Publications

Chapman, Alec R.; Lee, David F.; Cai, Wenting; Ma, Wenping; Li, Xiang; Sun, Wenjie; Xie, Xiaoliang Sunney "Correlated gene modules uncovered by high-precision single-cell transcriptomics," PNAS 119(51), e2206938119 DOI: 10.1073/pnas.2206938119 (2022)
Wu, Honggui; Li, Xiang; Jian, Fanchong; Yisimayi, Ayijiang; Zheng, Yinghui; Tan, Longzhi; Xing, Dong; Xie, X. Sunney "Highly sensitive single-cell chromatin accessibility assay andtranscriptome coassay with METATAC," PNAS 119(40), e2206450119 DOI: 10.1073/pnas.2206450119 (2022)
Cao, Yunlong; Wang, Jing; Jian, Fanchong; Xiao, Tianhe; Song, Weiliang; Yasimayi, Ayijiang; Huang, Weijin; Li, Qianqian; Wang, Peng; An, Ran; Wang, Jing; Wang, Yao; Niu, Xiao; Yang, Sijie; Liang, Hui; Sun, Haiyan; Li, Tao; Yu, Yuanling; Cui, Qianqian; Liu, Shuo; Yang, Xiaodong; Du, Shuo; Zhang, Zhiying; Hao, Xiaohua; Shao, Fei; Jin, Ronghua; Wang, Xiangxi; Xiao, Junyu; Wang, Youchun; Xie, Xiaoliang Sunney "Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies," Nature 602, 657-663 DOI: 10.1038/s41586-021-04385-3 (2021)
Du, Shuo; Liu, Pulan; Zhang, Zhiying; Xiao, Tianhe; Yasimayi, Ayijiang; Huang, Weijin; Wang, Youchun; Cao, Yunlong; Xie, Xiaoliang Sunney; Xiao, Junyu "Structures of SARS-CoV-2 B.1.351 neutralizing antibodies provide insights into cocktail design against concerning variants," Cell Research 31, 1130–1133 DOI: 10.1038/s41422-021-00555-0 (2021)
Cao, Yunlong; Yisimayi, Ayijiang; Bai, Yali; Huang, Weijin; Li, Xiaofeng; Zhang, Zhiying; Yuan, Tianjiao; An, Ran; Wang, Jing; Xiao, Tianhe; Du, Shuo; Ma, Wenping; Song, Liyang; Li, Yongzheng; Li, Xiang; Song, Weiliang; Wu, Jiajing; Liu, Shuo; Li, Xuemei; Zhang, Yonghong; Su, Bin; Guo, Xianghua; Wei, Yangyang; Gao, Chuanping; Zhang, Nana; Zhang, Yifei; Dou, Yang; Xu, Xiaoyu; Shi, Rui; Lu, Bai; Jin, Ronghua; Ma, Yingmin; Qin, Chengfeng; Wang, Youchun; Feng, Yingmei; Xiao, Junyu; Xie, Xiaoliang Sunney "Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines," Cell Research 31(7), 732-741 DOI: 10.1038/s41422-021-00514-9 (2021)
Xing, Dong; Tan, Longzhi; Chang, Chi-Han; Li, Heng; Xie, X. Sunney "Accurate SNV detection in single cells by transposon-based whole-genome amplification of complementary strands," PNAS 118(8), e2013106118 DOI: 10.1073/pnas.2013106118 (2021)
Tan, Longzhi; Ma, Wenping; Wu, Honggui; Sun, Wenjie; Zheng, Yinghui; Xing, Dong; Chen, Ritchie; Li, Xiang; Daley, Nicholas; Deisseroth, Karl; Xie, X. Sunney "Changes in genome architecture and transcriptional dynamics progress independently of sensory experience during post-natal brain development," Cell 184(3), 741-758 DOI: 10.1016/j.cell.2020.12.032 (2021)
Du, Shuo; Cao, Yunlong; Zhu, Qinyu; YU, Pin; Qi, Feifei; Wang, Guopeng; Du, Xiaoxia; Bao, Linlin; Deng, Wei; Zhu, Hua; Liu, Jiangning; Nie, Jianhui; Zheng, Yinghui; Liang, Haoyu; Liu, Ruixue; Gong, Shuran; Liu, Jiangning; Xu, Hua; Yisimayi, Ayijiang; Lv, Qi; Wang, Bo; He, Runsheng; Han, Yunlin; Zhao, Wenjie; Bai, Yali; Qu, Yajin; Gao, Xiang; Ji, Chenggong; Wang, Qisheng; Gao, Ning; Huang, Weijin; Wang, Youchun; Xie, X. Sunney; Su, Xiao-dong; Xiao, Junyu; Qin, Chuan "Structurally resolved SARS-CoV-2 antibody shows high efficacy in severely infected hamsters and provides a potent cocktail pairing strategy," Cell 183(4), 1013-1023.e13 DOI: 10.1016/j.cell.2020.09.035 (2020)
