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Pu, Y., Zhao, Z., Li, Y., Zou, J., Ma, Q., Zhao, Y., Ke, Y., Zhu, Y., Chen, H., Baker, M. A. B., Ge, H., Sun, Y., Xie, X. S., Bai, F. (2016) Enhanced Efflux Activity Facilitates Drug Tolerance in Dormant Bacterial Cells, Molecular Cell 62, 284-294.

Zhao, Z. W., Xie, X. S., Ge, H. (2016) Nonequilibrium Relaxation of Conformational Dynamics Facilitates Catalytic Reaction in an Elastic Network Model of T7 DNA Polymerase, J Phys Chem B 120(11), 2869–2877.

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Gu, C., Zhang, J., Yang, Y. I., Chen, X., Ge, H., Sun, Y., Su, X., Yang, L., Xie, X. S. and Gao, Y. Q. (2015) DNA Structural Correlation in Short and Long Ranges, J Phys Chem B 119(44), 13980–13990.

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 and Xie X. S. (2015) 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.

Tan, L., Li, Q., and Xie, X. S. (2015) Olfactory sensory neurons transiently express multiple olfactory receptors during development, Mol Syst Biol 11:844.

Cheng, J.-X. and Xie, X. S. (2015) Vibrational spectroscopic imaging of living systems: An emerging platform for biology and medicine, Science 350, aaa8870.

Ji, M., Lewis, S., Camelo-Piragua, S., Ramkissoon, S. H., Snuderl, M., Venneti, S., Fisher-Hubbard, A., Garrard, M., Fu, D., Wang, A. C., Heth, J. A., Maher, C. O., Sanai, N., Johnson, T. D., Freudiger, C. W., Sagher, O., Xie, X. S. and Orringer, D. A. (2015) Detection of human brain tumor infiltration with quantitative stimulated Raman scattering microscopy, Sci Transl Med 7(309), 309ra163.

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Xie, X. S. (2015) Single molecules meet genomics: pinpointing precision medicine, JAMA 313, 2021-2022.

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Chen, H., Shiroguchi, K., Ge, H., and Xie, X. S. (2015) Genome-wide study of mRNA degradation and transcript elongation in Escherichia coli, Mol Syst Biol 11, 781.

Chapman, A. R., He, Z., Lu, S. J., Yong, J., Tan, L. Z., Tang, F. C., and Xie, X. S. (2015) Single cell transcriptome amplification with MALBAC, Plos One 10.

Zhao, Z. W., Roy, R., Gebhardt, J. C., Suter, D. M., Chapman, A. R., and Xie, X. S. (2014) 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 111, 681-686.

Xie, X. S. (2014) Enzyme kinetics, past and present, Science 344, 360-360.

Wang, S. Y., Moffitt, J. R., Dempsey, G. T., Xie, X. S., and Zhuang, X. W. (2014) Characterization and development of photoactivatable fluorescent proteins for single-molecule-based superresolution imaging, P Natl Acad Sci USA 111, 8452-8457.

Jin, J. S., Lian, T. F., Xie, X. S., and Su, X. D. (2014) High-accuracy mapping of protein binding stability on nucleosomal DNA using a single-molecule method, J Mol Cell Biol 6, 438-440.

Fu, D., Zhou, J., Zhu, W. S., Manley, P. W., Wang, Y. K., Hood, T., Wylie, A., and Xie, X. S. (2014) Imaging the intracellular distribution of tyrosine kinase inhibitors in living cells with quantitative hyperspectral stimulated Raman scattering, Nat Chem 6, 615-623.

Fu, D., Yu, Y., Folick, A., Currie, E., Farese, R. V., Tsai, T. H., Xie, X. S., and Wang, M. C. (2014) In Vivo Metabolic Fingerprinting of Neutral Lipids with Hyperspectral Stimulated Raman Scattering Microscopy, Journal of the American Chemical Society 136, 8820-8828.

Fu, D., and Xie, X. S. (2014) Reliable Cell Segmentation Based on Spectral Phasor Analysis of Hyperspectral Stimulated Raman Scattering Imaging Data, Analytical Chemistry 86, 4115-4119.

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Chong, S. S., Chen, C. Y., Ge, H., and Xie, X. S. (2014) Mechanism of transcriptional bursting in bacteria, Cell 158, 314-326.

Bentley, J. N., Ji, M. B., Xie, X. S., and Orringer, D. A. (2014) Real-time image guidance for brain tumor surgery through stimulated Raman scattering microscopy, Expert Rev Anticanc 14, 359-361.

Xu, X. L., Ge, H., Gu, C., Gao, Y. Q., Wang, S. S., Thio, B. J. R., Hynes, J. T., Xie, X. S., and Cao, J. S. (2013) Modeling Spatial Correlation of DNA Deformation: DNA Allostery in Protein Binding, Journal of Physical Chemistry B 117, 13378-13387.

Xie, X. S. (2013) Enzyme Kinetics, Past and Present, Science 342, 1457-1459.

Tan, L. Z., Zong, C. H., and Xie, X. S. (2013) Rare event of histone demethylation can initiate singular gene expression of olfactory receptors, P Natl Acad Sci USA 110, 21148-21152.

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Lamb, E. S., Lefrancois, S., Ji, M. B., Wadsworth, W. J., Xie, X. S., and Wise, F. W. (2013) Fiber optical parametric oscillator for coherent anti-Stokes Raman scattering microscopy, Opt Lett 38, 4154-4157.

Kong, L. J., Ji, M. B., Holtom, G. R., Fu, D., Freudiger, C. W., and Xie, X. S. (2013) Multicolor stimulated Raman scattering microscopy with a rapidly tunable optical parametric oscillator, Opt Lett 38, 145-147.

