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234. Xie, X.S. Round-Trip Journey of a Physical Chemist. J. Phys. Chem. B 2023, 127(37), 7800-7809 DOI: 10.1021/acs.jpcb.3c05597

233. Hu, M.; Zhang, Y.; Yuan, Y.; Ma, W.; Zheng, Y.; Gu, Q.; Xie, X. S. Correlated protein modules revealing functional coordination of interacting proteins are detected by single-cell proteomics. J. Phys. Chem. B 2023, 127 (27), 6006-6014. DOI: 10.1021/acs.jpcb.3c00014.

232. Cao, Y.; Jian, F.; Wang, J.; Yu, Y.; Song, W.; Yisimayi, A.; Wang, J.; An, R.; Chen, X.; Zhang, N.; et al. Imprinted SARS-CoV-2 humoral immunity induces convergent Omicron RBD evolution. Nature 2023, 614 (7948), 521-529. DOI: 10.1038/s41586-022-05644-7.

231. 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.

230. Cao, Y.; Jian, F.; Zhang, Z.; Yisimayi, A.; Hao, X.; Bao, L.; Yuan, F.; Yu, Y.; Du, S.; Wang, J.; et al. Rational identification of potent and broad sarbecovirus-neutralizing antibody cocktails from SARS convalescents. Cell Rep. 2022, 41 (12). DOI: 10.1016/j.celrep.2022.111845.

229. Cao, Y.; Song, W.; Wang, L.; Liu, P.; Yue, C.; Jian, F.; Yu, Y.; Yisimayi, A.; Wang, P.; Wang, Y.; et al. Characterization of the enhanced infectivity and antibody evasion of Omicron BA.2.75. Cell Host Microbe 2022, 30 (11), 1527-1539.e1525. DOI: 10.1016/j.chom.2022.09.018.

228. Jian, F.; Yu, Y.; Song, W.; Yisimayi, A.; Yu, L.; Gao, Y.; Zhang, N.; Wang, Y.; Shao, F.; Hao, X.; et al. Further humoral immunity evasion of emerging SARS-CoV-2 BA.4 and BA.5 subvariants. Lancet Infect. Dis. 2022, 22 (11), 1535-1537. DOI: 10.1016/S1473-3099(22)00642-9.

227. Wu, H.; Li, X.; Jian, F.; Yisimayi, A.; Zheng, Y.; Tan, L.; Xing, D.; Xie, X. S. Highly sensitive single-cell chromatin accessibility assay and transcriptome coassay with METATAC. Proc. Natl. Acad. Sci. U.S.A. 2022, 119 (40), e2206450119. DOI: 10.1073/pnas.2206450119.

226. Cao, Y.; Yisimayi, A.; Jian, F.; Song, W.; Xiao, T.; Wang, L.; Du, S.; Wang, J.; Li, Q.; Chen, X.; et al. BA.2.12.1, BA.4 and BA.5 escape antibodies elicited by Omicron infection. Nature 2022, 608 (7923), 593-602. DOI: 10.1038/s41586-022-04980-y.

225. Cao, Y.; Wang, J.; Jian, F.; Xiao, T.; Song, W.; Yisimayi, A.; Huang, W.; Li, Q.; Wang, P.; An, R.; et al. Omicron escapes the majority of existing SARS-CoV-2 neutralizing antibodies. Nature 2021, 602 (7898), 657-663. DOI: 10.1038/s41586-021-04385-3.

224. Cao, Y.; Hao, X.; Wang, X.; Wu, Q.; Song, R.; Zhao, D.; Song, W.; Wang, Y.; Yisimayi, A.; Wang, W.; et al. Humoral immunogenicity and reactogenicity of CoronaVac or ZF2001 booster after two doses of inactivated vaccine. Cell Res. 2022, 32 (1), 107-109. DOI: 10.1038/s41422-021-00596-5.

223. 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 (10), 1130-1133. DOI: 10.1038/s41422-021-00555-0.