Cao, Yunlong; Su, Bin; Guo, Xianghua; Sun, Wenjie; Deng, Yongqiang; Bao, Linlin; Zhu, Qinyu; Zhang, Xu; Zheng, Yinghui; Geng, Chenyang; Chai, Xiaoran; He, Runsheng; Li, Xiaofeng; Lv, Qi; Zhu, Hua; Deng, Wei; Xu, Yanfeng; Wang, Yanjun; Qiao, Luxin; Tan, Yafang; Song, Liyang; Wang, Guopeng; Du, Xiaoxia; Gao, Ning; Liu, Jiangning; Xiao, Junyu; Su, Xiaodong; Du, Zongmin; Feng, Yingmei; Qin, Chuan; Qin, Chengfeng; Jin, Ronghua; Xie, X. Sunney "Potent Neutralizing Antibodies against SARS-CoV-2 Identified by High-Throughput Single-Cell Sequencing of Convalescent Patients' B Cells," Cell 182(1), 73-84.e16 DOI: 10.1016/j.cell.2020.05.025 (2020)
Di, Lin; Fu, Yusi; Sun, Yue; Li, Jie; Lu, Liu; Yao, Jiacheng; Wang, Guanbo; Wu, Yalei; Lao, kaiqin; Ding, Miao; Lee, Raymond W.; Zheng, Genhua; Xu, Jun; Oh, Juntaek; Wang, Dong; Xie, X. Sunney; Huang, Yanyi; Wang, Jianbin "RNA sequencing by direct tagmentation of RNA/DNA hybrids," PNAS 117(6), 2886-2893 DOI: 10.1073/pnas.1919800117 (2020)
Huang, Lei; Bogale, Berhan; Tang, Yaqiong; Lu, Sijia; Xie, X.Sunney; Racowsky, Catherine "Noninvasive preimplantation genetic testing for aneuploidy in spent medium may be more reliable than trophectoderm biopsy," PNAS 16(208), 14105-14112 DOI: 10.1073/pnas.1907472116 (2019)
Tan, Longzhi; Xing, Dong; Daley, Nicholas; Xie, X.Sunney "Three-dimensional genome structures of single sensory neurons in mouse visual and olfactory systems," Nat Struct Mol Biol 26, 297-307 DOI: 10.1038/s41594-019-0205-2 (2019)
Xiong, Luoxing; Huang, Lei; Tian, Feng; Lu, Sijia; Xie, X.Sunney "Bayesian model for accurate MARSALA (mutated allele revealed by sequencing with aneuploidy and linkage analyses)," J Assist Reprod Genet 36(6), 1263-1271 DOI: 10.1007/s10815-019-01451-8 (2019)
Tan, Longzhi; Xing, Dong; Chang, Chi-Han; Li, Heng; Xie, X.Sunney "Three-dimensional genome structures of single diploid human cells," Science 43, 924-928 DOI: 10.1126/science.aat5641 (2018)
Wu, Haitao; Shen, Xiaoting; Huang, Lei; Zeng, Yanhong; Gao, Yumei; Shao, Lin; Lu, Baomin; Zhong, Yiping; Miao, Benyu; Xu, Yanwen; Wang, Yali; Li, Yubin; Li, Yubin; Xiong, Luoxing; Lu, Sijia; Xie, X.Sunney; Zhou, Canquan "Genotyping single-sperm cells by universal MARSALA enables the acquisition of linkage information for combined pre-implantation genetic diagnosis and genome screening," J Assist Reprod Genet 35(6), 1071-1078 DOI: 10.1007/s10815-018-1158-9 (2018)
Blanshard, Robert C; Chen, Chongyi; Xie, X.Sunney; Hoffmann, Eva R "Single cell genomics to study DNA and chromosome changes in human gametes and embryos," Methods in Cell Biology 144, 441-457 DOI: 10.1016/bs.mcb.2018.03.037 (2018)
Tan, Longzhi; Xie, X.Sunney "A Near-complete Spatial Map of Olfactory Receptors in the Mouse Main Olfactory Epithelium," Chem Senses 43(6), 427-432 DOI: 10.1093/chemse/bjy030 (2018)
