Publications

Cao, Y.; Bai, Y.; Yuan, T.; Song, L.; Fan, Y.; Ren, L.; Song, W.; Peng, J.; An, R.; Gu, Q.; Zheng, Y.; Xie, X.S. Single-cell bisulfite-free 5mC and 5hmC sequencing with high sensitivity and scalability. Proc. Natl. Acad. Sci. U.S.A. 2023, 120(49), e2310367120 DOI: 10.1073/pnas.2310367120
Chapman, A.R.; Lee, D.F.; Cai, W.; Ma, W.; Li, X.; Sun, W.; Xie, X.S. Correlated gene modules uncovered by high-precision single-cell transcriptomics. Proc. Natl. Acad. Sci. U.S.A. 2022, 119(51), e2206938119 DOI: 10.1073/pnas.2206938119
Wu, H.; Li, X.; Jian, F.; Yisimayi, A.; Zheng, Y.; Tan, L.; Xing, D.; Xie, X.S. Highly sensitive single-cell chromatin accessibility assay andtranscriptome coassay with METATAC. Proc. Natl. Acad. Sci. U.S.A. 2022, 119(40), e2206450119 DOI: 10.1073/pnas.2206450119
Cao, Y.; Wang, J.; Jian, F.; Xiao, T.; Song, W.; Yasimayi, A.; Huang, W.; Li, Q.; Wang, P.; An, R.; Wang, J.; Wang, Y.; Niu, X.; Yang, S.; Liang, H.; Sun, H.; Li, T.; Yu, Y.; Cui, Q.; Liu, S.; Yang, X.; Du, S.; Zhang, Z.; Hao, X.; Shao, F.; Jin, R.; Wang, X.; Xiao, J.; Wang, Y.; Xie, X.S. Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. Nature 2021, 602, 657-663 DOI: 10.1038/s41586-021-04385-3
Du, S.; Liu, P.; Zhang, Z.; Xiao, T.; Yasimayi, A.; Huang, W.; Wang, Y.; Cao, Y.; Xie, X.S.; Xiao, J. Structures of SARS-CoV-2 B.1.351 neutralizing antibodies provide insights into cocktail design against concerning variants. Cell Res. 2021, 31, 1130–1133 DOI: 10.1038/s41422-021-00555-0
Cao, Y.; Yisimayi, A.; Bai, Y.; Huang, W.; Li, X.; Zhang, Z.; Yuan, T.; An, R.; Wang, J.; Xiao, T.; Du, S.; Ma, W.; Song, L.; Li, Y.; Li, X.; Song, W.; Wu, J.; Liu, S.; Li, X.; Zhang, Y.; Su, B.; Guo, X.; Wei, Y.; Gao, C.; Zhang, N.; Zhang, Y.; Dou, Y.; Xu, X.; Shi, R.; Lu, B.; Jin, R.; Ma, Y.; Qin, C.; Wang, Y.; Feng, Y.; Xiao, J.; Xie, X.S. Humoral immune response to circulating SARS-CoV-2 variants elicited by inactivated and RBD-subunit vaccines. Cell Res. 2021, 31(7), 732-741 DOI: 10.1038/s41422-021-00514-9
Xing, D.; Tan, L.; Chang, C.; Li, H.; Xie, X.S. Accurate SNV detection in single cells by transposon-based whole-genome amplification of complementary strands. Proc. Natl. Acad. Sci. U.S.A. 2021, 118(8), e2013106118 DOI: 10.1073/pnas.2013106118
Tan, L.; Ma, W.; Wu, H.; Sun, W.; Zheng, Y.; Xing, D.; Chen, R.; Li, X.; Daley, N.; Deisseroth, K.; Xie, X.S. Changes in genome architecture and transcriptional dynamics progress independently of sensory experience during post-natal brain development. Cell 2021, 184(3), 741-758 DOI: 10.1016/j.cell.2020.12.032
Du, S.; Cao, Y.; Zhu, Q.; YU, P.; Qi, F.; Wang, G.; Du, X.; Bao, L.; Deng, W.; Zhu, H.; Liu, J.; Nie, J.; Zheng, Y.; Liang, H.; Liu, R.; Gong, S.; Liu, J.; Xu, H.; Yisimayi, A.; Lv, Q.; Wang, B.; He, R.; Han, Y.; Zhao, W.; Bai, Y.; Qu, Y.; Gao, X.; Ji, C.; Wang, Q.; Gao, N.; Huang, W.; Wang, Y.; Xie, X.S.; Su, X.; Xiao, J.; Qin, C. Structurally resolved SARS-CoV-2 antibody shows high efficacy in severely infected hamsters and provides a potent cocktail pairing strategy. Cell 2020, 183(4), 1013-1023.e13 DOI: 10.1016/j.cell.2020.09.035
Cao, Y.; Su, B.; Guo, X.; Sun, W.; Deng, Y.; Bao, L.; Zhu, Q.; Zhang, X.; Zheng, Y.; Geng, C.; Chai, X.; He, R.; Li, X.; Lv, Q.; Zhu, H.; Deng, W.; Xu, Y.; Wang, Y.; Qiao, L.; Tan, Y.; Song, L.; Wang, G.; Du, X.; Gao, N.; Liu, J.; Xiao, J.; Su, X.; Du, Z.; Feng, Y.; Qin, C.; Qin, C.; Jin, R.; Xie, X.S. Potent Neutralizing Antibodies against SARS-CoV-2 Identified by High-Throughput Single-Cell Sequencing of Convalescent Patients' B Cells. Cell 2020, 182(1), 73-84.e16 DOI: 10.1016/j.cell.2020.05.025
