Weiss Lab:Publications

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Refereed Journal papers

1. Sternklar, S.; S., W.; Fischer, B., Controlling the self-frequency shift and intensity of oscillations with photorefractive crystals. Appl. Optics 1985, 24, 3121.

2. Sternklar, S.; S., W.; Fischer, B., Tunable frequency shifts of photorefractive oscillators. Opt. Lett 1986, 11, 165.

3. Fischer, B.; Sternklar, S.; Weiss, S., Photorefractive oscillation with intracavity image and multimode fiber. Applied Physics Letters 1986, 48, (23), 1567-9.

4. Sternklar, S.; Weiss, S.; Segev, M.; Fischer, B., Beam coupling and locking of lasers using photorefractive four-wave mixing. Opt. Lett. 1986, 11, 528.

5. Sternklar, S.; S., W.; Fischer, B., Double phase conjugate mirror: analysis, demonstration, and applications. Opt. Lett. 1986, 12, 114.

6. Sternklar, S., Weiss, S., Segev, M. and Fischer, B., Mach-Zehnder interferometer with multimode fibers using the double phase conjugate mirror. Appl. Optics 1986, 25, 4518.

7. Sternklar, S.; Weiss, S.; Segev, M.; Fischer, B., Image bearing photorefractive oscillators. Proc. of the 1986 International Optical Computing Conference, Jerusalem 1986, Proceedings of the SPIE, vol. 700, p.173.

8. Sternklar, S.; Weiss, S.; Fischer, B., Optical information processing with the double phase conjugate mirror. Optical Engineering (Bellingham, WA, United States) 1987, 26, (5), 423-7

9. Fischer, B.; S., W.; Sternklar, S., Spatial light modulation and filtering effects in photorefractive wave mixing. Appl. Phys. Lett. 1987, 50, 483.

10. Segev, M.; Weiss, S.; Fischer, B., Coupling of diode laser arrays with photorefractive passive phase conjugate mirrors. Applied Physics Letters 1987, 50, (20), 1397-9.

11. Weiss, S.; Segev, M.; Fischer, B., Line narrowing and self frequency scanning of laser diode arrays coupled to a photorefractive oscillator. IEEE J. Quantum Electron 1988, QE-24, 706.

12. Weiss, S., Segev, M.,Sternklar, S., and Fischer, B., Photorefractive Dynamic Optical Interconnects. Appl. Opt. 1988, 27, 3422.

13. Fischer, B.; Weiss, S., Solvable optimized four-wave mixing configuration with cubic photorefractive crystals. Appl. Phys. Lett. 1988, 53, 257.

14. Fischer, B.; Sternklar. S.; and Weiss, S., Photorefractive Oscillators. IEEE J. Quantum Electron 1989 QE-25, 550.

15. Weiss, S.; Werner, O.; and Fischer, B., Analysis of coupled photorefractive wave-mixing junctions. Opt. Lett. 1989 14, 186.

16. Weiss, S.; Fischer, B., Photorefractive saturable absorptive and dispersive optical bistability. Optics Communications 1989, 70, (6), 515-21.

17. Weiss, S.; Fischer, B., Instabilities and self-pulsation in a ring cavity with a photorefractive wave mixer. Opt. Lett. 1989, 14, (21), 1213-15. 18. Weiss, S.; Segev, S.; Sternklar, S.; Fischer, B., Photorefractive dynamical optical interconnects. Proc. of the 1988 Electro-Optic and Magneto-Optic Materials Conference, Hamburg 1989, Proceedings of the SPIE, vol. 1018.

19. Weiss, S.; Fischer, B., Dynamics of photorefractive nonlinear two-beam coupling and feedback effects. Optical and Quantum Electronics 1990, 22, (Spec. Issue), S17-S45.

20. Eisenstein. G; Wiesenfeld, J.M; Wegener, M.; Sucha, G.; Chemla, D.S.; Weiss, S.; Raybon, G.; and Koren, U., Ultrafast gain dynamics in 1.5m multiple quantum well optical amplifiers. A.P.L. 1990 58, 158.

21. Weiss, S.; Wiesenfeld, J.M; Chemla, D.S.; Raybon, G.; Sucha, G.; Wegener, M.; Eisenstein. G; Burrus, C.A.; Dentai, A.G.; Koren, U.; Miller, B.I.; Temkin, H.; Logan, R.A.; and Tanbun-Ek, T., Carrier capture times in 1.5m multiple quantum well optical amplifiers. A.P.L. 1992 60, 9.

22. Mycek, M. A.; Weiss, S.; Bigot, J. Y.; Schmitt-Rink, S.; Chemla, D. S.; Schaefer, W., Femtosecond time-resolved free-induction decay of room-temperature excitons in GaAs quantum wells. A.P.L. 1992, 60.

23. Weiss, S.; Mycek, M.; Bigot, J.; Schmitt-Rink, S.; Chemla, D. S., Collective effects in excitonic free induction decay: Do semiconductors and atoms emit coherent light in different ways? Physical Review Letters 1992, 69, (18), 2685-2688.