Ge, Hao; Wu, Pingping; Qian, Hong; Xie, Xiaoliang Sunney "Relatively slow stochastic gene-state switching in the presence of positive feedback significantly broadens the region of bimodality through stabilizing the uninduced phenotypic state," PLOS Computational Biology 14(3), e1006051 DOI: 10.1371/journal.pcbi.1006051 (2018)
Chen, Zitian; Zhou, Wenxiong; Qiao, Shuo; Kang, Li; Duan, Haifeng; Xie, X Sunney; Huang, Yanyi "Highly accurate fluorogenic DNA sequencing with information theory–based error correction," Nat Biotechnol 35(12), 1170-1178 DOI: 10.1038/nbt.3982 (2017)
Gao, Yan; Ni, Xiaohui; Guo, Hua; Su, Zhe; Ba, Yi; Tong, Zhongsheng; Guo, Zhi; Yao, Xin; Chen, Xixi; Yin, Jian; Yan, Zao; Liu, Ying; Bai, Fan; Xie, X. Sunney; Zhang, Ning "Single-cell sequencing deciphers a convergent evolution of copy number alterations from primary to circulating tumor cells," Genome Research 27, 1312-1322 DOI: 10.1101/gr.216788.116 (2017)
Chen, Chongyi; Xing, Dong; Tan, Longzhi; Li, Heng; Zhou, Guangyu; Huang, Lei; Xie, Xiaoliang S. "Single-cell whole-genome analyses by Linear Amplification via Transposon Insertion (LIANTI)," Science 356, 189-194 DOI: 10.1126/science.aak9787 (2017)
Xu, Jiawei; Zhang, Zhen; Niu, Wenbin; Yang, Qingling; Yao, Guidong; Shi, Senlin; Jin, Haixia; Song, Qingling; Yang, Wenyan; Yang, Qingling; Chen, Lei; Zhang, Xiangyang; Guo, Yihong; Su, Yingchun; Chen, Lei; Hu, Linli; Zhai, Jun; Chen, Lei; Zhang, Yile; Dong, Fangli; Gao, Yumei; Chen, Lei; Li, Wenhui; Bo, Shiping; Hu, Mintao; Ren, Jun; Huang, Lei; Lu, Sijia; Xie, Xiaoliang S.; Sun, Yingpu "Mapping allele with resolved carrier status of Robertsonian and reciprocal translocation in human preimplantation embryos," Proc Natl Acad Sci USA 114(41), E8695-E8702 DOI: 10.1073/pnas.1715053114 (2017)
Lee, David F.; Lu, Jenny; Chang, Seungwoo; Loparo, Joseph J.; Xie, Xiaoliang S. "Mapping DNA polymerase errors by single-molecule sequencing," Nucleic Acids Research , gkw436 DOI: 10.1093/nar/gkw436 (2016)
Zhao, Ziqing W; Xie, X.Sunney; Ge, Hao "Nonequilibrium Relaxation of Conformational Dynamics Facilitates Catalytic Reaction in an Elastic Network Model of T7 DNA Polymerase," J Phys Chem B120(11), 2869-2877 DOI: 10.1021/acs.jpcb.5b11002 (2016)
Xu, Juanjuan; Fang, Rui; Chen, Li; Chen, Daozhen; Xiao, Jian-Ping; Yang, Weimin; Wang, Honghua; Song, Xiaoqing; Ma, Ting; Bo, Shiping; Shi, Chong; Ren, Jun; Huang, Lei; Cai, Li-Yi; Yao, Bing; Xie, X.Sunney; Lu, Sijia "Noninvasive chromosome screening of human embryos by genome sequencing of embryo culture medium for in vitro fertilization," Proc Natl Acad Sci USA 113(42), 11907-11912 DOI: 10.1073/pnas.1613294113 (2016)
Chen, H.; Shiroguchi, K.; Ge, H.; Xie, X. S. "Genome-wide study of mRNA degradation and transcript elongation in Escherichia coli," Molecular Systems Biology 11(1), 781-781 DOI: 10.15252/msb.20145794 (2015)
Chapman, Alec R.; He, Zi; Lu, Sijia; Yong, Jun; Tan, Longzhi; Tang, Fuchou; Xie, X. Sunney "Single Cell Transcriptome Amplification with MALBAC," PLoS ONE 10(3), e0120889 DOI: 10.1371/journal.pone.0120889 (2015)
