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Key Publications

Single Cell Genomics

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

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

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 (6334), 189-194. DOI: 10.1126/science.aak9787.

Yan, L.; Huang, L.; Xu, L.; Huang, J.; Ma, F.; Zhu, X.; Tang, Y.; Liu, M.; Lian, Y.; Liu, P.; et al. Live births after simultaneous avoidance of monogenic diseases and chromosome abnormality by next-generation sequencing with linkage analyses. Proc. Natl. Acad. Sci. U.S.A. 2015, 112 (52), 15964-15969. DOI: 10.1073/pnas.1523297113.

Ni, X.; Zhuo, M.; Su, Z.; Duan, J.; Gao, Y.; Wang, Z.; Zong, C.; Bai, H.; Chapman, A. R.; Zhao, J.; et al. 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.

Hou, Y.; Fan, W.; Yan, L.; Li, R.; Lian, Y.; Huang, J.; Li, J.; Xu, L.; Tang, F.; Xie, X. S.; et al. Genome analyses of single human oocytes. Cell 2013, 155 (7), 1492-1506. DOI: 10.1016/j.cell.2013.11.040.

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.; et al. 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. Methods 2011, 8 (7), 575-580. DOI: 10.1038/nmeth.1629.

Coherent Raman Microscopy

Ji, M.; Orringer, D. A.; Freudiger, C. W.; Ramkissoon, S.; Liu, X.; Lau, D.; Golby, A. J.; Norton, I.; Hayashi, M.; Agar, N. Y. R.; et al. Rapid, label-free detection of brain tumors with stimulated Raman scattering microscopy. Sci Transl Med 2013, 5 (201), 201ra119-201ra119. DOI: 10.1126/scitranslmed.3005954.

Wang, M. C.; Min, W.; Freudiger, C. W.; Ruvkun, G.; Xie, X. S. RNAi screening for fat regulatory genes with SRS microscopy. Nat. Methods 2011, 8 (2), 135-138. DOI: 10.1038/nmeth.1556.

Saar, B. G.; Freudiger, C. W.; Reichman, J.; Stanley, C. M.; Holtom, G. R.; Xie, X. S. Video-rate molecular imaging in vivo with stimulated Raman scattering. Science 2010, 330 (6009), 1368-1370. DOI: 10.1126/science.1197236.

Freudiger, C. W.; Min, W.; Saar, B. G.; Lu, S.; Holtom, G. R.; He, C.; Tsai, J. C.; Kang, J. X.; Xie, X. S. Label-free biomedical imaging with high sensitivity by stimulated Raman scattering microscopy. Science 2008, 322 (5909), 1857-1861. DOI: 10.1126/science.1165758.

Evans, C. L.; Potma, E. O.; Puoris'haag, M.; Côté, D.; Lin, C. P.; Xie, X. S. Chemical imaging of tissue in vivo with video-rate coherent anti-Stokes Raman scattering microscopy. Proc. Natl. Acad. Sci. U.S.A. 2005, 102 (46), 16807-16812. DOI: 10.1073/pnas.0508282102.

Zumbusch, A.; Holtom, G. R.; Xie, X. S. Three-dimensional vibrational imaging by coherent anti-Stoke Raman scattering. Phys. Rev. Lett. 1999, 82 (20), 4142-4145. DOI: 10.1103/PhysRevLett.82.4142.

Gene Expression and Regulation - Live Cell Single Molecule Studies

Taniguchi, Y.; Choi, P. J.; Li, G. W.; Chen, H.; Babu, M.; Hearn, J.; Emili, A.; Xie, X. S. Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science 2010, 329 (5991), 533-538. DOI: 10.1126/science.1188308.

Choi, P. J.; Cai, L.; Frieda, K.; Xie, X. S. A stochastic single-molecule event triggers phenotype switching of a bacterial cell. Science 2008, 322 (5900), 442-446. DOI: 10.1126/science.1161427.

Elf, J.; Li, G. W.; Xie, X. S. Probing transcription factor dynamics at the single-molecule level in a living cell. Science 2007, 316 (5828), 1191-1194. DOI: 10.1126/science.1141967.

Yu, J.; Xiao, J.; Ren, X.; Lao, K.; Xie, X. S. Probing gene expression in live cells, one protein molecule at a Time. Science 2006, 311 (5767), 1600-1603. DOI: 10.1126/science.1119623.

Cai, L.; Friedman, N.; Xie, X. S. Stochastic protein expression in individual cells at the single molecule level. Nature 2006, 440 (7082), 358-362. DOI: 10.1038/nature04599.

Single Molecule Enzymology

Chong, S.; Chen, C.; Ge, H.; Xie, X. S. Mechanism of transcriptional bursting in bacteria. Cell 2014, 158 (2), 314-326. DOI: 10.1016/j.cell.2014.05.038.

Kim, S.; Broströmer, E.; Xing, D.; Jin, J.; Chong, S.; Ge, H.; Wang, S.; Gu, C.; Yang, L.; Gao, Y. Q.; et al. Probing allostery through DNA. Science 2013, 339 (6121), 816-819. DOI: 10.1126/science.1229223.

English, B. P.; Min, W.; van Oijen, A. M.; Lee, K. T.; Luo, G.; Sun, H.; Cherayil, B. J.; Kou, S. C.; Xie, X. S. Ever-fluctuating single enzyme molecules: Michaelis-Menten equation revisited. Nat. Chem. Biol. 2006, 2 (2), 87-94. DOI: 10.1038/nchembio759.