24. Bigot, J.; Mycek, M.; Weiss, S.; Ulbrich, R. G.; Chemla, D. S., Instantaneous frequency dynamics of coherent wave mixing in semiconductor quantum wells. Physical Review Letters 1993, 70, (21), 3307-3310.

25. Weiss, S.; Ogletree, D. F.; Botkin, D.; Salmeron, M.; Chemla, D. S., Ultrafast scanning probe microscopy. Appl. Phys. Lett. 1993, 63, 2567.

26. Weiss, S.; Ogletree, D. F.; Botkin, D.; Salmeron, M.; Chemla, D. S., Towards ultrafast movies of moving atoms. Optics and Photonics News 1993, 36, 4-12.

27. Botkin, D.; Weiss, S.; Sucha, G.; Chemla, D. S.; Wiesenfeld, J. M., Ultrafast dynamics of the optical mode of a 1.5mm multiple quantum well optical amplifier. Appl. Phys. Lett. 1994, 64, 2861.

28. Wiesenfeld, J. M.; Weiss, S.; Botkin, D.; Chemla, D. S., Carrier transport effects in multiple quantum well optical amplifiers. Optical and Quantum Electronics 1994, 26, S731.

29. Bigot, J. Y.; Mycek, M. A.; Weiss, S.; Ulbrich, R. G.; Chemla, D. S., Amplitude decay and instantaneous frequency dynamics of excitonic polarization in semiconductor quantum wells. Coherent Optical Interactions in Semiconductors, edited by R.T. Phillips, Plenum Press, New York, 1994.

30. Chemla, D. S.; Bigot, J.; Mycek, M.; Weiss, S.; Schafer, W., Ultrafast phase dynamics of coherent emission from excitons in GaAs quantum wells. Physical Review. B. Condensed Matter. 1994, 50, (12), 8439-8453.

31. Botkin, D.; Weiss, S.; Ogletree, D. F.; Salmeron, M.; Chemla, D. S., Ultrafast scanning probe microscopy. Proceedings of the SPIE, vol. 2116, Los Angeles 1994.

32. Weiss, S.; Botkin, D.; Ogletree, D. F.; Salmeron, M.; Chemla, D. S., The Ultrafast Response of a scanning Tunneling Microscope. Phys. Stat. Sol. (b) 1995, 188, 343.

33. Botkin, D.; Weiss, S.; Ogletree, D. F.; Salmeron, M.; Chemla, D. S., Design considerations in an ultrafast scanning tunneling microscope. Rev. Sci. Instrum. 1995, 66, 4130.

34. Sucha, G.; Bolton, S. R.; Weiss, S.; Chemla, D. S., Period doubling and quasiperiodicity in additive pulse modelocked lasers. Opt. Lett. 1995, 20, 1794.

35. Ha, T.; Enderle, T.; Ogletree, D. F.; Chemla, D. S.; Selvin, P. R.; Weiss, S., Probing the interaction between two single molecules: fluorescence resonance energy transfer between a single donor and a single acceptor. Proc Natl Acad Sci U S A 1996, 93, (13), 6264-8.

36. Botkin, D.; Glass, J.; Chemla, D. S.; Ogletree, D. F.; Salmeron, M.; Weiss, S., Advances in ultrafast scanning tunneling microscopy. Appl. Phys. Lett. 1996, 69, 1321.

37. Ha, T.; Enderle, T.; Chemla, S.; Selvin, R.; Weiss, S., Single Molecule Dynamics Studied by Polarization Modulation. Physical Review Letters 1996, 77, (19), 3979-3982.

38. Ha, T.; Enderle, T.; Chemla, D. S.; Weiss, S., Dual-molecule spectroscopy: molecular rulers for the study of biological macromolecules. IEEE Journal of Special Topics in Quantum Electronics 1996, 2, 1115.

39. Enderle, T.; Ha, T.; Chemla, D. S.; Magowan, C.; Weiss, S., Surface specific mapping and co-localization of malarial and host proteins in red-blood-cell membrane by dual-color near-field scanning optical microscopy. Proc. Natl. Acad. Sci. USA 1997, 94, 520.

40. Ha, T.; Chemla, D. S.; Enderle, T.; Weiss, S., Single molecule spectroscopy with automated positioning. Appl. Phys. Lett. 1997, 70, 782.

41. Ha, T.; Enderle, T.; Selvin, P. R.; Chemla, D. S.; Weiss, S., Room temperature observation of quantum jumps. Chem. Phys. Lett. 1997, 271, 1.

42. Ha, T.; Chemla, D. S.; Enderle, T.; Weiss, S., Strategy for room temperature spectroscopy of single molecules. Bioimaging 1997, 5, 99.

43. Ha, T.; Glass, J.; Chemla, D. S.; Weiss, S., Hindered rotational diffusion and rotational jumps of single molecules. Phys. Rev. Lett. 1998, 80, 2093.