222. Cao, Y.; Yisimayi, A.; Bai, Y.; Huang, W.; Li, X.; Zhang, Z.; Yuan, T.; An, R.; Wang, J.; Xiao, T.; et al. 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.

221. Xing, D.; Tan, L.; Chang, C.-H.; 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.

220. Tan, L.; Ma, W.; Wu, H.; 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.e717. DOI: 10.1016/j.cell.2020.12.032.

219. Chen, C.; Li, J.; Di, L.; Jing, Q.; Du, P.; Song, C.; Li, J.; Li, Q.; Cao, Y.; Xie, X. S.; et al. MINERVA: a facile strategy for SARS-CoV-2 whole-genome deep sequencing of clinical samples. Mol. Cell 2020, 80 (6), 1123-1134.e1124. DOI: 10.1016/j.molcel.2020.11.030.

218. Du, S.; Cao, Y.; Zhu, Q.; Yu, P.; Qi, F.; Wang, G.; Du, X.; Bao, L.; Deng, W.; Zhu, H.; et al. 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.e1013. DOI: 10.1016/j.cell.2020.09.035.

217. Cao, Y.; Su, B.; Guo, X.; Sun, W.; Deng, Y.; Bao, L.; Zhu, Q.; Zhang, X.; Zheng, Y.; Geng, C.; et al. 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.

216. Su, Q. P.; Zhao, Z. W.; Meng, L.; Ding, M.; Zhang, W.; Li, Y.; Liu, M.; Li, R.; Gao, Y. Q.; Xie, X. S.; et al. Superresolution imaging reveals spatiotemporal propagation of human replication foci mediated by CTCF-organized chromatin structures. Proc. Natl. Acad. Sci. U.S.A. 2020, 117 (26), 15036-15046. DOI: 10.1073/pnas.2001521117.

215. Di, L.; Fu, Y.; Sun, Y.; Li, J.; Liu, L.; Yao, J.; Wang, G.; Wu, Y.; Lao, K.; Lee, R. W.; et al. 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.

214. Huang, L.; Bogale, B.; Tang, Y.; Lu, S.; Xie, X. S.; 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, 116 (28), 14105-14112. DOI: 10.1073/pnas.1907472116.

213. Xiong, L.; Huang, L.; Tian, F.; Lu, S.; Xie, X. S. 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.

212. Tan, L.; Xing, D.; Daley, N.; Xie, X. S. Three-dimensional genome structures of single sensory neurons in mouse visual and olfactory systems. Nat. Struct. Mol. Biol. 2019, 26 (4), 297-307. DOI: 10.1038/s41594-019-0205-2.

211. Ji, M.; Arbel, M.; Zhang, L.; Freudiger, C. W.; Hou, S. S.; Lin, D.; Yang, X.; Bacskai, B. J.; Xie, X. S. Label-free imaging of amyloid plaques in Alzheimer's disease with stimulated Raman scattering microscopy. Sci. Adv. 2018, 4 (11), eaat7715. DOI: 10.1126/sciadv.aat7715.

210. Tan, L.; Xing, D.; Chang, C. H.; Li, H.; Xie, X. S. Three-dimensional genome structures of single diploid human cells. Science 2018, 361 (6405), 924-928. DOI: 10.1126/science.aat5641.

209. Wu, H.; Shen, X.; Huang, L.; Zeng, Y.; Gao, Y.; Shao, L.; Lu, B.; Zhong, Y.; Miao, B.; Xu, Y.; et al. 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.

208. Tan, L.; Xie, X. S. 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.

207. 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.

206. 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.

205. Xu, J.; Zhang, Z.; Niu, W.; Yang, Q.; Yao, G.; Shi, S.; Jin, H.; Song, W.; Chen, L.; Zhang, X.; et al. Mapping allele with resolved carrier status of Robertsonian and reciprocal translocation in human preimplantation embryos. Proc. Natl. Acad. Sci. U.S.A. 2017, 114 (41), E8695-E8702. DOI: 10.1073/pnas.1715053114.