Di, L.; Fu, Y.; Sun, Y.; Li, J.; Lu, L.; Yao, J.; Wang, G.; Wu, Y.; Lao, k.; Ding, M.; Lee, R.W.; Zheng, G.; Xu, J.; Oh, J.; Wang, D.; Xie, X.S.; Huang, Y.; Wang, J. RNA sequencing by direct tagmentation of RNA/DNA hybrids. Proc. Natl. Acad. Sci. U.S.A. 2020, 117(6), 2886-2893 DOI: 10.1073/pnas.1919800117
Huang, L.; Bogale, B.; Tang, Y.; Lu, S.; Xie, X.; Racowsky, C. Noninvasive preimplantation genetic testing for aneuploidy in spent medium may be more reliable than trophectoderm biopsy. Proc. Natl. Acad. Sci. U.S.A. 2019, 16(208), 14105-14112 DOI: 10.1073/pnas.1907472116
Tan, L.; Xing, D.; Daley, N.; Xie, X. Three-dimensional genome structures of single sensory neurons in mouse visual and olfactory systems. Nat Struct Mol Biol 2019, 26, 297-307 DOI: 10.1038/s41594-019-0205-2
Xiong, L.; Huang, L.; Tian, F.; Lu, S.; Xie, X. Bayesian model for accurate MARSALA (mutated allele revealed by sequencing with aneuploidy and linkage analyses). J Assist Reprod Genet 2019, 36(6), 1263-1271 DOI: 10.1007/s10815-019-01451-8
Tan, L.; Xing, D.; Chang, C.; Li, H.; Xie, X. Three-dimensional genome structures of single diploid human cells. Science 2018, 361, 924-928 DOI: 10.1126/science.aat5641
Wu, H.; Shen, X.; Huang, L.; Zeng, Y.; Gao, Y.; Shao, L.; Lu, B.; Zhong, Y.; Miao, B.; Xu, Y.; Wang, Y.; Li, Y.; Li, Y.; Xiong, L.; Lu, S.; Xie, X.; Zhou, C. 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 2018, 35(6), 1071-1078 DOI: 10.1007/s10815-018-1158-9
Blanshard, R.C.; Chen, C.; Xie, X.; Hoffmann, E.R. Single cell genomics to study DNA and chromosome changes in human gametes and embryos. Methods in Cell Biology 2018, 144, 441-457 DOI: 10.1016/bs.mcb.2018.03.037
Tan, L.; Xie, X. A Near-complete Spatial Map of Olfactory Receptors in the Mouse Main Olfactory Epithelium. Chem Senses 2018, 43(6), 427-432 DOI: 10.1093/chemse/bjy030
Ge, H.; Wu, P.; Qian, H.; Xie, X.S. 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 Comput. Biol. 2018, 14(3), e1006051 DOI: 10.1371/journal.pcbi.1006051
Chen, Z.; Zhou, W.; Qiao, S.; Kang, L.; Duan, H.; Xie, X.S.; Huang, Y. Highly accurate fluorogenic DNA sequencing with information theory–based error correction. Nat Biotechnol 2017, 35(12), 1170-1178 DOI: 10.1038/nbt.3982
Gao, Y.; Ni, X.; Guo, H.; Su, Z.; Ba, Y.; Tong, Z.; Guo, Z.; Yao, X.; Chen, X.; Yin, J.; Yan, Z.; Liu, Y.; Bai, F.; Xie, X.S.; Zhang, N. Single-cell sequencing deciphers a convergent evolution of copy number alterations from primary to circulating tumor cells. Genome Res. 2017, 27, 1312-1322 DOI: 10.1101/gr.216788.116
Chen, C.; Xing, D.; Tan, L.; Li, H.; Zhou, G.; Huang, L.; Xie, X.S. Single-cell whole-genome analyses by Linear Amplification via Transposon Insertion (LIANTI). Science 2017, 356, 189-194 DOI: 10.1126/science.aak9787
Xu, J.; Zhang, Z.; Niu, W.; Yang, Q.; Yao, G.; Shi, S.; Jin, H.; Song, Q.; Yang, W.; Yang, Q.; Chen, L.; Zhang, X.; Guo, Y.; Su, Y.; Chen, L.; Hu, L.; Zhai, J.; Chen, L.; Zhang, Y.; Dong, F.; Gao, Y.; Chen, L.; Li, W.; Bo, S.; Hu, M.; Ren, J.; Huang, L.; Lu, S.; Xie, X.S.; Sun, Y. Mapping allele with resolved carrier status of Robertsonian and reciprocal translocation in human preimplantation embryos. Proc Natl Acad Sci USA 2017, 114(41), E8695-E8702 DOI: 10.1073/pnas.1715053114