44. Enderle, T.; Ha, T.; Chemla, D. S.; Weiss, S., Near-field fluorescence microscopy of cells. Ultramicroscopy 1998, 71, (1-4), 303-9.

45. Bruchez, M., Jr.; Moronne, M.; Gin, P.; Weiss, S.; Alivisatos, A. P., Semiconductor nanocrystals as fluorescent biological labels. Science 1998, 281, (5385), 2013-6.

46. U. Banin, M. Bruchez, A.P. Alivisatos, T. Ha, S. Weiss and D.S. Chemla,

Ha, T.; Weiss, S., Dual- and single-molecule fluorescence spectroscopy: towards kinetic observation of single-molecule reactions. Organic Mesoscopic Chemistry 1999, 61-74.

48. Weiss, S., Fluorescence spectroscopy of single biomolecules. Science 1999, 283, (5408), 1676-83.

49. Deniz, A. A.; Dahan, M.; Ha, T.; Grunwell, J.; Faulhaber, A.; Chemla, D. S.; Weiss, S.; Schultz, P. G., Ratiometric single pair FRET on freely diffusing molecules - observation of Förster distance dependence and of sub-populations. Proc. Natl. Acad. Sci. USA 1999, 96, 3670-3675. PMID: 10097095 PMCID: PMC22352.

50. Ha, T.; Ting, A. Y.; Liang, J.; Deniz, A. A.; Chemla, D. S.; Schultz, P. G.; Weiss, S., Temporal fluctuations of fluorescence resonance energy transfer between two dyes conjugated to a single protein. Chemical Physics 1999, 247, (1), 107-118.

51. Dahan, M.; Deniz, A. A.; Ha, T.; Chemla, D. S.; Schultz, P. G.; Weiss, S., Ratiometric measurement and identification of single diffusing molecules. Chemical Physics 1999, 247, (1), 85-106.

52. Ha, T.; Ting, A. Y.; Liang, J.; Caldwell, W. B.; Deniz, A. A.; Chemla, D. S.; Schultz, P. G.; Weiss, S., Single-molecule fluorescence spectroscopy of enzyme conformational dynamics and cleavage mechanism. Proc Natl Acad Sci U S A 1999, 96, (3), 893-8. PMID: 9927664 PMCID: PMC 15321

53. Ha, T.; Laurence, T. A.; Chemla, D. S.; Weiss, S., Polarization Spectroscopy of Single Fluorescent Molecules. Journal of Physical Chemistry B 1999, 103, (33), 6839-6850.

54. Deniz, A.A., Laurence, T.A., Beligere,G.S., Dahan, M., Martin, A.B., Chemla, D.S., Dawson, P.E., Schultz, P.G., and Weiss S., Single-molecule protein folding: Diffusion fluorescence resonance energy transfer studies of the denaturation of chymotrypsin inhibitor 2. Proc Natl Acad Sci U S A 2000, 97, (10), 5179-84.PMid: 10792044 PMCID: PMC25802

55. Lacoste, T. D.; Michalet, X.; Pinaud, F.; Chemla, D. S.; Alivisatos, A. P.; Weiss, S., Ultrahigh-resolution multicolor colocalization of single fluorescent probes. Proc Natl Acad Sci U S A 2000, 97, (17), 9461-6. PMID:10931959 PMCID: PMC16886

56. Weiss, S., Measuring conformational dynamics of biomolecules by single molecule fluorescence spectroscopy. Nat Struct Biol 2000, 7, (9), 724-9. PMID: 10966638

57. Deniz, A. A.; Laurence, T. A.; Dahan, M.; Chemla, D. S.; Schultz, P. G.; Weiss, S., Ratiometric single-molecule studies of freely diffusing biomolecules. Annu Rev Phys Chem 2001, 52, 233-53.PMID: 11326065

58. Dahan, M.; Laurence, T.; Herten, D. P.; Schumacher, A.; Chemla, D. S.; Alivisatos, A. P.; Sauer, M.; Weiss, S., Time-gated biological imaging using colloidal quantum dots. Optics Lett. 2001, 26, (825-827).PMID:18040463

59. Gerion, D.; Pinaud, F.; Williams, S. C.; Parak, W. J.; Zanchet, D.; Weiss, S.; Alivisatos, A. P., Synthesis and Properties of Biocompatible Water-Soluble Silica-Coated CdSe/ZnS Semiconductor Quantum Dots. Journal of Physical Chemistry B 2001, 105, (37), 8861-8871.

60. Michalet, X.; Lacoste, T. D.; Weiss, S., Ultrahigh-resolution colocalization of spectrally separable point-like fluorescent probes. Methods 2001, 25, (1), 87-102. PMID:11559000

61. Michalet, X.; Pinaud, F.; Lacoste, T. D.; Dahan, M.; Bruchez, M. P.; Alivisatos, A. P.; Weiss, S., Properties of fluorescent semiconductor nanocrystals and their application to biological labeling. Single Molecules 2001, 2, (4), 261-276.