204. Gao, Y.; Ni, X.; Guo, H.; Su, Z.; Ba, Y.; Tong, Z.; Guo, Z.; Yao, X.; Chen, X.; Yin, J.; et al. Single-cell sequencing deciphers a convergent evolution of copy number alterations from primary to circulating tumor cells. Genome Res. 2017, 27 (8), 1312-1322. DOI: 10.1101/gr.216788.116.

203. 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.

202. Zhou, Y.; Wang, P.; Tian, F.; Gao, G.; Huang, L.; Wei, W.; Xie, X. S. Painting a specific chromosome with CRISPR/Cas9 for live-cell imaging. Cell Res. 2017, 27 (2), 298-301. DOI: 10.1038/cr.2017.9.

201. Yang, W.; Li, A.; Suo, Y.; Lu, F. K.; Sunney Xie, X. Simultaneous two-color stimulated Raman scattering microscopy by adding a fiber amplifier to a 2 ps OPO-based SRS microscope. Opt. Lett. 2017, 42 (3), 523-526. DOI: 10.1364/OL.42.000523.

200. Fu, D.; Yang, W.; Xie, X. S. Label-free imaging of neurotransmitter acetylcholine at neuromuscular junctions with stimulated Raman scattering. J. Am. Chem. Soc. 2017, 139 (2), 583-586. DOI: 10.1021/jacs.6b10727.

199. Tian, F.; Yang, W.; Mordes, D. A.; Wang, J.-Y.; Salameh, J. S.; Mok, J.; Chew, J.; Sharma, A.; Leno Duran, E.; Suzuki-Uematsu, S.; et al. Monitoring peripheral nerve degeneration in ALS by label-free stimulated Raman scattering imaging. Nat. Commun. 2016, 7 (1), 13283. DOI: 10.1038/ncomms13283.

198. Xu, J.; Fang, R.; Chen, L.; Chen, D.; Xiao, J.-P.; Yang, W.; Wang, H.; Song, X.; Ma, T.; Bo, S.; et al. Noninvasive chromosome screening of human embryos by genome sequencing of embryo culture medium for in vitro fertilization. Proc. Natl. Acad. Sci. U.S.A. 2016, 113 (42), 11907-11912. DOI: 10.1073/pnas.1613294113.

197. 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, 44 (13), e118-e118. DOI: 10.1093/nar/gkw436.

196. Lu, F.; Calligaris, D.; Olubiyi, O. I.; Norton, I.; Yang, W.; Santagata, S.; Xie, X. S.; Golby, A. J.; Agar, N. Y. R. Label-free neurosurgical pathology with stimulated Raman imaging. Cancer Res. 2016, 76 (12), 3451-3462. DOI: 10.1158/0008-5472.CAN-16-0270.

195. Pu, Y.; Zhao, Z.; Li, Y.; Zou, J.; Ma, Q.; Zhao, Y.; Ke, Y.; Zhu, Y.; Chen, H.; Baker, Matthew A. B.; et al. Enhanced efflux activity facilitates drug tolerance in dormant bacterial cells. Mol. Cell 2016, 62 (2), 284-294. DOI: 10.1016/j.molcel.2016.03.035.

194. Zhao, Z. W.; Xie, X. S.; Ge, H. Nonequilibrium relaxation of conformational dynamics facilitates catalytic reaction in an elastic network model of T7 DNA polymerase. J. Phys. Chem. B 2016, 120 (11), 2869-2877. DOI: 10.1021/acs.jpcb.5b11002.

193. 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.

192. Tan, L.; Li, Q.; Xie, X. S. Olfactory sensory neurons transiently express multiple olfactory receptors during development. Mol. Syst. Biol. 2015, 11 (12), 844. DOI: 10.15252/msb.20156639.

191. Cheng, J. X.; Xie, X. S. Vibrational spectroscopic imaging of living systems: an emerging platform for biology and medicine. Science 2015, 350 (6264), aaa8870. DOI: 10.1126/science.aaa8870.