Yang, H.; Luo, G.; Karnchanaphanurach, P.; Louie, T. M.; Rech, I.; Cova, S.; Xun, L.; Xie, X. S. Protein conformational dynamics probed by single-molecule electron transfer. Science 2003, 302 (5643), 262-266. DOI: 10.1126/science.1086911.

Lu, H. P.; Xun, L.; Xie, X. S. Single-molecule enzymatic dynamics. Science 1998, 282 (5395), 1877-1882. DOI: 10.1126/science.282.5395.1877.

Single Molecule Spectroscopy and Imaging

Chong, S.; Min, W.; Xie, X. S. Ground-state depletion microscopy: detection sensitivity of single-molecule optical absorption at room temperature. J. Phys. Chem. Lett. 2010, 1 (23), 3316-3322. DOI: 10.1021/jz1014289.

Min, W.; Lu, S.; Chong, S.; Roy, R.; Holtom, G. R.; Xie, X. S. Imaging chromophores with undetectable fluorescence by stimulated emission microscopy. Nature 2009, 461 (7267), 1105-1109. DOI: 10.1038/nature08438.

Sánchez, E. J.; Novotny, L.; Xie, X. S. Near-field fluorescence microscopy based on two-photon excitation with metal tips. Phys. Rev. Lett. 1999, 82 (20), 4014-4017. DOI: 10.1103/PhysRevLett.82.4014.

Lu, H. P.; Xie, X. S. Single-molecule spectral fluctuations at room temperature. Nature 1997, 385, 143-146.

Sánchez, E. J.; Novotny, L.; Holtom, G. R.; Xie, X. S. Room-temperature fluorescence imaging and spectroscopy of single molecules by two-photon excitation. J. Phys. Chem. A 1998, 102 (25), 4948-4948. DOI: 10.1021/jp981638o.

Xie, X. S.; Dunn, R. C. Probing single molecule dynamics. Science 1994, 265 (5170), 361-364. DOI: 10.1126/science.265.5170.361.


Cao, Y.; Jian, F.; Wang, J.; Yu, Y.; Song, W.; Yisimayi, A.; Wang, J.; An, R.; Chen, X.; Zhang, N.; Wang, Y.; Wang, P.; Zhao, L.; Sun, H.; Yu, L.; Yang, S.; Xiao, T.; Gu, Q.; Shao, F.; Hao, X.; Xu, Y.; Jin, R.; Shen, Z.; Wang, Y.; Xie, X.S. Imprinted SARS-CoV-2 humoral immunity induces convergent Omicron RBD evolution. Nature 2023, 614, 521-529 DOI: 10.1038/s41586-022-05644-7

Cao, Y.; Jian, F.; Zhang, Z.; Yisimayi, A.; Hao, X.; Bao, L.; Yuan, F.; Yu, Y.; Du, S.; Wang, J.; Xiao, T.; Song, W.; Zhang, Y.; Liu, P.; An, R.; Wang, P.; Wang, Y.; Yang, S.; Niu, X.; Zhang, Y.; Gu, Q.; Shao, F.; Hu, Y.; Yin, W.; Zheng, A.; Wang, Y.; Qin, C.; Jin, R.; Xiao, J.; Xie, X.S. Rational identification of potent and broad sarbecovirus-neutralizing antibody cocktails from SARS convalescents. Cell Rep. 2022, 41(12), 111845 DOI: 10.1016/j.celrep.2022.111845

Cao, Y.; Song, W.; Wang, L.; Liu, P.; Yue, C.; Jian, F.; Yu, Y.; Wang, Y.; Yisimayi, A.; Wang, P.; Wang, Y.; Zhu, Q.; Deng, J.; Fu, W.; Yu, L.; Zhang, N.; Wang, J.; Xiao, T.; An, R.; Wang, J.; Liu, L.; Yang, S.; Niu, X.; Gu, Q.; Shao, F.; Hao, X.; Meng, B.; Gupta, R.K.; Jin, R.; Wang, Y.; Xie, X.S.; Wang, X. Characterization of the enhanced infectivity and antibody evasion of Omicron BA.2.75. Cell Host Microbe 2022, 30(11), 1527-1539 DOI: 10.1016/j.chom.2022.09.018

Cao, Y.; Yisimayi, A.; Jian, F.; Song, W.; Xiao, T.; Wang, L.; Du, S.; Wang, J.; Wang, J.; Li, Q.; Chen, X.; Yu, Y.; Wang, P.; Zhang, Z.; Liu, P.; An, R.; Hao, X.; Wang, Y.; Wang, J.; Feng, R.; Sun, H.; Zhao, L.; Zhang, W.; Zhao, D.; Zheng, J.; Yu, L.; Li, C.; Zhang, N.; Wang, R.; Niu, X.; Yang, S.; Song, X.; Chai, Y.; He, Y.; Shi, Y.; Zheng, L.; Li, Z.; Gu, Q.; Shao, F.; Huang, W.; Jin, R.; Shen, Z.; Wang, Y.; Wang, X.; Xiao, J.; Xie, X.S. BA.2.12.1, BA.4 and BA.5 escape antibodies elicited by Omicron infection. Nature 2022, 608, 593-602 DOI: 10.1038/s41586-022-04980-y

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

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

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