62. Michalet, X.; Lacoste, T. D.; Pinaud, F.; Chemla, D. S.; Alivisatos, A. P.; Weiss, S., Ultrahigh Resolution Multicolor Colocalization of Single Fluorescent Nanocrystals. Proceedings of SPIE 2001, 4258, 8-15.

63. Michalet, X.; Weiss, S., Single-molecule spectroscopy and microscopy. Comptes Rendus Physique 2002, 3, (5), 619-644.

64. Kapanidis, A. N.; Weiss, S., “Fluorescent probes and bioconjugation chemistries for single-molecule fluorescence analysis of biomolecules”. The Journal of Chemical Physics 2002, 24, 10953-10964.

65. Michalet, X.; Kapanidis, A. N.; Laurence, T.; Pinaud, F.; Doose, S.; Pflughoefft, M.; Weiss, S., The power and prospects of fluorescence microscopies and spectroscopies. Annu Rev Biophys Biomol Struct 2003, 32, 161-82. PMID: 12598370

66. Licht, S. S.; Sonnleitner, A.; Weiss, S.; Schultz, P. G., A rugged energy landscape mechanism for trapping of transmembrane receptors during endocytosis. Biochemistry 2003, 42, (10), 2916-25. PMID: 12627957

67. Tsay, J. M.; Pflughoefft, M.; Bentolila, L. A.; Weiss, S., Hybrid approach to the synthesis of highly luminescent CdTe/ZnS and CdHgTe/ZnS nanocrystals. J Am Chem Soc 2004, 126, (7), 1926-7.PMID: 14971912

68. Baer, R.; Neuhauser, D.; Weiss, S., Enhanced Absorption Induced by a Metallic Nanoshell. Nano Letters 2004, 4, (1), 85-88.

69. Laurence, T. A.; Kapanidis, A. N.; Kong, X.; Chemla, D. S.; Weiss, S., Photon arrival-time interval distribution (PAID): A novel tool for analyzing molecular interactions. J. of Phys. Chem. B 2004, 108, (9), 3051-3067.

70. Pinaud, F.; King, D.; Moore, H. P.; Weiss, S., Bioactivation and Cell Targeting of Semiconductor CdSe/ZnS Nanocrystals with Phytochelatin-related Peptides. J. Am. Chem. Soc. 2004, 126, 6115-6123. PMID:15137777

71. Hertzog, D. E.; Michalet, X.; Jager, M.; Kong, X.; Santiago, J.; Weiss, S.; Bakajin, O., Femtomole Mixer for Microsecond Kinetic Studies of Protein Folding. Analytical Chemistry 2004, 76 (24), 7169 – 7178. PMID: 15595857 PMCID: PMC1413504

72. Kapanidis, A.N.; Lee, N.K.; Laurence, T.A.; Doose, S.; Margeat, E.; Weiss, S., Fluorescence-aided molecule sorting: Analysis of structure and interactions by alternating-laser excitation of single molecules, Proc Natl Acad Sci, 2004, 101 (24), 8936-8941 15175430 PMID: 15175420 PMCID: PMC428450

73. Michalet, X.; Pinaud, F.; Bentolila, L. A.; Tsay, J.; Doose, S; Li, J.; Sundaresan, G.; Wu, A. M.; Gambhir, S.S.; Weiss, S., Quantum Dots for Live Cells and in vivo Imaging, Diagnostics and Beyond, Science 2005, 307 (5709), 538-544 PMID:15681376 PMID: 15681376 PMCID: PMC1201471

74. Tsay, J.; Doose, S.; Pinaud, F.; Weiss, S., Enhancing the photoluminescence of peptide-coated CdSe nanocrystals with shell composition and UV irradiation, J. Phys. Chem B. 2005, 109, 1669-1674 PMID:164299593 PMCID: PMC1315301

75. Doose, S.; Tsay, J. M.; Pinaud, F.; Weiss, S., Comparison of Photophysical and Colloidal Properties of Biocompatible Semiconductor Nanocrystals Using Fluorescence Correlation Spectroscopy, Anal Chem. 2005 , 77(7):2235-42. PMID:1580158

76. Lee N.K., Kapanidis A.N., Michalet X., Mukhophadyay J., Ebright R.H., Weiss S., Towards structure from single biomolecules: accurate FRET through alternating-laser excitation. Biophys J, 2005, 88 (4), 2939–2953. PMID: 15653725 PMCID: PMC1282518

77. Kapanidis, A.N.; Laurence, T.A.; Lee, N.K.; Margeat, E.; Kong, X.; Weiss, S., Alternating-laser excitation of single molecules, Accounts of Chemical Research (Special Issue on Single-Molecule Spectroscopy) 2005, 38, 532-533 PMID:16028886

78. Jager, M.; Michalet, X.; Weiss, S., Protein-protein interactions as a tool for site specific labeling of proteins, Protein Science, 2005, 14, 2059-2068. PMID: 15987886 PMCID: PMC2279317

79. Li, J.J.; Tsay, J.; Michalet, X.; Weiss, S., Wave-function engineering: from quantum wells to near-infrared type-II colloidal quantum dots synthesized by layer-by-layer colloidal epitaxy, Chemical Physics (Special Issue on Molecular Nanoscience-In Honor of Daniel S. Chemla on his 65th Birthday), 2005, 318, 82–90.