190. Gu, C.; Zhang, J.; Yang, Y. I.; Chen, X.; Ge, H.; Sun, Y.; Su, X.; Yang, L.; Xie, S.; Gao, Y. Q. DNA structural correlation in short and long ranges. J. Phys. Chem. B 2015, 119 (44), 13980-13990. DOI: 10.1021/acs.jpcb.5b06217.

189. Ji, M.; Lewis, S.; Camelo-Piragua, S.; Ramkissoon, S. H.; Snuderl, M.; Venneti, S.; Fisher-Hubbard, A.; Garrard, M.; Fu, D.; Wang, A. C.; et al. Detection of human brain tumor infiltration with quantitative stimulated Raman scattering microscopy. Sci Transl Med 2015, 7 (309), 309ra163-309ra163. DOI: 10.1126/scitranslmed.aab0195.

188. 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. U.S.A. 2015, 112 (38), 11923-11928. DOI: 10.1073/pnas.1513988112.

187. Lu, F. K.; Basu, S.; Igras, V.; Hoang, M. P.; Ji, M.; Fu, D.; Holtom, G. R.; Neel, V. A.; Freudiger, C. W.; Fisher, D. E.; et al. Label-free DNA imaging in vivo with stimulated Raman scattering microscopy. Proc. Natl. Acad. Sci. U.S.A. 2015, 112 (37), 11624-11629. DOI: 10.1073/pnas.1515121112.

186. Huang, L.; Ma, F.; Chapman, A.; Lu, S.; Xie, X. S. Single-cell whole-genome amplification and sequencing: methodology and applications. Annu Rev Genomics Hum Genet 2015, 16 (1), 79-102. DOI: 10.1146/annurev-genom-090413-025352.

185. Xie, X. S. Single molecules meet genomics: pinpointing precision medicine. JAMA 2015, 313 (20), 2021-2022. DOI: 10.1001/jama.2015.5533.

184. Chen, Z.; Duan, H.; Qiao, S.; Zhou, W.; Qiu, H.; Kang, L.; Xie, X. S.; Huang, Y. Fluorogenic sequencing using halogen-fluorescein-labeled nucleotides. Chembiochem 2015, 16 (8), 1153-1157. DOI: 10.1002/cbic.201500117.

183. 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.

182. Ge, H.; Qian, H.; Xie, X. S. Stochastic phenotype transition of a single cell in an Intermediate region of gene state switching. Phys. Rev. Lett. 2015, 114 (7), 078101. DOI: 10.1103/PhysRevLett.114.078101.

181. 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. DOI: 10.15252/msb.20145794.

180. Kou, S. C.; Xie, X. S. Generalized langevin equation with fractional gaussian noise: subdiffusion within a single protein molecule. Phys. Rev. Lett. 2004, 93 (18), 180603. DOI: 10.1103/PhysRevLett.93.180603.

179. Jin, J.; Lian, T.; Sunney Xie, X.; Su, X.-D. High-accuracy mapping of protein binding stability on nucleosomal DNA using a single-molecule method. J Mol Cell Biol 2014, 6 (5), 438-440. DOI: 10.1093/jmcb/mju033.

178. 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.

177. Fu, D.; Zhou, J.; Zhu, W. S.; Manley, P. W.; Wang, Y. K.; Hood, T.; Wylie, A.; Xie, X. S. Imaging the intracellular distribution of tyrosine kinase inhibitors in living cells with quantitative hyperspectral stimulated Raman scattering. Nat. Chem. 2014, 6 (7), 614-622. DOI: 10.1038/nchem.1961.

176. Fu, D.; Yu, Y.; Folick, A.; Currie, E.; Farese, R. V., Jr.; Tsai, T. H.; Xie, X. S.; Wang, M. C. In vivo metabolic fingerprinting of neutral lipids with hyperspectral stimulated Raman scattering microscopy. J. Am. Chem. Soc. 2014, 136 (24), 8820-8828. DOI: 10.1021/ja504199s.

