פרופ' שמעון וייס

פרופ'
פרופ' שמעון וייס
טלפון: 
דוא"ל: 

תחומי מחקר

General area: Biophysics, Biophysical Chemistry, Nano-Spectroscopy, Bio-Nano-Technology, Molecular Imaging.

Topics: Single molecule detection and spectroscopy, application of single molecule detection to biology, dynamic structural/molecular biology, bacterial and eukaryotic transcription, protein folding, protein-protein and protein-DNA interactions, single molecule enzymology, novel Bio-Nano-Technology probes, semiconductor nanocrystals, quantum dots, semiconductor nanocrystals voltage sensors,  fluorescence microscopy/spectroscopy, superresolution microscopy, physics/chemistry of mesoscopic systems.

קורות חיים

2009- to date                        The Dean Willard Chair in Chemistry and Biochemistry

2011-to date                         Distinguished Professor

2001-to date                         Professor of Chemistry, Biochemistry and Physiology , UCLA

1998-to 2001                       Staff Scientist at Lawrence Berkeley National Laboratory, Physical Biosciences Division.

1990-to 2001                       Staff Scientist at Lawrence Berkeley National Laboratory, Materials Sciences Division.

1989-1990                            Post-doctoral position at AT&T Bell Laboratories. Conducted research on ultrafast dynamics of semiconductors multiple quantum-well structures.

                                                Advisor: Dr. Daniel Chemla

1989                                       D.Sc. in Electrical Engineering, Technion, Israel Institute of Technology.

                                                Advisor: Dr. Baruch Fischer

1985-1989                            Graduate student in the Electrical Engineering Department, Technion, Israel Institute of Technology. Conducted research on dynamics of photorefractive oscillators.

1984                                       B.Sc. (Cum Laude) in Electrical Engineering, Technion, Israel Institute of Technology.

 

פירסומים

as of 11/22/15:                                    ISI                                          Google Scholar

Sum of the Times Cited:                    22,666 (22,045)                   33,569

Average Citations per Item:              125.23

h-index:                                                 56                                           66

 

 

PATENTS

as of 11/22/15:                    USPTO                   EPO

issued patents                       32                           17

published patents                                33

 

 

a] Books, Book Chapters

1.             Ha, T.; Weiss, S., “Dual- and single-molecule fluorescence spectroscopy: towards kinetic observation of single molecule reactions.” a chapter in "Mesoscopic Chemistry - a Chemistry for the 21st century monograph" Masuhara H.; De Schryver, F.; Eds. International Union of Pure and Applied Chemistry, Blackwell Science, 1999, ISBN 0632051256, pg 61-74. 1999.

 

2.             Michalet, X.; Weiss, S., Laser in Physics: Single Molecule Spectroscopy. Chapter in Encyclopedia of Modern Optics Guenther, B.; Miller, A.; Bayvel L.; Midwinter, J.; Eds.  Elsevier Physics, pg 147-162. 2005.

 

3.             Michalet, X.; Bentolila, L.A.;  Weiss, S.; chapter on “Molecular Imaging” in Advances in Medical Physics: An Overview for Generalists, chapter 7, pg. 181 Wolbarst, A.B.; Zamenhof, R.G.; Hendee, W.R.; Eds., Medical Physics Publishing, Madison, 2006.

 

4.             Laurence, T.A.; Michalet, X.; Jäger, M.; and Weiss, S., Chapter on “Protein Dynamics and Interactions” in Single Molecule Dynamics, Yanagida, T.; Ishii, Y. Eds.,  Wiley-VCH, 2007.

 

5.             Nir, E.; Jäger, M.; and Weiss, S., “Alternating Laser Excitation Spectroscopy of freely diffusing single molecules: Application to biomolecular structure, dynamics and interactions”, Handai Nanophotonics, volume 3, Masuhara, H.; Kawata, S.; and Tokunaga, F. Eds., Elsevier B.V. 2007.

 

6.             Michalet, X.; Bentolila, L.A.; and Weiss S. Chapter on “The physics of quantum dots” in Advances in Medical Physics, Vol. II, Wolbarst A.B., Zamenhof R.G. and Hendee W.R., Eds., Medical Physics Publishing, Madison, Wisconsin, 2007.