Kim, S., Brostromer, E., Xing, D., Jin, J. S., Chong, S. S., Ge, H., Wang, S. Y., Gu, C., Yang, L. J., Gao, Y. Q., Su, X. D., Sun, Y. J., and Xie, X. S. (2013) Probing Allostery Through DNA, Science 339, 816-819.

Ji, M., Orringer, D. A., Freudiger, C. W., Ramkissoon, S., Liu, X., Lau, D., Golby, A. J., Norton, I., Hayashi, M., Agar, N. Y., Young, G. S., Spino, C., Santagata, S., Camelo-Piragua, S., Ligon, K. L., Sagher, O., and Xie, X. S. (2013) Rapid, label-free detection of brain tumors with stimulated Raman scattering microscopy, Sci Transl Med 5, 201ra119.

Hou, Y., Fan, W., Yan, L. Y., Li, R., Lian, Y., Huang, J., Li, J. S., Xu, L. Y., Tang, F. C., Xie, X. S., and Qiao, J. (2013) Genome Analyses of Single Human Oocytes, Cell 155, 1492-1506.

Graziano, V., Mcgrath, W. J., Suomalainen, M., Greber, U. F., Freimuth, P., Blainey, P. C., Luo, G. B., Xie, X. S., and Mangel, W. F. (2013) Regulation of a Viral Proteinase by a Peptide and DNA in One-dimensional Space I. Binding to DNA and to Hexon of the Precursor to Protein VI, pVI, of Human Adenovirus, Journal of Biological Chemistry 288, 2059-2067.

Graziano, V., Luo, G. B., Blainey, P. C., Perez-Berna, A. J., Mcgrath, W. J., Flint, S. J., Martin, C. S., Xie, X. S., and Mangel, W. F. (2013) Regulation of a Viral Proteinase by a Peptide and DNA in One-dimensional Space II. Adenovirus Proteinase is Activated in an Unusual One-dimensional Biochemical Reaction Journal of Biological Chemistry 288, 2068-2080.

Gebhardt, J. C. M., Suter, D. M., Roy, R., Zhao, Z. Q. W., Chapman, A. R., Basu, S., Maniatis, T., and Xie, X. S. (2013) Single-molecule imaging of transcription factor binding to DNA in live mammalian cells, Nature Methods 10, 421-+.

Fu, D., Holtom, G., Freudiger, C., Zhang, X., and Xie, X. S. (2013) Hyperspectral Imaging with Stimulated Raman Scattering by Chirped Femtosecond Lasers, Journal of Physical Chemistry B 117, 4634-4640.

Blainey, P. C., Graziano, V., Perez-Berna, A. J., McGrath, W. J., Flint, S. J., Martin, C. S., Xie, X. S., and Mangel, W. F. (2013) 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, Journal of Biological Chemistry 288, 2092-2102.

Zong, C. H., Lu, S. J., Chapman, A. R., and Xie, X. S. (2012) Genome-Wide Detection of Single-Nucleotide and Copy-Number Variations of a Single Human Cell, Science 338, 1622-1626.

Zhang, X., Roeffaers, M. B. J., Basu, S., Daniele, J. R., Fu, D., Freudiger, C. W., Holtom, G. R., and Xie, X. S. (2012) Label-Free Live-Cell Imaging of Nucleic Acids Using Stimulated Raman Scattering Microscopy, Chemphyschem 13, 1054-1059.

Yu, Z. L., Chen, T., Zhang, X. N., Fu, D., Liao, X., Shen, J., Liu, X. X., Zhang, B., Xie, X. S., Su, X. D., Chen, J. Y., and Huang, Y. Y. (2012) Label-free chemical imaging in vivo: three-dimensional non-invasive microscopic observation of amphioxus notochord through stimulated Raman scattering (SRS), Chem Sci 3, 2646-2654.

Shiroguchi, K., Jia, T. Z., Sims, P. A., and Xie, X. S. (2012) Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes, P Natl Acad Sci USA 109, 1347-1352.

Lu, S. J., Zong, C. H., Fan, W., Yang, M. Y., Li, J. S., Chapman, A. R., Zhu, P., Hu, X. S., Xu, L. Y., Yan, L. Y., Bai, F., Qiao, J., Tang, F. C., Li, R. Q., and Xie, X. S. (2012) Probing Meiotic Recombination and Aneuploidy of Single Sperm Cells by Whole-Genome Sequencing, Science 338, 1627-1630.

Lu, F. K., Ji, M., Fu, D., Ni, X., Freudiger, C. W., Holtom, G., and Xie, X. S. (2012) Multicolor stimulated Raman scattering (SRS) microscopy, Mol Phys 110, 1927-1932.

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

Fu, D., Lu, F. K., Zhang, X., Freudiger, C., Pernik, D. R., Holtom, G., and Xie, X. S. (2012) Quantitative Chemical Imaging with Multiplex Stimulated Raman Scattering Microscopy, Journal of the American Chemical Society 134, 3623-3626.

Freudiger, C. W., Pfannl, R., Orringer, D. A., Saar, B. G., Ji, M. B., Zeng, Q., Ottoboni, L., Ying, W., Waeber, C., Sims, J. R., De Jager, P. L., Sagher, O., Philbert, M. A., Xu, X. Y., Kesari, S., Xie, X. S., and Young, G. S. (2012) Multicolored stain-free histopathology with coherent Raman imaging, Lab Invest 92, 1492-1502.

Wang, W. Q., Li, G. W., Chen, C. Y., Xie, X. S., and Zhuang, X. W. (2011) Chromosome Organization by a Nucleoid-Associated Protein in Live Bacteria, Science 333, 1445-1449.

Wang, M. C., Min, W., Freudiger, C. W., Ruvkun, G., and Xie, X. S. (2011) RNAi screening for fat regulatory genes with SRS microscopy, Nature Methods 8, 135-U152.