175. Wang, S.; Moffitt, J. R.; Dempsey, G. T.; Xie, X. S.; Zhuang, X. Characterization and development of photoactivatable fluorescent proteins for single-molecule–based superresolution imaging. Proc. Natl. Acad. Sci. U.S.A. 2014, 111 (23), 8452-8457. DOI: 10.1073/pnas.1406593111.

174. Fu, D.; Xie, X. S. Reliable cell segmentation based on spectral phasor analysis of hyperspectral stimulated Raman scattering imaging data. Anal. Chem. 2014, 86 (9), 4115-4119. DOI: 10.1021/ac500014b.

173. Bentley, J. N.; Ji, M.; Xie, X. S.; Orringer, D. A. Real-time image guidance for brain tumor surgery through stimulated Raman scattering microscopy. Expert Rev Anticancer Ther 2014, 14 (4), 359-361. DOI: 10.1586/14737140.2013.877844.

172. Freudiger, C. W.; Yang, W.; Holtom, G. R.; Peyghambarian, N.; Xie, X. S.; Kieu, K. Q. Stimulated Raman scattering microscopy with a robust fibre laser source. Nat. Photonics 2014, 8 (2), 153-159. DOI: 10.1038/nphoton.2013.360.

171. Zhao, Z. W.; Roy, R.; Gebhardt, J. C. M.; Suter, D. M.; Chapman, A. R.; Xie, X. S. Spatial organization of RNA polymerase II inside a mammalian cell nucleus revealed by reflected light-sheet superresolution microscopy. Proc. Natl. Acad. Sci. U.S.A. 2014, 111 (2), 681-686. DOI: 10.1073/pnas.1318496111.

170. Tan, L.; Zong, C.; Xie, X. S. Rare event of histone demethylation can initiate singular gene expression of olfactory receptors. Proc. Natl. Acad. Sci. U.S.A. 2013, 110 (52), 21148-21152. DOI: 10.1073/pnas.1321511111.

169. 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.

168. Xie, X. S. Enzyme kinetics, past and present. Science 2013, 342 (6165), 1457-1459. DOI: 10.1126/science.1248859.

167. 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.

166. 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.

165. Lamb, E. S.; Lefrancois, S.; Ji, M.; Wadsworth, W. J.; Sunney Xie, X.; Wise, F. W. Fiber optical parametric oscillator for coherent anti-Stokes Raman scattering microscopy. Opt. Lett. 2013, 38 (20), 4154-4157. DOI: 10.1364/OL.38.004154.

164. 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.

163. Gebhardt, J. C. M.; Suter, D. M.; Roy, R.; Zhao, Z. W.; Chapman, A. R.; Basu, S.; Maniatis, T.; Xie, X. S. Single-molecule imaging of transcription factor binding to DNA in live mammalian cells. Nat. Methods 2013, 10 (5), 421-426. DOI: 10.1038/nmeth.2411.

162. Fu, D.; Holtom, G.; Freudiger, C.; Zhang, X.; Xie, X. S. Hyperspectral imaging with stimulated Raman scattering by chirped femtosecond lasers. J. Phys. Chem. B 2013, 117 (16), 4634-4640. DOI: 10.1021/jp308938t.

161. 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.

160. Blainey, P. C.; Graziano, V.; Pérez-Berná, A. J.; McGrath, W. J.; Flint, S. J.; San Martín, C.; Xie, X. S.; Mangel, W. F. Regulation of a viral proteinase by a peptide and DNA in one-dimensional Space: IV. viral proteinase slides along DNA to locate and process its substrates. J. Biol. Chem. 2013, 288 (3), 2092-2102. DOI: 10.1074/jbc.M112.407460.

159. Kong, L.; Ji, M.; Holtom, G. R.; Fu, D.; Freudiger, C. W.; Xie, X. S. Multicolor stimulated Raman scattering microscopy with a rapidly tunable optical parametric oscillator. Opt. Lett. 2013, 38 (2), 145-147. DOI: 10.1364/OL.38.000145.