 

7.             Kapanidis, A.N.; Heilemann, M.; Margeat, E.; Kong, X.; Nir, E.; Weiss, S.; Chapter on “Alternating-Laser Excitation of Single Molecules” in The Single Molecule Manual, chapter 6, Selvin, P.; Ha, T.; Eds., Cold Spring Harbor Laboratory Press, Woodbury, NY 2007.

 

8.             Bentolila, L.A.; Michalet, X.; and Weiss, S., “Quantum Optics: Colloidal Fluorescent Semiconductor Nanocrystals (Quantum dots) in Single-Molecule Detection and Imaging”,  Springer Series in Biophysics: Single Molecules and Nanotechnology, Rigler, R.; Vogel, H.; Eds. Springer-Verlag, Heidelberg, Germany 2008.

 

9.             Kapanidis, A.N.; Weiss, S.; chapter on “Single-molecule FRET analysis of the path from transcription initiation to elongation”, in RNA Polymerases as Molecular Motors, Buc, H.; Strick, T.; Eds., Royal Society of Chemistry, London 2009.

 

10.          Bentolila, L.A.; Doose, S.; Ebenstein, Y.; Iyer, G.; Li, J.J.; Michalet, X.; Pinaud, F.; Tsay, J.; Weiss, S.; “Peptide-Functionalized Quantum Dots for Live Diagnostic Imaging and Therapeutic Applications”, in “Inorganic Nanoprobes for Biological Sensing and Imaging”, Mattoussi, H.; Cheon, J.; Eds. Artech House, 2009.

 

11.          Ebenstein, Y.; Weiss, S.; “Mapping Transcription Factors on Stretched DNA – A Single Molecule Approach”, in the Nobel Symposium book on “Single Molecule Spectroscopy in Chemistry, Physics, and Biology”, Sånga Säby, June 2008, Ed. by Gräslund, A.; Rigler, R.; Widengren, J.; Springer, 2009.

 

12.          Kapanidis, A.N.; Majumdar, D.; Heilemann, M.; Nir, E.; Weiss, S.; “Alternating Laser Excitation for Solution-based Single Molecule FRET”, Imaging Techniques volume, Optical Imaging Techniques manual, Cold Spring Harbor Laboratory Press, 2010.

 

13.          Iyer, G.; Michalet, X.; Chang, Y.P.; Weiss, S.; “Tracking Single Proteins in Live Cells using Single Chain Antibody Fragment-Fluorescent Quantum Dot Affinity Pair” in Methods in Enzymology, Walter, N.G. Ed., Elsevier 2010, 475, 61-79.

 

14.          Iyer, G.; Xu, J.; Weiss, S.; “Bioconjugating semiconductor quantum dots”, in “Methods in Molecular Biology”, Book chapter for Bioconjugation Protocols, 2nd Ed., Springer, 2010.

 

15.          Dertinger, T.; Colyer, R.; Vogel, R.; Heilemann, M.; Sauer, M.; Enderlein, J,; Weiss, S.; “Superresolution Optical Fluctuation Imaging (SOFI)”, in Advances in Experimental Medicine and Biology, Zahavi, E.; Ordentlich, A.; Itzhaki, S.; Shafferman, A.; Eds., NANO-BIOTECHNOLOGY FOR BIOMEDICAL AND DIAGNOSTIC RESEARCH, Springer, 2012, Volume 733, 17-21, http://dx.doi.org/10.1007/978-94-007-2555-3_2

 

 

b] Refereed Journal papers

1) Published

1.             Sternklar, S.; S., W.; Fischer, B., Controlling the self-frequency shift and intensity of oscillations with photorefractive crystals. Appl. Optics 1985, 24, 3121. PMID: 18224013

 

2.             Sternklar, S.; S., W.; Fischer, B., Tunable frequency shifts of photorefractive oscillators. Opt. Lett 1986, 11, 165. PMID: 19730567

 

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. PMID: 19738678

 

5.             Sternklar, S.; S., W.; Fischer, B., Double phase conjugate mirror: analysis, demonstration, and applications. Opt. Lett. 1986, 12, 114. PMID:19738810