Wang, K., Freudiger, C. W., Lee, J. H., Saar, B. G., Xie, X. S., and Xu, C. (2011) All fiber, 1064-nm time-lens source for coherent anti-Stokes Raman scattering and stimulated Raman scattering microscopy, Proc Spie 7903.

Sims, P. A., Greenleaf, W. J., Duan, H., and Xie, X. S. (2011) Fluorogenic DNA sequencing in PDMS microreactors, Nat Methods 8, 575-580.

Saar, B. G., Johnston, R. S., Freudiger, C. W., Xie, X. S., and Seibel, E. J. (2011) Coherent Raman scanning fiber endoscopy, Opt Lett 36, 2396-2398.

Saar, B. G., Contreras-Rojas, L. R., Xie, X. S., and Guy, R. H. (2011) Imaging Drug Delivery to Skin with Stimulated Raman Scattering Microscopy, Mol Pharmaceut 8, 969-975.

Roeffaers, M. B. J., Zhang, X., Freudiger, C. W., Saar, B. G., van Ruijven, M., van Dalen, G., Xiao, C. H., and Xie, X. S. (2011) Label-free imaging of biomolecules in food products using stimulated Raman microscopy, Journal of Biomedical Optics 16.

Min, W., Freudiger, C. W., Lu, S. J., and Xie, X. S. (2011) Coherent Nonlinear Optical Imaging: Beyond Fluorescence Microscopy, Annu Rev Phys Chem 62, 507-530.

Li, G. W., and Xie, X. S. (2011) Central dogma at the single-molecule level in living cells, Nature 475, 308-315.

Imitola, J., Cote, D., Rasmussen, S., Xie, X. S., Liu, Y. R., Chitnis, T., Sidman, R. L., Lin, C. P., and Khoury, S. J. (2011) Multimodal coherent anti-Stokes Raman scattering microscopy reveals microglia-associated myelin and axonal dysfunction in multiple sclerosis-like lesions in mice, Journal of Biomedical Optics 16.

Freudiger, C. W., Roeffaers, M. B. J., Zhang, X., Saar, B. G., Min, W., and Xie, X. S. (2011) Optical Heterodyne-Detected Raman-Induced Kerr Effect (OHD-RIKE) Microscopy, Journal of Physical Chemistry B 115, 5574-5581.

Freudiger, C. W., Min, W., Holtom, G. R., Xu, B. W., Dantus, M., and Xie, X. S. (2011) Highly specific label-free molecular imaging with spectrally tailored excitation-stimulated Raman scattering (STE-SRS) microscopy, Nature Photonics 5, 103-109.

Zeng, Y. N., Saar, B. G., Friedrich, M. G., Chen, F., Liu, Y. S., Dixon, R. A., Himmel, M. E., Xie, X. S., and Ding, S. Y. (2010) Imaging Lignin-Downregulated Alfalfa Using Coherent Anti-Stokes Raman Scattering Microscopy, Bioenerg Res 3, 272-277.

Xie, X. S. (2010) Enzymology and Life at the Single Molecule Level, Springer Series Chem 96, 435-448.

Wang, K., Freudiger, C. W., Lee, J. H., Saar, B. G., Xie, X. S., and Xu, C. (2010) Synchronized time-lens source for coherent Raman scattering microscopy, Opt Express 18, 24019-24024.

Taniguchi, Y., Choi, P. J., Li, G. W., Chen, H. Y., Babu, M., Hearn, J., Emili, A., and Xie, X. S. (2010) Quantifying E-coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells, Science 329, 533-538.

Saar, B. G., Zeng, Y. N., Freudiger, C. W., Liu, Y. S., Himmel, M. E., Xie, X. S., and Ding, S. Y. (2010) Label-Free, Real-Time Monitoring of Biomass Processing with Stimulated Raman Scattering Microscopy, Angew Chem Int Edit 49, 5476-5479.

Saar, B. G., Freudiger, C. W., Reichman, J., Stanley, C. M., Holtom, G. R., and Xie, X. S. (2010) Video-Rate Molecular Imaging in Vivo with Stimulated Raman Scattering, Science 330, 1368-1370.

Min, W., Jiang, L., and Xie, X. S. (2010) Complex Kinetics of Fluctuating Enzymes: Phase Diagram Characterization of a Minimal Kinetic Scheme, Chem-Asian J 5, 1129-1138.

Lu, S. J., Min, W., Chong, S. S., Holtom, G. R., and Xie, X. S. (2010) Label-free imaging of heme proteins with two-photon excited photothermal lens microscopy, Appl Phys Lett 96.

Kim, S., Schroeder, C. M., and Xie, X. S. (2010) Single-Molecule Study of DNA Polymerization Activity of HIV-1 Reverse Transcriptase on DNA Templates, Journal of Molecular Biology 395, 995-1006.

Chong, S. S., Min, W., and Xie, X. S. (2010) Ground-State Depletion Microscopy: Detection Sensitivity of Single-Molecule Optical Absorption at Room Temperature, J Phys Chem Lett 1, 3316-3322.

Choi, P. J., Xie, X. S., and Shakhnovich, E. I. (2010) Stochastic Switching in Gene Networks Can Occur by a Single-Molecule Event or Many Molecular Steps, Journal of Molecular Biology 396, 230-244.

Sims, P. A., and Xie, X. S. (2009) Probing Dynein and Kinesin Stepping with Mechanical Manipulation in a Living Cell, Chemphyschem 10, 1511-1516.

Saar, B. G., Holtom, G. R., Freudiger, C. W., Ackermann, C., Hill, W., and Xie, X. S. (2009) Intracavity wavelength modulation of an optical parametric oscillator for coherent Raman microscopy, Opt Express 17, 12532-12539.