158. 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.

157. 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.

156. Freudiger, C. W.; Pfannl, R.; Orringer, D. A.; Saar, B. G.; Ji, M.; Zeng, Q.; Ottoboni, L.; Ying, W.; Waeber, C.; Sims, J. R.; et al. Multicolored stain-free histopathology with coherent Raman imaging. Lab. Invest. 2012, 92 (10), 1492-1502. DOI: 10.1038/labinvest.2012.109.

155. Lu, F. K.; Ji, M.; Fu, D.; Ni, X.; Freudiger, C. W.; Holtom, G.; Xie, X. S. Multicolor stimulated Raman scattering microscopy. Mol Phys 2012, 110 (15-16), 1927-1932. DOI: 10.1080/00268976.2012.695028.

154. Lefrancois, S.; Fu, D.; Holtom, G. R.; Kong, L.; Wadsworth, W. J.; Schneider, P.; Herda, R.; Zach, A.; Sunney Xie, X.; Wise, F. W. Fiber four-wave mixing source for coherent anti-Stokes Raman scattering microscopy. Opt. Lett. 2012, 37 (10), 1652-1654. DOI: 10.1364/OL.37.001652.

153. Yu, Z.; Chen, T.; Zhang, X.; Fu, D.; Liao, X.; Shen, J.; Liu, X.; Zhang, B.; Xie, X. S.; Su, X. D.; et al. Label-free chemical imaging in vivo: three-dimensional non-invasive microscopic observation of amphioxus notochord through Stimulated Raman Scattering (SRS). Chem. Sci. 2012, 3 (8), 2646-2654, 10.1039/C2SC20316B. DOI: 10.1039/C2SC20316B.

152. Zhang, X.; Roeffaers, M. B. J.; Basu, S.; Daniele, J. R.; Fu, D.; Freudiger, C. W.; Holtom, G. R.; Xie, X. S. Label-free live-cell imaging of nucleic acids using stimulated Raman scattering microscopy. Chemphyschem 2012, 13 (4), 1054-1059. DOI: 10.1002/cphc.201100890.

151. Fu, D.; Lu, F. K.; Zhang, X.; Freudiger, C.; Pernik, D. R.; Holtom, G.; Xie, X. S. Quantitative chemical imaging with multiplex stimulated Raman scattering microscopy. J. Am. Chem. Soc. 2012, 134 (8), 3623-3626. DOI: 10.1021/ja210081h.

150. 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.

149. Wang, W.; Li, G. W.; Chen, C.; Xie, X. S.; Zhuang, X. Chromosome organization by a nucleoid-associated protein in live bacteria. Science 2011, 333 (6048), 1445-1449. DOI: 10.1126/science.1204697.

148. 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.

147. Saar, B. G.; Johnston, R. S.; Freudiger, C. W.; Xie, X. S.; Seibel, E. J. Coherent Raman scanning fiber endoscopy. Opt. Lett. 2011, 36 (13), 2396-2398. DOI: 10.1364/OL.36.002396.

146. Li, G. W.; Xie, X. S. Central dogma at the single-molecule level in living cells. Nature 2011, 475 (7356), 308-315. DOI: 10.1038/nature10315.

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38. Bai, C.; Wang, C.; Xie, X. S.; Wolynes, P. G. Single molecule physics and chemistry. Proc. Natl. Acad. Sci. U.S.A. 1999, 96 (20), 11075-11076. DOI: 10.1073/pnas.96.20.11075.

37. Lu, H. P.; Xie, X. S. Single-molecule spectroscopy studies of molecular dynamics in chemical and biological systems. Z Phys Chem (N F) 1999, 212 (1), 59-66. DOI: 10.1524/zpch.1999.212.Part_1.059.

36. Xie, X. S.; Lu, H. P. Single-molecule enzymology. J. Biol. Chem. 1999, 274 (23), 15967-15970. DOI: 10.1074/jbc.274.23.15967.