Xie, Xiaoliang Sunney "Single Molecules Meet Genomics: Pinpointing Precision Medicine," JAMA 313(20), 2021 DOI: 10.1001/jama.2015.5533 (2015)
Huang, Lei; Ma, Fei; Chapman, Alec; Lu, Sijia; Xie, Xiaoliang Sunney "Single-Cell Whole-Genome Amplification and Sequencing: Methodology and Applications," Annu. Rev. Genom. Human Genet. 16(1), 79-102 DOI: 10.1146/annurev-genom-090413-025352 (2015)
Fu, Yusi; Li, Chunmei; Lu, Sijia; Zhou, Wenxiong; Tang, Fuchou; Xie, X. Sunney; Huang, Yanyi "Uniform and accurate single-cell sequencing based on emulsion whole-genome amplification," Proc Natl Acad Sci USA 112(38), 11923-11928 DOI: 10.1073/pnas.1513988112 (2015)
Tan, L.; Li, Q.; Xie, X. S. "Olfactory sensory neurons transiently express multiple olfactory receptors during development," Molecular Systems Biology 11(12), 844-844 DOI: 10.15252/msb.20156639 (2015)
Yan, Liying; Huang, Lei; Xu, Liya; Huang, Jin; Ma, Fei; Zhu, Xiaohui; Tang, Yaqiong; Liu, Mingshan; Lian, Ying; Liu, Ping; Li, Rong; Lu, Sijia; Tang, Fuchou; Qiao, Jie; Xie, X. Sunney "Live births after simultaneous avoidance of monogenic diseases and chromosome abnormality by next-generation sequencing with linkage analyses," Proc Natl Acad Sci USA 112(52), 15964-15969 DOI: 10.1073/pnas.1523297113 (2015)
Hou, Yu; Fan, Wei; Yan, Liying; Li, Rong; Lian, Ying; Huang, Jin; Li, Jinsen; Xu, Liya; Tang, Fuchou; Xie, X. Sunney; Qiao, Jie "Genome Analyses of Single Human Oocytes," Cell 155(7), 1492-1506 DOI: 10.1016/j.cell.2013.11.040 (2013)
Ni, X.; Zhuo, M.; Su, Z.; Duan, J.; Gao, Y.; Wang, Z.; Zong, C.; Bai, H.; Chapman, A. R.; Zhao, J.; Xu, L.; An, T.; Ma, Q.; Wang, Y.; Wu, M.; Sun, Y.; Wang, S.; Li, Z.; Yang, X.; Yong, J.; Su, X.-D.; Lu, Y.; Bai, F.; Xie, X. S.; Wang, J. "Reproducible copy number variation patterns among single circulating tumor cells of lung cancer patients," Proceedings of the National Academy of Sciences 110(52), 21083-21088 DOI: 10.1073/pnas.1320659110 (2013)
Xu, Xinliang; Ge, Hao; Gu, Chan; Gao, Yi Qin; Wang, Siyuan S.; Thio, Beng Joo Reginald; Hynes, James T.; Xie, X. Sunney; Cao, Jianshu "Modeling Spatial Correlation of DNA Deformation: DNA Allostery in Protein Binding," J. Phys. Chem. B 117(42), 13378-13387 DOI: 10.1021/jp4047243 (2013)
Zong, C.; Lu, S.; Chapman, A. R.; Xie, X. S. "Genome-Wide Detection of Single-Nucleotide and Copy-Number Variations of a Single Human Cell," Science 338(6114), 1622-1626 DOI: 10.1126/science.1229164 (2012)
Lu, S.; Zong, C.; Fan, W.; Yang, M.; Li, J.; Chapman, A. R.; Zhu, P.; Hu, X.; Xu, L.; Yan, L.; Bai, F.; Qiao, J.; Tang, F.; Li, R.; Xie, X. S. "Probing Meiotic Recombination and Aneuploidy of Single Sperm Cells by Whole-Genome Sequencing," Science 338(6114), 1627-1630 DOI: 10.1126/science.1229112 (2012)
Shiroguchi, K.; Jia, T. Z.; Sims, P. A.; Xie, X. S. "Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes," Proceedings of the National Academy of Sciences 109(4), 1347-1352 DOI: 10.1073/pnas.1118018109 (2012)
Sims, Peter A; Greenleaf, William J; Duan, Haifeng; Xie, X Sunney "Fluorogenic DNA sequencing in PDMS microreactors," Nat Meth 8(7), 575-580 DOI: 10.1038/nmeth.1629 (2011)