. 51(D1):D1102-D1108.

Yimin Wang#, Yunchao Ling#, Jiao Gong#, Xiaohan Zhao, Hanwen Zhou, Bo Xie, Haiyi Lou, Xinhao Zhuang, Li Jin, Shaohua Fan*, Guo-Qing Zhang*, Shuhua Xu*. PGG.SV: a whole-genome-sequencing-based structural variant resource and data analysis platform. Nucleic Acids Research. 2022. 51(D1):D1109–D1116.

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.

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

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.

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.

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.

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

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.

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.

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.

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.

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.

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.