Murugkar, S., Evans, C. L., Xie, X. S., and Anis, H. (2009) Chemically specific imaging of cryptosporidium oocysts using coherent anti-Stokes Raman scattering (CARS) microscopy, J Microsc-Oxford 233, 244-250.

Min, W., Xie, X. S., and Bagchi, B. (2009) Role of conformational dynamics in kinetics of an enzymatic cycle in a nonequilibrium steady state, J Chem Phys 131, 065104.

Min, W., Lu, S. J., Rueckel, M., Holtom, G. R., and Xie, X. S. (2009) Near-Degenerate Four-Wave-Mixing Microscopy, Nano Lett 9, 2423-2426.

Min, W., Lu, S. J., Chong, S. S., Roy, R., Holtom, G. R., and Xie, X. S. (2009) Imaging chromophores with undetectable fluorescence by stimulated emission microscopy, Nature 461, 1105-1109.

Min, W., Lu, S., Holtom, G. R., and Xie, X. S. (2009) Triple-Resonance Coherent Anti-Stokes Raman Scattering Microspectroscopy, Chemphyschem 10, 344-347.

Lyn, R. K., Kennedy, D. C., Sagan, S. M., Blais, D. R., Rouleau, Y., Pegoraro, A. F., Xie, X. S., Stolow, A., and Pezacki, J. P. (2009) Direct imaging of the disruption of hepatitis C virus replication complexes by inhibitors of lipid metabolism, Virology 394, 130-142.

Lu, J., Min, W., Conchello, J. A., Xie, X. S., and Lichtman, J. W. (2009) Super-Resolution Laser Scanning Microscopy through Spatiotemporal Modulation, Nano Lett 9, 3883-3889.

Kieu, K., Saar, B. G., Holtom, G. R., Xie, X. S., and Wise, F. W. (2009) High-power picosecond fiber source for coherent Raman microscopy, Opt Lett 34, 2051-2053.

Friedman, N., Cai, L., and Xie, X. S. (2009) Stochasticity in Gene Expression as Observed by Single-molecule Experiments in Live Cells, Isr J Chem 49, 333-342.

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Blainey, P. C., Luo, G., Kou, S. C., Mangel, W. F., Verdine, G. L., Bagchi, B., and Xie, X. S. (2009) Nonspecifically bound proteins spin while diffusing along DNA, Nat Struct Mol Biol 16, 1224-1229.

Xie, X. S., Choi, P. J., Li, G. W., Lee, N. K., and Lia, G. (2008) Single-molecule approach to molecular biology in living bacterial cells, Annual Review of Biophysics 37, 417-444.

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Nan, X., Sims, P. A., and Xie, X. S. (2008) Organelle tracking in a living cell with microsecond time resolution and nanometer spatial precision, Chemphyschem 9, 707-712.

Min, W., Xie, X. S., and Bagchi, B. (2008) Two-dimensional reaction free energy surfaces of catalytic reaction: Effects of protein conformational dynamics on enzyme catalysis, Journal of Physical Chemistry B 112, 454-466.

Li, J. J., Chu, Y., Lee, B. Y., and Xie, X. S. (2008) Enzymatic signal amplification of molecular beacons for sensitive DNA detection, Nucleic Acids Res 36, e36.

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Choi, P. J., Cai, L., Frieda, K., and Xie, X. S. (2008) A stochastic single-molecule event triggers phenotype switching of a bacterial cell, Science 322, 442-446.

Bagchi, B., Blainey, P. C., and Xie, X. S. (2008) Diffusion constant of a nonspecifically bound protein undergoing curvilinear motion along DNA, Journal of Physical Chemistry B 112, 6282-6284.

Xiao, J., Elf, J., Li, G., Yu, J., and Xie, X. S. (2007) Imaging gene expression in living cells at the single-molecule level, Single Molecule Techniques: A Laboratory Manual Edited by Paul R. Selvin and Taekjip Ha, Cold Spring Harbor Laboratory Press, Cold Spring Harbor 149-170.

Wright, A. J., Poland, S. P., Girkin, J. M., Freudiger, C. W., Evans, C. L., and Xie, X. S. (2007) Adaptive optics for enhanced signal in CARS microscopy, Opt Express 15, 18209-18219.

Saar, B. G., Park, H. S., Xie, X. S., and Lavrentovich, O. D. (2007) Three-dimensional imaging of chemical bond orientation in liquid crystals by coherent anti-stokes Raman scattering microscopy, Opt Express 15, 13585-13596.

Luo, G., Wang, M., Konigsberg, W. H., and Xie, X. S. (2007) Single-molecule and ensemble fluorescence assays for a functionally important conformational change in T7 DNA polymerase, P Natl Acad Sci USA 104, 12610-12615.

Kim, S. J., Blainey, P. C., Schroeder, C. M., and Xie, X. S. (2007) Multiplexed single-molecule assay for enzymatic activity on flow-stretched DNA, Nature Methods 4, 397-399.

Evans, C. L., Xu, X. Y., Kesari, S., Xie, X. S., Wong, S. T. C., and Young, G. S. (2007) Chemically-selective imaging of brain structures with CARS microscopy, Opt Express 15, 12076-12087.

Elf, J., Li, G. W., and Xie, X. S. (2007) Probing transcription factor dynamics at the single-molecule level in a living cell, Science 316, 1191-1194.

Yu, J., Xiao, J., Ren, X., Lao, K., and Xie, X. S. (2006) Probing gene expression in live cells, one protein molecule at a time, Science 311, 1600-1603.

Xie, X. S., Yu, J., and Yang, W. Y. (2006) Perspective - Living cells as test tubes, Science 312, 228-230.

Xie, X. S., Cheng, J.-X., and Potma, E. (2006) Coherent anti-stokes Raman scattering microscopy, In Handbook of biological confocal microscopy 3rd ed. Edited by James Pawley, Springer Science, New York, pp 595-606, Springer.