 

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. PMID:20454049

 

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. PMID: 20539392

 

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. PMID:19749864

 

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. PMID: 19759638

 

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. PMID: 10046558

 

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. PMID: 10053835

 

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.PMID: 9974862

 

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. PMID: 8692803 PMCID: PMC39010

http://www.pnas.org/content/93/13/6264.full.pdf+html

 

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. PMID: 100623577

http://prl.aps.org/pdf/PRL/v77/i19/p3979_1

 

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. PMID: 9012816 PMCID: PMC19545

 

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.

http://www.sciencedirect.com/science/article/pii/S0009261497004405

 

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.

http://prl.aps.org/pdf/PRL/v80/i10/p2093_1

 

44.          Enderle, T.; Ha, T.; Chemla, D. S.; Weiss, S., Near-field fluorescence microscopy of cells. Ultramicroscopy 1998, 71, (1-4), 303-9. PMID: 9566345

 

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. PMID:9748157

http://www.sciencemag.org/content/281/5385/2013.full.pdf

 

46.          U. Banin, M. Bruchez, A.P. Alivisatos, T. Ha, S. Weiss and D.S. Chemla, “Evidence for a thermal contribution to emission intermittency in single CdSe/CdS core/shell nanocrystals”, J. Chem. Phys., 110, 1195-1201 (1999).

 

47.          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.

http://www.sciencemag.org/content/283/5408/1676.full.pdf

 

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.

http://www.pnas.org/content/96/7/3670.full.pdf

 

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.

http://www.sciencedirect.com/science/article/pii/S0301010499001494

 

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.

http://www.sciencedirect.com/science/article/pii/S0301010499001329

 

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

http://www.pnas.org/content/96/3/893.full.pdf+html

 

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.

http://pubs.acs.org/doi/pdf/10.1021/jp990948j

 

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

http://www.pnas.org/content/97/10/5179.full.pdf+html

 

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

http://www.pnas.org/content/97/17/9461.full.pdf+html

 

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

http://www.nature.com/nsmb/journal/v7/n9/pdf/nsb0900_724.pdf

 

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

http://www.annualreviews.org/doi/pdf/10.1146/annurev.physchem.52.1.233

 

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

http://www.opticsinfobase.org/abstract.cfm?URI=ol-26-11-825

 

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.

http://pubs.acs.org/doi/pdf/10.1021/jp0105488

 

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

http://www.sciencedirect.com/science/article/pii/S1046202301912186

 

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.

http://onlinelibrary.wiley.com/doi/10.1002/1438-5171(200112)2:4%3C261::AID-SIMO261%3E3.0.CO;2-P/pdf

 

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.

http://www.chem.ucla.edu/~michalet/papers/SPIE2001.pdf

 

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

http://www.chem.ucla.edu/~michalet/papers/CRAS2002.pdf

 

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.

http://scitation.aip.org/getpdf/servlet/GetPDFServlet?filetype=pdf&id=JCPSA6000117000024010953000001&idtype=cvips&doi=10.1063/1.1521158&prog=normal

 

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

http://www.annualreviews.org/doi/pdf/10.1146/annurev.biophys.32.110601.142525

 

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

http://pubs.acs.org/doi/pdf/10.1021/bi026059v

 

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

http://pubs.acs.org/doi/pdf/10.1021/ja039227v

 

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

http://pubs.acs.org/doi/pdf/10.1021/nl034902k

 

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.

http://pubs.acs.org/doi/pdf/10.1021/jp036499b

 

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

http://pubs.acs.org/doi/pdf/10.1021/ja031691c

 

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

http://pubs.acs.org/doi/pdf/10.1021/ac048661s

 

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

http://www.pnas.org/content/101/24/8936.full.pdf+html

 

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

http://www.sciencemag.org/content/307/5709/538.full.pdf

 

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

http://pubs.acs.org/doi/pdf/10.1021/jp046828f

 

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

http://pubs.acs.org/doi/pdf/10.1021/ac050035n

 

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

http://www.sciencedirect.com/science/article/pii/S0006349505733464

 

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

http://pubs.acs.org/doi/pdf/10.1021/ar0401348

 