80. Laurence, T. A.; Kong, X.; Jager, M.; Weiss, S., Probing structural heterogeneities and fluctuations of nucleic acids and denatured proteins, Proc Natl Acad Sci U S A., 2005, 102 (48), 17348-53 (Epub 2005 Nov 15). PMID: 16287971 PMCID: PMC12976781

81. Margeat, E.; Kapanidis, A.N.; Tinnefeld, P.; Wang, Y; Mukhopadhyay, J.; Ebright, R.H.; and Weiss, S., Direct observation of abortive initiation and promoter escape within single immoblized transcription complexes, Biophys J., 2006,90,1419-1431. PMID:: 16299085 PMCID: PMC1367292

82. Kapanidis, A.N.; Margeat, E.; Laurence, T.A.; Doose, S.; Ho, S.O.; Kortkhonjia, M.E.; Mekler, V.; Ebright, R.H.; and Weiss, S.; Retention of transcription initation factor σ70 in transcription elongation: single molecule analysis, Molecular Cell, 2005, 20 (3), 347-56. PMID: 16285917

83. Michalet, X., Pinaud, F. F., Bentolila, L.A., Tsay, J. M., Doose, S., Li, J. J., Iyer, G., Weiss, S., Peptide-coated semiconductor nanocrystals for biomedical applications, Proceedings of SPIE, 2005, 5704, 57-68.

84. Tsay, J.M.; Doose, S.; Pinaud, F.; and Weiss, S., Enhancing the Photoluminescence of Peptide-coated Nanocrystals, Proceedings of SPIE on Progress on Biomedical Optics and imaging: Nanobiophotonics and Biomedical Applications II, 2005 Vol. 6, no. 20, pages 139-147. PMID: 16448137 PMCID: PMC 1315301

85. Pinaud, F.; Michalet, X.; Tsay, J.M.; Doose, S.; Li, J.J.; Iyer, G.; Weiss, S.; Advances in fluorescence imaging with quantum dot bio-probes, Biomaterials 2006, 27 (9), 1679-87 . PMID: 16318871 PMCID: PMC3073483

86. Tsay, J.M.; Doose, S.; and Weiss, S.; Rotational and Translational Diffusion of CdSe/CdS/ZnS Nanorods Studied by Fluorescence Correlation Spectroscopy, J. Am. Chem. Soc., 2006,128(5),1639. PMID: 16648137 PMCID: PMC2535805

87. Jäger M.; Nir E.; Weiss S., Site-specific labeling of proteins for single molecule FRET by combining chemical and enzymatic modification, Protein Science, 2006,15:640-646. PMID: 16452617 PMCID: PMC 2249784

88. Bentolila, L. A.; Weiss, S., Single-Step Multicolor Fluorescence in situ Hybridization Analysis using Semiconductor Quantum Dot-DNA Conjugates, Cell Biochemistry and Biophysics, 2006, 45, 59-70. PMID:16679564 PMCID:PMC3084375

89. Michalet, X.; Weiss, S.; Jäger, M.; Single-molecule Fluorescence Studies of Protein Folding and

            Conformational Dynamics, Chemical Reviews, 2006, 106(5): 1785-813.
            PMID: 16683755 PMCID: PMC 2569857

90. Michalet, X.; Siegmund, O.H.W.; Vallerga, J.V.; Jelinsky, P.; Millaud, J.E.; Weiss, S.; Photon-Counting H33D Detector for Biological Fluorescence Imaging, Nuclear Instruments and Methods in Phyiscs Research, 2006, 567, 133. PMID:20151021 PMCID:PMC2819128

91. Nir, E.; Michalet, X.; Hamadani. K.; Laurence, T.A.; Neuhauser, D.; Kovchegov, Y.; and Weiss, S., Shot-noise limited single-molecule FRET histogram: comparison between theory and experiments, J. Phys. Chem. B 2006, 110, 22103-22124. PMID: 17078646 PMCID:PMC3085016

92. Kapanidis, A.N.; Margeat, E.; Ho, S.O.; Kortkhonjia, E.; Weiss, S.; and Ebright, R.H., Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism, Science, 2006, 314: 1144-1147. PMID: 17110578 PMID:PMC2754788

93. Iyer, G.; Pinaud, F.; Tsay, J.M.; Li, J.J.; Bentolila, L.A.; Michalet, X.; and Weiss, S., Peptide coated quantum dots for biological applications, IEEE Transactions on Nanobioscience, 2006, 5: 231-8.PMID: 17181021 PMCID: PMC3074086