Rakic, B., Sagan, S. M., Noestheden, M., Belanger, S., Nan, X. L., Evans, C. L., Xie, X. S., and Pezacki, J. P. (2006) Peroxisome proliferator-activated receptor alpha antagonism inhibits hepatitis C virus replication, Chem Biol 13, 23-30.

Qian, H., and Xie, X. S. (2006) Generalized Haldane equation and fluctuation theorem in the steady-state cycle kinetics of single enzymes, Phys Rev E 74.

Potma, E. O., Evans, C. L., and Xie, X. S. (2006) Heterodyne coherent anti-Stokes Raman scattering (CARS) imaging, Opt Lett 31, 241-243.

Nan, X. L., Potma, E. O., and Xie, X. S. (2006) Nonperturbative chemical imaging of organelle transport in living cells with coherent anti-stokes Raman scattering microscopy, Biophys J 91, 728-735.

Min, W., and Xie, X. S. (2006) Kramers model with a power-law friction kernel: Dispersed kinetics and dynamic disorder of biochemical reactions, Phys Rev E 73.

Min, W., Gopich, I. V., English, B. P., Kou, S. C., Xie, X. S., and Szabo, A. (2006) When does the Michaelis-Menten equation hold for fluctuating enzymes?, Journal of Physical Chemistry B 110, 20093-20097.

Luo, G., Andricioaei, I., Xie, X. S., and Karplus, M. (2006) Dynamic distance disorder in proteins is caused by trapping, The Journal of Physical Chemistry B 110, 9363-9367.

Legare, F., Evans, C. L., Ganikhanov, F., and Xie, X. S. (2006) Towards CARS endoscopy, Opt Express 14, 4427-4432.

Lee, J. B., Hite, R. K., Hamdan, S. M., Xie, X. S., Richardson, C. C., and van Oijen, A. M. (2006) DNA primase acts as a molecular brake in DNA replication, Nature 439, 621-624.

Ganikhanov, F., Evans, C. L., Saar, B. G., and Xie, X. S. (2006) High-sensitivity vibrational imaging with frequency modulation coherent anti-Stokes Raman scattering (FM CARS) microscopy, Opt Lett 31, 1872-1874.

Ganikhanov, F., Carrasco, S., Xie, X. S., Katz, M., Seitz, W., and Kopf, D. (2006) Broadly tunable dual-wavelength light source for coherent anti-Stokes Raman scattering microscopy, Opt Lett 31, 1292-1294.

Friedman, N., Cai, L., and Xie, X. S. (2006) Linking Stochastic Dynamics to Population Distribution: An Analytical Framework of Gene Expression, Physical Review Letters 97.

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

Cai, L., Friedman, N., and Xie, X. S. (2006) Stochastic protein expression in individual cells at the single molecule level, Nature 440, 358-362.

Blainey, P. C., van Oijent, A. M., Banerjee, A., Verdine, G. L., and Xie, X. S. (2006) A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA, P Natl Acad Sci USA 103, 5752-5757.

Potma, E. O., and Xie, X. S. (2005) Direct visualization of lipid phase segregation in single lipid bilayers with coherent anti-stokes Raman scattering microscopy, Chemphyschem 6, 77-79.

Nan, X. L., Sims, P. A., Chen, P., and Xie, X. S. (2005) Observation of individual microtubule motor steps in living cells with endocytosed quantum dots, Journal of Physical Chemistry B 109, 24220-24224.

Min, W., Luo, G. B., Cherayil, B. J., Kou, S. C., and Xie, X. S. (2005) Observation of a power law memory kernel for distance fluctuation within a single protein molecule, Fluctuations and Noise in Biological, Biophysical, and Biomedical Systems III 5841, 194-204.

Min, W., Luo, G., Cherayil, B. J., Kou, S. C., and Xie, X. S. (2005) Observation of a power-law memory kernel for fluctuations within a single protein molecule, Phys Rev Lett 94, 198302.

Min, W., Jiang, L., Yu, J., Kou, S. C., Qian, H., and Xie, X. S. (2005) Nonequilibrium steady state of a nanometric biochemical system: Determining the thermodynamic driving force from single enzyme turnover time traces, Nano Lett 5, 2373-2378.

Min, W., English, B. P., Luo, G., Cherayil, B. J., Kou, S. C., and Xie, X. S. (2005) Fluctuating enzymes: lessons from single-molecule studies, Acc Chem Res 38, 923-931.

Krug, J. T., Sanchez, E. J., and Xie, X. S. (2005) Fluorescence quenching in tip-enhanced nonlinear optical microscopy, Appl Phys Lett 86.

Kou, S. C., Cherayil, B. J., Min, W., English, B. P., and Xie, X. S. (2005) Single-molecule Michaelis-Menten equations, Journal of Physical Chemistry B 109, 19068-19081.

Kou, S., Sunney Xie, X., and Liu, J. S. (2005) Bayesian analysis of single molecule experimental data, Journal of the Royal Statistical Society: Series C (Applied Statistics) 54, 469-506.

Evans, C. L., Potma, E. O., Puoris'haag, M., Cote, D., Lin, C. P., and Xie, X. S. (2005) Chemical imaging of tissue in vivo with video-rate coherent anti-Stokes Raman scattering microscopy, P Natl Acad Sci USA 102, 16807-16812.

Debnath, P., Min, W., Xie, X. S., and Cherayil, B. J. (2005) Multiple time scale dynamics of distance fluctuations in a semiflexible polymer: a one-dimensional generalized Langevin equation treatment, J Chem Phys 123, 204903.