35. 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.

34. 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.

33. 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.

32. Ying, L.; Xie, X. S. Fluorescence spectroscopy, exciton dynamics, and photochemistry of single allophycocyanin trimers. J. Phys. Chem. B 1998, 102 (50), 10399-10409. DOI: 10.1021/jp983227d.

31. Xie, X. S.; Trautman, J. K. Optical studies of single molecules at room temperature. Annu Rev Phys Chem 1998, 49 (1), 441-480. DOI: 10.1146/annurev.physchem.49.1.441.

30. 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.

29. Novotny, L.; Sánchez, E. J.; Xie, X. S. Near-field optical imaging using metal tips illuminated by higher-order Hermite–Gaussian beams. Ultramicroscopy 1998, 71 (1), 21-29. DOI: 10.1016/S0304-3991(97)00077-6.

28. Novotny, L.; Bian, R. X.; Xie, X. S. Theory of nanometric optical tweezers. Phys. Rev. Lett. 1997, 79 (4), 645-648. DOI: 10.1103/PhysRevLett.79.645.

27. Lu, H. P.; Xie, X. S. Single-molecule kinetics of interfacial electron transfer. J. Phys. Chem. B 1997, 101 (15), 2753-2757. DOI: 10.1021/jp9634518.

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

25. Xie, X. S. Single-molecule spectroscopy and dynamics at room temperature. Acc. Chem. Res. 1996, 29 (12), 598-606. DOI: 10.1021/ar950246m.

24. Bian, R. X.; Dunn, R. C.; Xie, X. S.; Leung, P. T. Single molecule emission characteristics in near-field microscopy. Phys. Rev. Lett. 1995, 75 (26), 4772-4775. DOI: 10.1103/PhysRevLett.75.4772.

23. Holtom, G. R.; Crowell, R. A.; Xie, X. S. High-repetition-rate femtosecond optical parametric oscillator–amplifier system near 3 μm. J. Opt. Soc. Am. B 1995, 12 (9), 1723-1731. DOI: 10.1364/JOSAB.12.001723.

22. Dunn, R. C.; Xie, X. S. Characterization of the temporal behavior of ultrashort pulses emerging from a near-field fiber probe. Ultramicroscopy 1995, 57 (2), 169-172. DOI: 10.1016/0304-3991(94)00130-F.

21. Dunn, R. C.; Allen, E. V.; Joyce, S. A.; Anderson, G. A.; Sunney Xie, X. Near-field fluorescent imaging of single proteins. Ultramicroscopy 1995, 57 (2), 113-117. DOI: 10.1016/0304-3991(94)00121-3.

20. Crowell, R. A.; Holtom, G. R.; Xie, X. S. Infrared free induction decay of liquid water molecules. J. Phys. Chem. 1995, 99 (7), 1840-1842. DOI: 10.1021/j100007a009.

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

18. Du, M.; Xie, X.; Mets, L.; Fleming, G. R. Direct observation of ultrafast energy-transfer processes in light harvesting complex II. J. Phys. Chem. 1994, 98 (17), 4736-4741. DOI: 10.1021/j100068a041.

17. Dunn, R. C.; Holtom, G. R.; Mets, L.; Xie, X. S. Near-field fluorescence imaging and fluorescence lifetime measurement of light harvesting complexes in intact photosynthetic membranes. J. Phys. Chem. 1994, 98 (12), 3094-3098. DOI: 10.1021/j100063a010.

16. Du, M.; Xie, X.; Jia, Y.; Mets, L.; Fleming, G. R. Direct observation of ultrafast energy transfer in PSI core antenna. Chem. Phys. Lett. 1993, 201 (5), 535-542. DOI: 10.1016/0009-2614(93)85113-3.

15. Du, M.; Rosenthal, S. J.; Xie, X.; DiMagno, T. J.; Schmidt, M.; Hanson, D. K.; Schiffer, M.; Norris, J. R.; Fleming, G. R. Femtosecond spontaneous-emission studies of reaction centers from photosynthetic bacteria. Proc. Natl. Acad. Sci. U.S.A. 1992, 89 (18), 8517-8521. DOI: doi:10.1073/pnas.89.18.8517.