94. Lee, N.K.; Kapanidis, A.N.; Koh, H.R.; Korlann, Y.; Ho, S.O.; Kim; Y.;Gassman, N.; Kim, S.K.; and Weiss, S., Three-color alternating-laser excitation of single molecules: simultaneous monitoring of multiple interactions and distances, Biophysical Journal, 2007, 92: 303-12.PMCID: PMC1697855

95. Michalet, X.; Siegmund, O.H.W.; Vallerga, J.V.; Jelinsky,P.; Millaud, J.E. and Weiss, S, Detectors for ingle -molecule fluorescence imaging and spectroscopy, Journal of Modern Optics, 2007, 54: 239–81.PMID: 2057633 PMCID :PMC2821066

96. Doose, S.; Heilemann, M.; Michalet, X.; Weiss, S.; and Kapanidis A.N., “Periodic Acceptor excitation spectroscopy of single molecules”, European Biophysical J., 2007, 36:669–674, DOI 10.1007/s00249-007-0133-7. PMID: 17279362 PMCID: PMC3084376

97. Majumdar, D.S.; Smirnova, I.; Kasho, V.; Nir, E.; Kong, X.; Weiss, S.; Kaback, H.R.; “Single-molecule FRET Reveals a Sugar-Induced Conformational Dynamics in LacY”, Proc Natl Acad Sci U S A., 2007; 104(31); 12640–12645. PMCID: PMC1937519

98. Iyer, G; Pinaud, F.; Tsay, J.M.; Weiss, S; “Solubilization of quantum dots with a recombinant peptide from E.coli”, Small, 2007, 3, 793 – 798. PMID: 17393550 PMCID: PMC3081612

99. Tsay, J.M.; Trzoss, M.; Shi, L.; Komg, X.; Selke, M.; Jung, M.E.; Weiss, S.; “Singlet Oxygen Production by Peptide-coated Quantum Dot-Photosensitizer Conjugates”, J. Am. Chem. Soc., 2007; 129(21); 6865-6871. PMCID#PMC2527466

100. Kong, X.; Nir, E.;Hamadani, K.; Weiss, S.; “Photobleaching Pathways in Single Molecule FRET Experiments”, J. Am. Chem. Soc,. 2007, 129, 4643-4654. PMCID: PMC2569857

101. Schipper, M.L.; Cheng, Z.; Lee, S.W.; Keren, S.; Bentolila, L.A.; Sundaresan, G.; Iyer, G.; Gheysens,O.; Ebenstein, Y.; Li, J.; Rao, J.; Chen, X.; Wu, A.M.; Weiss, S.; Gambhir, S.S.; “MicroPET-Based Biodistribution of Quantum Dots in Living Mice”, J. of Nuclear Medicine, 2007; 48, 1511-1518. DOI: http://pubs.acs.org/10.2967/jnumed.107.040071 . PMCID: PMC2299220

102. Kim, Y.; Ho, S.O.; Gassman, N.R.; Korlann, Y.; Landrof, E.V.; Collart, F.; Weiss, S.; “Efficient site-specific labeling of proteins via cysteines”, Bioconjugate Chemistry, 2008, 19 (3), 786–791, DOI: http://pubs.acs.org/10.1021/bc7002499 . PMID: 18275130 PMCID: PMC3085854

103. Hamadani, K.M.; Weiss, S.; “Non-equilibrium Single Molecule Protein Folding in a Co-axial Mixer”, Biophysical Journal, 2008, 95, 352–365, BioFAST: First Published March 13, 2008. DOI: http://pubs.acs.org/10.1529/biophysj.107.127431 .PMID: 18339751 PMCID:PMC62426651

104. Chang, Y.P.; Pinaud, F.; Michalet, X.; Iyer, G.; and Weiss, S.; “Tracking bio-molecules in live cells using quantum dots”, Journal of Biophotonics, 2008, 4, 287–298; DOI: http://pubs.acs.org/10.1002/jbio.200810029 .PMID: 19343652 PMCID: PMC3075916

105. Korlann, Y.; Dertinger, T.; Michalet, X.; Weiss, S.; Enderlein, J.; “Measuring diffusion with polarization-modulation dual-focus Fluorescence Correlation Spectroscopy”, Optics Express, 2008, 16, 14609-16 DOI: http://pubs.acs.org/10.1364/OE.16.014609 . PMID: 18794997 PMCID:PMC 2832597

106. Iyer, G.; Michalet, X.; Pinaud, F.F.; Matyas, C.E.; Chang, Y.P.; Payne, G.; Weiss, S.; “High Affinity scFv-hapten Pair as a Tool for Quantum Dot Labeling and Tracking of Single Proteins in Live Cells”, Nano Lett., 2008, 8, 4618-23; ASAP, DOI: http://pubs.acs.org/doi/pdf/10.1021/nl8032284. PMID:19053789 PMCID: PMC3084663