Rech, I., Luo, G., Ghioni, M., Yang, H., Xie, X. S., and Cova, S. (2004) Photon-timing detector module for single-molecule spectroscopy with 60-ps resolution, Selected Topics in Quantum Electronics, IEEE Journal of 10, 788-795.

Potma, E. O., Xie, X. S., Muntean, L., Preusser, J., Jones, D., Ye, J., Leone, S. R., Hinsberg, W. D., and Schade, W. (2004) Chemical imaging of photoresists with coherent anti-Stokes Raman scattering (CARS) microscopy, Journal of Physical Chemistry B 108, 1296-1301.

Potma, E. O., and Xie, X. S. (2004) CARS microscopy for biology and medicine, Optics and photonics news 15, 40-45.

Nan, X., Yang, W. Y., and Xie, X. (2004) CARS microscopy lights up lipids in living cells, Biophotonics International 11, 44-47.

Kou, S. C., and Xie, X. S. (2004) Generalized Langevin Equation with Fractional Gaussian Noise: Subdiffusion within a Single Protein Molecule, Physical Review Letters 93, 180603.

Evans, C. L., Potma, E. O., and Xie, X. S. (2004) Coherent anti-stokes raman scattering spectral interferometry: determination of the real and imaginary components of nonlinear susceptibility chi(3) for vibrational microscopy, Opt Lett 29, 2923-2925.

Cotlet, M., Masuo, S., Luo, G., Hofkens, J., Van der Auweraer, M., Verhoeven, J., Mullen, K., Xie, X. S., and De Schryver, F. (2004) Probing conformational dynamics in single donor-acceptor synthetic molecules by means of photoinduced reversible electron transfer, Proc Natl Acad Sci U S A 101, 14343-14348.

Cheng, J. X., and Xie, X. S. (2004) Coherent anti-Stokes Raman scattering microscopy: Instrumentation, theory, and applications, Journal of Physical Chemistry B 108, 827-840.

Yang, H., Luo, G. B., Karnchanaphanurach, P., Louie, T. M., Rech, I., Cova, S., Xun, L. Y., and Xie, X. S. (2003) Protein conformational dynamics probed by single-molecule electron transfer, Science 302, 262-266.

van Oijen, A. M., Blainey, P. C., Crampton, D. J., Richardson, C. C., Ellenberger, T., and Xie, X. S. (2003) Single-molecule kinetics of lambda exonuclease reveal base dependence and dynamic disorder, Science 301, 1235-1238.

Potma, E. O., and Xie, X. S. (2003) Detection of single lipid bilayers with coherent anti-Stokes Raman scattering (CARS) microscopy, J Raman Spectrosc 34, 642-650.

Potma, E. O., Evans, C., Xie, X. S., Jones, R. J., and Ye, J. (2003) Picosecond-pulse amplification with an external passive optical cavity, Opt Lett 28, 1835-1837.

Pautot, S., Frisken, B. J., Cheng, J.-X., Xie, X. S., and Weitz, D. (2003) Spontaneous formation of lipid structures at oil/water/lipid interfaces, Langmuir 19, 10281-10287.

Nan, X. L., Cheng, J. X., and Xie, X. S. (2003) Vibrational imaging of lipid droplets in live fibroblast cells with coherent anti-Stokes Raman scattering microscopy, J Lipid Res 44, 2202-2208.

Louie, T. M., Xie, X. S., and Xun, L. Y. (2003) Coordinated production and utilization of FADH(2) by NAD(P)H-flavin oxidoreductase and 4-hydroxyphenylacetate 3-monooxygenase, Biochemistry-Us 42, 7509-7517.

Hartschuh, A., Sanchez, E. J., Xie, X. S., and Novotny, L. (2003) High-resolution near-field Raman microscopy of single-walled carbon nanotubes, Physical Review Letters 90.

Dufresne, E. R., Corwin, E. I., Greenblatt, N. A., Ashmore, J., Wang, D. Y., Dinsmore, A. D., Cheng, J. X., Xie, X. S., Hutchinson, J. W., and Weitz, D. A. (2003) Flow and Fracture in Drying Nanoparticle Suspensions, Physical Review Letters 91.

Cheng, J. X., and Xie, X. S. (2003) CARS microscopy: 3D vibrational imaging of proteins, DNA, and lipids in living cells, Springer Ser Chem Ph 71, 608-610.

Cheng, J. X., Pautot, S., Weitz, D. A., and Xie, X. S. (2003) Ordering of water molecules between phospholipid bilayers visualized by coherent anti-Stokes Raman scattering microscopy, P Natl Acad Sci USA 100, 9826-9830.

Yang, H., and Xie, X. S. (2002) Statistical approaches for probing single-molecule dynamics photon-by-photon, Chem Phys 284, 423-437.

Yang, H., and Xie, X. S. (2002) Probing single-molecule dynamics photon by photon, J Chem Phys 117, 10965-10979.

Xie, X. S. (2002) Single-molecule approach to dispersed kinetics and dynamic disorder: Probing conformational fluctuation and enzymatic dynamics, J Chem Phys 117, 11024-11032.

Volkmer, A., Book, L. D., and Xie, X. S. (2002) Time-resolved coherent anti-Stokes Raman scattering microscopy: Imaging based on Raman free induction decay, Appl Phys Lett 80, 1505-1507.

Sanchez, E. J., Krug, J. T., and Xie, X. S. (2002) Ion and electron beam assisted growth of nanometric SimOn structures for near-field microscopy, Rev Sci Instrum 73, 3901-3907.

Potma, E. O., Jones, D. J., Cheng, J. X., Xie, X. S., and Ye, J. (2002) High-sensitivity coherent anti-Stokes Raman scattering microscopy with two tightly synchronized picosecond lasers, Opt Lett 27, 1168-1170.