Lee, D.F.; Lu, J.; Chang, S.; Loparo, J.J.; Xie, X.S. Mapping DNA polymerase errors by single-molecule sequencing. Nucleic Acids Res. 2016, , gkw436 DOI: 10.1093/nar/gkw436
Zhao, Z.W.; Xie, X.; Ge, H. Nonequilibrium Relaxation of Conformational Dynamics Facilitates Catalytic Reaction in an Elastic Network Model of T7 DNA Polymerase. J Phys Chem 2016, B120(11), 2869-2877 DOI: 10.1021/acs.jpcb.5b11002
Xu, J.; Fang, R.; Chen, L.; Chen, D.; Xiao, J.; Yang, W.; Wang, H.; Song, X.; Ma, T.; Bo, S.; Shi, C.; Ren, J.; Huang, L.; Cai, L.; Yao, B.; Xie, X.; Lu, S. Noninvasive chromosome screening of human embryos by genome sequencing of embryo culture medium for in vitro fertilization. Proc Natl Acad Sci USA 2016, 113(42), 11907-11912 DOI: 10.1073/pnas.1613294113
Chen, H.; Shiroguchi, K.; Ge, H.; Xie, X.S. Genome-wide study of mRNA degradation and transcript elongation in Escherichia coli. Mol. Syst. Biol. 2015, 11(1), 781-781 DOI: 10.15252/msb.20145794
Chapman, A.R.; He, Z.; Lu, S.; Yong, J.; Tan, L.; Tang, F.; Xie, X.S. Single Cell Transcriptome Amplification with MALBAC. PLoS ONE 2015, 10(3), e0120889 DOI: 10.1371/journal.pone.0120889
Xie, X.S. Single Molecules Meet Genomics: Pinpointing Precision Medicine. JAMA 2015, 313(20), 2021 DOI: 10.1001/jama.2015.5533
Huang, L.; Ma, F.; Chapman, A.; Lu, S.; Xie, X.S. Single-Cell Whole-Genome Amplification and Sequencing: Methodology and Applications. Annu. Rev. Genom. Human Genet. 2015, 16(1), 79-102 DOI: 10.1146/annurev-genom-090413-025352
Fu, Y.; Li, C.; Lu, S.; Zhou, W.; Tang, F.; Xie, X.S.; Huang, Y. Uniform and accurate single-cell sequencing based on emulsion whole-genome amplification. Proc Natl Acad Sci USA 2015, 112(38), 11923-11928 DOI: 10.1073/pnas.1513988112
Tan, L.; Li, Q.; Xie, X.S. Olfactory sensory neurons transiently express multiple olfactory receptors during development. Mol. Syst. Biol. 2015, 11(12), 844-844 DOI: 10.15252/msb.20156639
Yan, L.; Huang, L.; Xu, L.; Huang, J.; Ma, F.; Zhu, X.; Tang, Y.; Liu, M.; Lian, Y.; Liu, P.; Li, R.; Lu, S.; Tang, F.; Qiao, J.; Xie, X.S. Live births after simultaneous avoidance of monogenic diseases and chromosome abnormality by next-generation sequencing with linkage analyses. Proc Natl Acad Sci USA 2015, 112(52), 15964-15969 DOI: 10.1073/pnas.1523297113
Hou, Y.; Fan, W.; Yan, L.; Li, R.; Lian, Y.; Huang, J.; Li, J.; Xu, L.; Tang, F.; Xie, X.S.; Qiao, J. Genome Analyses of Single Human Oocytes. Cell 2013, 155(7), 1492-1506 DOI: 10.1016/j.cell.2013.11.040
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.; Lu, Y.; Bai, F.; Xie, X.S.; Wang, J. Reproducible copy number variation patterns among single circulating tumor cells of lung cancer patients. Proc. Natl. Acad. Sci. U.S.A. 2013, 110(52), 21083-21088 DOI: 10.1073/pnas.1320659110
Xu, X.; Ge, H.; Gu, C.; Gao, Y.Q.; Wang, S.S.; Thio, B.J.R.; Hynes, J.T.; Xie, X.S.; Cao, J. Modeling Spatial Correlation of DNA Deformation: DNA Allostery in Protein Binding. J. Phys. Chem. B 2013, 117(42), 13378-13387 DOI: 10.1021/jp4047243
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 2012, 338(6114), 1622-1626 DOI: 10.1126/science.1229164
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 2012, 338(6114), 1627-1630 DOI: 10.1126/science.1229112
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. Proc. Natl. Acad. Sci. U.S.A. 2012, 109(4), 1347-1352 DOI: 10.1073/pnas.1118018109
Sims, P.A.; Greenleaf, W.J.; Duan, H.; Xie, X.S. Fluorogenic DNA sequencing in PDMS microreactors. Nat Meth 2011, 8(7), 575-580 DOI: 10.1038/nmeth.1629