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

http://onlinelibrary.wiley.com/doi/10.1110/ps.051384705/pdf

 

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.

http://www.sciencedirect.com/science/article/pii/S0301010405001461

 

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

http://www.pnas.org/content/102/48/17348.full.pdf+html

 

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

http://www.cell.com/biophysj/abstract/S0006-3495(06)72332-3

 

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

http://www.cell.com/molecular-cell/abstract/S1097-2765(05)01682-5

 

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.

http://scitation.aip.org/getpdf/servlet/GetPDFServlet?filetype=pdf&id=PSISDG005704000001000057000001&idtype=cvips&doi=10.1117/12.589498&prog=normal

 

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

https://www.google.com/url?sa=t&rct=j&q=&esrc=s&source=web&cd=3&ved=0CD4QFjAC&url=http%3A%2F%2Fspiedigitallibrary.org%2Fdata%2FConferences%2FSPIEP%2F26225%2F139_1.pdf&ei=tYBtUqGBLaOpiQK2iIGQCg&usg=AFQjCNElmW8YJt0F__fbkpjM2fm7XI1Ivw&sig2=t6PqKxWTLq2Uww3QUmU8kg&bvm=bv.55123115,d.cGE

 

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

http://www.chem.ucla.edu/~michalet/papers/BM2006.pdf

 

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

http://pubs.acs.org/doi/pdf/10.1021/ja056162i

 

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

http://onlinelibrary.wiley.com/doi/10.1110/ps.051851506/pdf

 

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

http://www.springerlink.com/content/3q0u881w4t5j3037/fulltext.pdf

 

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

http://www.chem.ucla.edu/~michalet/papers/CR2006.pdf

 

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

http://www.sciencedirect.com/science/article/pii/S0168900206008916

 

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

http://pubs.acs.org/doi/pdf/10.1021/jp063483n

 

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

http://www.sciencemag.org/content/314/5802/1144.full.pdf

 

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

http://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=04016045

 

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

http://www.sciencedirect.com/science/article/pii/S0006349507708287

 

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

http://www.tandfonline.com/doi/pdf/10.1080/09500340600769067

 

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

http://www.springerlink.com/content/8pmk214820082600/fulltext.pdf

 

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

http://www.pnas.org/content/104/31/12640.full.pdf+html

 

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

http://onlinelibrary.wiley.com/doi/10.1002/smll.200600516/pdf

 

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

http://pubs.acs.org/doi/pdf/10.1021/ja070713i

 

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

http://pubs.acs.org/doi/pdf/10.1021/ja068002s

 

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. PMCID: PMC2299220

http://jnm.snmjournals.org/content/48/9/1511.full.pdf+html

 

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, PMID: 18275130 PMCID: PMC3085854

http://pubs.acs.org/doi/pdf/10.1021/bc7002499

 

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. PMID: 18339751 PMCID:PMC62426651

http://www.cell.com/biophysj/abstract/S0006-3495(08)70309-6

 

104.        Chang, Y.P.; Pinaud, F.; Antelman, J.; and Weiss, S.; “Tracking bio-molecules in live cells using quantum dots”, Journal of Biophotonics, 2008, 4, 287–298; PMCID: PMC3075916

http://onlinelibrary.wiley.com/doi/10.1002/jbio.200810029/pdf

 

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-PMID: 18794997 PMCID:PMC 2832597

http://www.opticsinfobase.org/abstract.cfm?URI=oe-16-19-14609

 

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

http://pubs.acs.org/doi/pdf/10.1021/nl8032284

 

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; PMID: 19051182 PMCID: PMC3084659

http://onlinelibrary.wiley.com/doi/10.1002/smll.200800003/pdf

 

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., PMID: 19436489 PMCID: PMC 2645578

http://www.tandfonline.com/doi/pdf/10.2976/1.3013702

 

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; PMID: 19111618 PMCID: PMC3084661

http://www.sciencedirect.com/science/article/pii/S1046592808003069

 

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.   PMCID:PMC 2766537

http://onlinelibrary.wiley.com/doi/10.1111/j.1600-0854.2009.00902.x/pdf

 

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. PMID;19374434 PMCID: PMC 2748936.