Louie, T. M., Yang, H., Karnchanaphanurach, P., Xie, X. S., and Xun, L. Y. (2002) FAD is a preferred substrate and an inhibitor of Escherichia coli general NAD(P)H : flavin oxidoreductase, Journal of Biological Chemistry 277, 39450-39455.

Krug, J. T., Sanchez, E. J., and Xie, X. S. (2002) Design of near-field optical probes with optimal field enhancement by finite difference time domain electromagnetic simulation, J Chem Phys 116, 10895-10901.

Jones, D. J., Potma, E. O., Cheng, J. X., Burfeindt, B., Pang, Y., Ye, J., and Xie, X. S. (2002) Synchronization of two passively mode-locked, picosecond lasers within 20 fs for coherent anti-Stokes Raman scattering microscopy, Rev Sci Instrum 73, 2843-2848.

Cheng, J. X., and Xie, X. S. (2002) Green's function formulation for third-harmonic generation microscopy, J Opt Soc Am B 19, 1604-1610.

Cheng, J. X., Volkmer, A., and Xie, X. S. (2002) Theoretical and experimental characterization of coherent anti-Stokes Raman scattering microscopy, J Opt Soc Am B 19, 1363-1375.

Cheng, J. X., Volkmer, A., Book, L. D., and Xie, X. S. (2002) Multiplex coherent anti-stokes Raman scattering microspectroscopy and study of lipid vesicles, Journal of Physical Chemistry B 106, 8493-8498.

Cheng, J. X., Potma, E., and Xie, S. X. (2002) Coherent anti-Stokes Raman scattering correlation spectroscopy: Probing dynamical processes with chemical selectivity, J Phys Chem A 106, 8561-8568.

Cheng, J. X., Jia, Y. K., Zheng, G. F., and Xie, X. S. (2002) Laser-scanning coherent anti-stokes Raman scattering microscopy and applications to cell biology, Biophys J 83, 502-509.

Xie, X. S. (2001) Single-molecule approach to enzymology, Single Mol 2, 229-236.

Volkmer, A., Cheng, J. X., and Xie, X. S. (2001) Vibrational imaging with high sensitivity via epidetected coherent anti-Stokes Raman scattering microscopy, Physical Review Letters 87.

Cheng, J. X., Volkmer, A., Book, L. D., and Xie, X. S. (2001) An epi-detected coherent anti-stokes raman scattering (E-CARS) microscope with high spectral resolution and high sensitivity, Journal of Physical Chemistry B 105, 1277-1280.

Cheng, J. X., Book, L. D., and Xie, X. S. (2001) Polarization coherent anti-Stokes Raman scattering microscopy, Opt Lett 26, 1341-1343.

Zumbusch, A., Holtom, G. R., and Xie, X. S. (1999) Three-dimensional vibrational imaging by coherent anti-Stokes Raman scattering, Physical Review Letters 82, 4142-4145.

Xie, X. S., and Lu, H. P. (1999) Single-molecule enzymology, Journal of Biological Chemistry 274, 15967-15970.

Schenter, G. K., Lu, H. P., and Xie, X. S. (1999) Statistical analyses and theoretical models of single-molecule enzymatic dynamics, J Phys Chem A 103, 10477-10488.

Sanchez, E. J., Novotny, L., and Xie, X. S. (1999) Near-field fluorescence microscopy based on two-photon excitation with metal tips, Physical Review Letters 82, 4014-4017.

Lu, H. P., and Xie, X. S. (1999) Single-molecule spectroscopy studies of molecular dynamics in chemical and biological systems, Z Phys Chem 212, 59-66.

Bai, C. L., Wang, C., Xie, X. S., and Wolynes, P. G. (1999) Single molecule physics and chemistry, P Natl Acad Sci USA 96, 11075-11076.

Ying, L. M., and Xie, X. S. (1998) Fluorescence spectroscopy, exciton dynamics, and photochemistry of single allophycocyanin trimers, Journal of Physical Chemistry B 102, 10399-10409.

Xie, X. S., and Trautman, J. K. (1998) Optical studies of single molecules at room temperature, Annual Review of Physical Chemistry 49, 441-480.

Novotny, L., Sanchez, E. J., and Xie, X. S. (1998) Optical microscopy and spectroscopy beyond the diffraction limit, Laser Techniques for Condensed-Phase and Biological Systems 3273, 194-202.

Novotny, L., Sanchez, E. J., and Xie, X. S. (1998) Near-field optical imaging using metal tips illuminated by higher-order Hermite-Gaussian beams, Ultramicroscopy 71, 21-29.

Lu, H. P., Xun, L. Y., and Xie, X. S. (1998) Single-molecule enzymatic dynamics, Science 282, 1877-1882.

Sanchez, E. J., Novotny, L., Holtom, G. R., and Xie, X. S. (1997) Room-temperature fluorescence imaging and spectroscopy of single molecules by two-photon excitation, J Phys Chem A 101, 7019-7023.

Novotny, L., Bian, R. X., and Xie, X. S. (1997) Theory of nanometric optical tweezers, Physical Review Letters 79, 645-648.

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

Lu, H. P., and Xie, X. S. (1997) Single-molecule kinetics of interfacial electron transfer, Journal of Physical Chemistry B 101, 2753-2757.

Xie, X. S. (1996) Single-moleculespectroscopy and dynamics at room temperature, Accounts Chem Res 29, 598-606.

Xie, X. S., and Dunn, R. C. (1995) Near-Field Single Molecule Spectroscopy, P Soc Photo-Opt Ins 2385, 95-102.

Holtom, G. R., Crowell, R. A., and Xie, X. S. (1995) High-repetition-rate femtosecond optical parametric oscillator–amplifier system near 3 μm, J Optic Soc Am B 12, 1723-1731.