107. Schipper, M.L., Iyer, G., Koh, A.L., Cheng, Z., Ebenstein, Y., Aharoni, A., Keren, S., Bentolila, L.A., Li, J., Rao, J., Chen, X., Banin, U., Wu, A.M., Sinclair, R., Weiss, S., Gambhir, S.S., “Particle Size, Surface Coating, and Pegylation Influence the Biodistribution of Quantum Dots in Living Mice”, Small, 2009, 5, 126–34; DOI: http://dx.doi.org/10.1002/smll.200800003. PMID: 19051182 PMCID: PMC3084659

108. Waldauer, S.; Bakajin, O.; Ball, T.; Chen, Y.; DeCamp, S.; Kopka, M.; Jäger,, M.; Singh, V.R.; Wedemeyer, W.J.; Weiss, S.; Yao, S.; Lapidus, L.J.; “Ruggedness in the Folding Landscape of Protein L”, HFSP J., 2009, 2, 388-395., DOI: http://dx.doi.org/10.2976/1.3013702. PMID: 19436489 PMCID: PMC 2645578

109. Gassman, N.R.; Ho, S.O.; Korlann, Y.; Chiang, J.; Wu, Y.; Perry, J.; Kim, Y.; Weiss, S.; “In-vivo assembly and single molecule characterization of the transcription machinery from Shewanella Oneidensis MR-1”, Protein Expression and Purification, 2009, 65, 66–76; DOI: http://dx.doi.org/10.1016/j.pep.2008.11.013.

             PMID: 19111618 PMCID: PMC3084661

110. Pinaud, F.; Michalet, X.; Iyer, G.; Margeat, E.; Moore, H.P.; Weiss, S.; “Dynamic Partitioning of a GPI-Anchored Protein in Glycosphingolipid-Rich Microdomains of the Cell Membrane”, Traffic, 2009,10, 691-712. DOI: 11387465[uid]http://dx.doi.org/10.1111/j.1600-0854.2009.00902 PMID:19416475 PMCID:PMC 2766537

111. Antelman, J.; Ebenstein, Y.; Chang, C.W.; Weiss, S.; Michalet, X.; “Nanometer Distance Measurements Between Multicolor Quantum Dots”, Nano Letters, 2009, 9, 2199-2205. DOI: http://dx.doi.org/10.1021/nl901163k .PMID;19374434 PMCID: PMC 2748936

112. Ebenstein, Y.; Gassman, N.R.; Antelman, J.; Kim, Y.; Kim, S.; Ho, S.O.; Samuel, R.; Michalet, X.; Weiss, S.; “Lighting up Individual DNA Binding Proteins with Quantum Dots”, Nano Lett., 2009, 9, 1598–1603. DOI: http://dx.doi.org/10.1021/nl803820b . PMID:1920670 PMCID: PMC 3084662

113. Bentolila, L.A.; Ebenstein, Y.; Weiss, S.; “Quantum Dots for in vivo Small Animal Imaging”, J. of Nuclear Medicine, 2009, 50, 493-6. DOI: http://dx.doi.org/0.2967/jnumed.108.053561 . PMID: 19289434 PMCID:PMC3081879

114. Ebenstein, Y.; Gassman, N.R.; Kim, S.; Antelman, J.; Weiss, S.; “Combining Atomic Force and Fluorescence microscopy For Analysis of Quantum-dot labeled Protein–DNA Complexes”, Journal of Molecular Recognition, 2009, DOI: http://dx.doi.org/10.1002/jmr.956 .PMID:19452448 PMCID: PMC3085854

115. Antelman, J.; Ebenstein, Y.; Michalet, X.; Weiss, S.; “Suppression of quantum dots’ blinking in DTT-doped polymer films”, J. Phys. Chem. C, 2009, 113, 11541-45, DOI: http://dx.doi.org/10.1021/jp811078e PMID: 20161096 PMCID:PMC 2745152

116. Tremsin, A.S.; Siegmund, O.H.W.; Vallerga, J.V.; Raffanti, R.; Weiss, S.; Michalet, X.; “High Speed Multichannel Charge Sensitive Data Acquisition System with Self-Triggered Event Timing”, IEEE Trans. Nucl. Sci., 2009, 56, 1148-52, DOI: http://dx.doi.org/10.1109/TNS.2009.2015302 .PMID: 20174482 PMCID:PMC 2824915

117. Barat, B.; Sirk, S.; McCabe K.; Li, J.; Lepin, Remenyi, R.; E.; Koh, AL.; Olafsen, T.; Gambhir, SS.; Weiss, S.; and Wu, AM.; “Cys-antibody-quantum dot conjugates (immunoQdots) for cancer marker detection”, Bioconjugate Chemistry, 2009, 20, 1474-8, DOI: http://dx.doi.org/10.1021/bc800421f . PMID: 19642689 PMCID:PMC 2891877

118. Michalet, X.; Colyer, R.A.; Antelman, J.; Siegmund, O.H.W.; Tremsin, A.; Vallerga, J.V.; Weiss, S.; “Single-Quantum Dot Imaging with a Photon Counting Camera”, Current Pharmaceutical Biotechnology, 2009, 10, 543-58. PMID:19689323 PMCID:PMC 2830710