14. Lewis, J. W.; Goldbeck, R. A.; Kliger, D. S.; Xie, X.; Dunn, R. C.; Simon, J. D. Time-resolved circular dichroism spectroscopy: experiment, theory, and applications to biological systems. J. Phys. Chem. 1992, 96 (13), 5243-5254. DOI: 10.1021/j100192a016.

13. Rosenthal, S. J.; Xie, X.; Du, M.; Fleming, G. R. Femtosecond solvation dynamics in acetonitrile: observation of the inertial contribution to the solvent response. J. Chem. Phys. 1991, 95 (6), 4715-4718. DOI: 10.1063/1.461742.

12. Xie, X.; Simon, J. D. Protein conformational relaxation following photodissociation of carbon monoxide from carbonmonoxymyoglobin: picosecond circular dichroism and absorption studies. Biochemistry 1991, 30 (15), 3682-3692. DOI: 10.1021/bi00229a013.

11. Xie, X.; Simon, J. D. A picosecond circular dichroism study of photosynthetic reaction centers from Rhodobacter sphaeroides. Biochim Biophys Acta Bioenerg 1991, 1057 (1), 131-139. DOI: 10.1016/S0005-2728(05)80093-3.

10. Xie, X.; Simon, J. D. Picosecond magnetic circular dichroism spectroscopy. J. Phys. Chem. 1990, 94 (21), 8014-8016. DOI: 10.1021/j100384a006.

9. Xie, X.; Simon, J. D. Picosecond time-resolved circular dichroism study of protein relaxation in myoglobin following photodissociation of carbon monoxide. J. Am. Chem. Soc. 1990, 112 (21), 7802-7803. DOI: 10.1021/ja00177a054.

8. Xie, X.; Simon, J. D. Picosecond circular dichroism spectroscopy: a Jones matrix analysis. J. Opt. Soc. Am. B 1990, 7 (8), 1673-1684. DOI: 10.1364/JOSAB.7.001673.

7. Xie, X.; Simon, J. D. Picosecond time resolved absorption studies of the solvation of Cr(CO)5 in alcohols: a unimolecular kinetic model for the formation of Cr(CO)5(OHR) from photogenerated Cr(CO)5(ROH). J. Am. Chem. Soc. 1990, 112 (3), 1130-1136. DOI: 10.1021/ja00159a037.

6. Xie, X.; Simon, J. D. Picosecond time‐resolved circular dichroism spectroscopy: experimental details and applications. Rev. Sci. Instrum. 1989, 60 (8), 2614-2627. DOI: 10.1063/1.1140681.

5. Xie, X.; Simon, J. D. Photodissociation of chromium hexacarbonyl and hexakis(phenyl isocyanide)chromium in tetrahydrofuran. J. Phys. Chem. 1989, 93 (11), 4401-4404. DOI: 10.1021/j100348a006.

4. Xie, X.; Simon, J. D. High energy and tunable picosecond laser pulses at 1 kHz: synchronously pumping a dye laser with a mode-locked, Q-switched and cavity dumped Nd:YAG laser system. Opt. Commun. 1989, 69 (3), 303-307. DOI: 10.1016/0030-4018(89)90121-1.

3. Simon, J. D.; Xie, X. Photodissociation of chromium hexacarbonyl in 1-propanol and 2-propanol: effect of solvent structure on the mechanisms of formation of Cr(CO)5(OHR) from photogenerated Cr(CO)5(ROH). J. Phys. Chem. 1989, 93 (1), 291-293. DOI: 10.1021/j100338a059.

2. Simon, J. D.; Xie, X. Time-resolved studies of solvation: the photodissociation of hexacarbonylchromium in pentanol. J. Phys. Chem. 1987, 91 (22), 5538-5540. DOI: 10.1021/j100306a007.

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