Dunn, R. C., and Xie, X. S. (1995) Characterization of the temporal behavior of ultrashort pulses emerging from a near-field fiber probe, Ultramicroscopy 57, 169-172.

Dunn, R. C., Allen, E. V., Joyce, S. A., Anderson, G. A., and Xie, X. S. (1995) Near-Field Fluorescent Imaging of Single Proteins, Ultramicroscopy 57, 113-117.

Crowell, R. A., Holtom, G. R., and Xie, X. S. (1995) Infrared Free Induction Decay of Liquid Water Molecules, The Journal of Physical Chemistry 99, 1840-1842.

Bian, R. X., Dunn, R. C., Xie, X. S., and Leung, P. T. (1995) Single molecule emission characteristics in near-field microscopy, Physical Review Letters 75, 4772-4775.

Xie, X. S., Holtom, G. R., Mets, L., and Dunn, R. C. (1994) Near-field Time-Resolved Spectroscopy on Single Molecules and Photosynthetic Membranes, Ultrafast Phenomena IX, (Springer-Verlag) 124.

Xie, X. S., and Dunn, R. C. (1994) Probing Single-Molecule Dynamics, Science 265, 361-364.

Dunn, R. C., Holtom, G. R., Mets, L., and Xie, X. S. (1994) Near-field fluorescence imaging and fluorescence lifetime measurement of light harvesting complexes in intact photosynthetic membranes, The Journal of Physical Chemistry 98, 3094-3098.

Du, M., Xie, X., Mets, L., and Fleming, G. R. (1994) Direct observation of ultrafast energy-transfer processes in light harvesting complex II, The Journal of Physical Chemistry 98, 4736-4741.

Crowell, R., Holtom, G., and Xie, Y. (1994) Liquid-water dynamics probed by femtosecond infrared spectroscopy, Ultrafast Phenomena IX, (Springer-Verlag) 60, 156-156.

Rosenthal, S., Du, M., Xie, X., and DiMagno, T. (1993) Femtosecond Spontaneous Emission Studies of Photosynthetic Bacterial Reaction Centers, Ultrafast Phenomena VIII (Springer-Verlag) 539.

Dunn, R. C., Xie, X., and Simon, J. D. (1993) Real-time spectroscopic techniques for probing conformational dynamics of heme proteins, Metallobiochemistry Part C: Spectroscopic and Physical Methods for Probing Metal Ion Environments in Metalloenzymes and Metalloproteins, Academic Press Inc. , 177-198.

Du, M., Xie, X., Mets, L., and Fleming, G. (1993) Direct Observation of Ultrafast Energy Transfer Step in PSI Core Antenna, Chem Phys Lett 201, 535-542.

Rosenthal, S., Scherer, N., Cho, M., Xie, X., Schmidt, M., and Fleming, G. (1992) Femtosecond Solvation Dynamics Studied by Time Resolved Fluorescence and Transient Birefringence, Ultrafast Phenomena VIII (Springer-Verlag) 617.

Lewis, J. W., Goldbeck, R. A., Kliger, D. S., Xie, X., Dunn, R. C., and Simon, J. D. (1992) Time-resolved circular dichroism spectroscopy: experiment, theory, and applications to biological systems, The Journal of Physical Chemistry 96, 5243-5254.

Du, M., Rosenthal, S. J., Xie, X., DiMagno, T. J., Schmidt, M., Hanson, D. K., Schiffer, M., Norris, J. R., and Fleming, G. R. (1992) Femtosecond spontaneous-emission studies of reaction centers from photosynthetic bacteria, Proceedings of the National Academy of Sciences 89, 8517-8521.

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

Xie, X., and Simon, J. D. (1991) A picosecond circular dichroism study of photosynthetic reaction centers from Rhodobacter sphaeroides, Biochimica et Biophysica Acta (BBA)-Bioenergetics 1057, 131-139.

Rosenthal, S. J., Xie, X., Du, M., and Fleming, G. R. (1991) Femtosecond solvation dynamics in acetonitrile: Observation of the inertial contribution to the solvent response, The Journal of chemical physics 95, 4715-4718.

Xie, X., and Simon, J. D. (1990) 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), Journal of the American Chemical Society 112, 1130-1136.

Xie, X., and Simon, J. D. (1990) Picosecond circular dichroism spectroscopy: a Jones matrix analysis, J Optic Soc Am B 7, 1673-1684.

Xie, X., and Simon, J. D. (1990) Picosecond time-resolved circular dichroism study of protein relaxation in myoglobin following photodissociation of carbon monoxide, Journal of the American Chemical Society 112, 7802-7803.

Xie, X., and Simon, J. D. (1989) Picosecond Polarization Studies of Protein Motion, Ultrafast Phenomena VII (Springer-Verlag), eds. Harris, C.B.; Ippen, E.P; Mourou, G.A.; Zewail, A.H.

Xie, X., and Simon, J. D. (1989) 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, Optics communications 69, 303-307.

Xie, X., and Simon, J. D. (1989) Photodissociation of chromium hexacarbonyl and hexakis (phenyl isocyanide) chromium in tetrahydrofuran, The Journal of Physical Chemistry 93, 4401-4404.

Xie, X., and Simon, J. D. (1989) Picosecond time resolved circular dichroism spectroscopy: experimental details and applications, Rev Sci Instrum 60, 2614-2627.

Simon, J. D., and Xie, X. (1989) 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), The Journal of Physical Chemistry 93, 291-293.

Simon, J. D., and Xie, X. (1987) Time-resolved studies of solvation: the photodissociation of hexacarbonylchromium in pentanol, Journal of Physical Chemistry 91, 5538-5540.

Simon, J. D., and Xie, X. (1986) Photodissociation of chromium hexacarbonyl in solution: direct observation of the formation of pentacarbonyl (methanol) chromium, The Journal of Physical Chemistry 90, 6751-6753.