119. Liu, C.; Chung, S.; Lee, S.; Weiss, S.; Neuhauser, D.; “Adsorbate induced absorption red-shift in an organic cluster conjugate: electronic effects of surfactants and organic adsorbate on band edge excitations in a methanethiol CdSe conjugate”, J. Chem. Phys, 2009, 131, 174705-1/-8., DOI: http://dx.doi.org/10.1063/1.3251774 PMID: 19895033 PMCID:PMC 2787060

120. Dertinger, T.; Colyer, R.; Iyer, G.; Weiss, S.; Enderlein, J.; “Fast, background-free, 3D superresolution optical fluctuation imaging (SOFI)”, Proc Natl Acad Sci, 2009, 106, 22287-92, DOI: http://dx.doi.org/10.1073/pnas.0907866106 PMID:20018714 PMCID:PMC 2799731

121. Dertinger, T.; Colyer, R.; Vogel, R.; Enderlein, J.; Weiss, S.; “Achieving increased resolution and more pixels with Superresolution Optical Fluctuation Imaging (SOFI)”, Optics Express, 2010, 18. 18875-85. DOI: http://dx.doi.org/10.1364/OE.18.018875 PMID: 20940780 PMCID: PMC3072111

122. Dertinger, T.; Heilemann, M.; Vogel, R.; Sauer, M.; Weiss, S.; “Superresolution Optical Fluctuation Imaging with Organic Dyes”, accepted, Angew. Chem. 2010, 49, 1–4. DOI: http://dx.doi.org/10.1002/anie.201004138 PMID:21031383 PMCID: PMC 3007670

123. Colyer, R.A.; Scalia, G.; Rech, I.; Gulinatti, A.; Ghioni, M.; Cova, S.; Weiss, S.; Michalet, X.; “High-throughput FCS using an LCOS spatial light modulator and an 8x1 SPAD array”, Biomedical Optics Express. 2010, 1, 1408-31. DOI: http://dx.doi.org/10.1364/BOE.1.001408PMID: 21258559 PMCID:PMC 3018120

124. Kim, S.; Streets, A.M.; Lin, R.R.; Quake, S.R.; Weiss, S.; Majumdar, D.S.; “High Throughput Single Molecule Optofluidics”, Nature Methods, 2011, Advanced online publication: DOI: http://dx.doi.org/10.1038/nmeth.1569 PMID: 212976618 PMCID: PMC 3075913

125. Iyer, G.; Pinaud, F.; Xu, J.; Ebenstein, Y.; Li, J.; Dahan, M.; Weiss, S.; “Aromatic Aldehyde and Hydrazine Activated Peptide Coated Quantum Dots for Easy Bioconjugation and Live Cell Imaging”, submitted, Bioconjugation Chemistry, 2011. DOI: http://dx.doi.org/10.1021/bc100593

126. Colyer, R.A.; Siegmund, O.H.W.; Tremsin, A.S.; Vallerga, J.V.; Weiss, S.; Michalet, X.; “Phasor Imaging with a Widefield Photon-Counting Detector”, accepted, Journal of Biomedical Optics.

127. Dertinger, T.; Weiss, S.; “Advances in Superresolution Optical Fluctuation Imaging”, accepted, Quarterly Reviews of Biophysics.

128. Voelz, V.A.; Jäger, M.; Yao, S.; Chen, Y.; Zhu, L.; Waldauer, S.A.; Bowman, G.R.; Friedrichs, M.; Bakajin, O.; Lapidus, L.J.; Weiss, S.; Pande, V.S.; “Surprising complexity to protein folding revealed by theory and experiment”, submitted to Nature Communications.

129. Kim, S.; Gottfried, A.; Lin, R.R.; Dertinger, T.; Kim, A.; Chang, S.; Weinhold, E.; Weiss, S.; Ebenstein, Y.; “Enzymatically incorporated genomic tags for optical mapping of DNA binding proteins”, submitted to Angewandte Chemie.

130. Lijun Xu, L.; Feng, Z.; Sinha, D.; Ebenstein, Y.; Gauron, C.; Lin, S.; Weiss, S.; Jullien, L.; Vriz, S.; Bensimon, D.; “Spatio-temporal control of retinoic acid activity in zebrafish hindbrain development”, submitted to Development.

131. Cordes, T.; Robb, N.C.; Hwang, L.C.; Gryte1, Santoso, Y.; Ebright, R.H.; Weiss, S.; Kapanidis, A.N.; “Single-molecule FRET reveals functionally important conformational dynamics in the bacterial transcription open complex”, submitted to Journal of Molecular Biology.

132. Dertinger, T.; Xu, J.; Foroutan Naini, O.; Vogel, R.; Weiss, S.; “SOFI-based 3D superresolution sectioning with a wide-field microscope”, submitted to Optical Nanoscopy.


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