http://pubs.acs.org/doi/pdf/10.1021/nl901163k

 

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.  PMID:1920670 PMCID: PMC 3084662

http://pubs.acs.org/doi/pdf/10.1021/nl803820b

 

113.        Bentolila, L.A.; Ebenstein, Y.; Weiss, S.; “Quantum Dots for in vivo Small Animal Imaging”, J. of Nuclear Medicine, 2009, 50, 493-6. PMID: 19289434 PMCID:PMC3081879

http://jnm.snmjournals.org/content/50/4/493.full.pdf+html

 

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, 22, 397-402. PMID:19452448 PMCID: PMC3085854

http://onlinelibrary.wiley.com/doi/10.1002/jmr.956/pdf

 

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, PMID: 20161096 PMCID:PMC 2745152

http://pubs.acs.org/doi/pdf/10.1021/jp811078e

 

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,.PMID: 20174482 PMCID:PMC 2824915

http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=5075944

 

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,. PMID: 19642689  PMCID:PMC 2891877

http://pubs.acs.org/doi/pdf/10.1021/bc800421f

 

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

http://www.chem.ucla.edu/~michalet/papers/CPB2009.pdf

 

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., PMID: 19895033 PMCID:PMC 2787060

http://scitation.aip.org/getpdf/servlet/GetPDFServlet?filetype=pdf&id=JCPSA6000131000017174705000001&idtype=cvips&doi=10.1063/1.3251774&prog=normal

 

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, PMID:20018714 PMCID:PMC 2799731

http://www.pnas.org/content/106/52/22287.full.pdf+html

 

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. PMID: 20940780 PMCID: PMC3072111

http://www.opticsinfobase.org/abstract.cfm?URI=oe-18-18-18875

 

122.        Dertinger, T.; Heilemann, M.; Vogel, R.; Sauer, M.; Weiss, S.; “Superresolution Optical Fluctuation Imaging with Organic Dyes”,  Angew. Chem. 2010, 49, 1–4. PMID:21031383 PMCID: PMC 3007670

http://onlinelibrary.wiley.com/doi/10.1002/anie.201004138/pdf

 

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. PMID:21258559 PMCID:PMC3018120.

http://www.opticsinfobase.org/abstract.cfm?URI=boe-1-5-1408

 

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, 8, 242-7. PMID: 212976618 PMCID: PMC 3075913

http://www.nature.com/nmeth/journal/v8/n3/pdf/nmeth.1569.pdf

 

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”,, Bioconjugation Chemistry, 2011, 22, 1006–1011.  PMID: 21553893, PMCID: PMC3116077.

http://pubs.acs.org/doi/pdf/10.1021/bc100593m

 

126.        Yim, S.W.; Kim, T.; Laurence, T.A.; Partono, S.; Kim, D.; Kim. Y.; Weiss, S.; Reitmair, A.; “Four-Color Alternating-Laser Excitation Single-Molecule Fluorescence Spectroscopy for Next-Generation Biodetection Assays”, Clinical Chemistry, 2012 58:4. PMID: 22266381.

http://www.clinchem.org/content/early/2012/01/12/clinchem.2011.176958.full.pdf+html

 

127.        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”, Journal of Biomedical Optics, 2012, 17, 016008. PMID: 22352658, PMCID: PMC3380817.

http://scitation.aip.org/getpdf/servlet/GetPDFServlet?filetype=pdf&id=JBOPFO000017000001016008000001&idtype=cvips&doi=10.1117/1.JBO.17.1.016008&prog=normal

 

128.        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”,  Angewandte Chemie, 2012, 51, 1-5. PMID: 22344826, PMC3417104.

http://onlinelibrary.wiley.com/doi/10.1002/anie.201107714/pdf

 

129.        Dertinger, T.; Xu, J.;  Foroutan Naini, O.; Vogel, R.; Weiss, S.; “SOFI-based 3D superresolution sectioning with a wide-field microscope”, Optical Nanoscopy, 2012, 1, 2. PMC in process NIHMSID#454827

http://www.optnano.com/content/pdf/2192-2853-1-2.pdf

 

130.        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.; “Slow Unfolded-State Structuring in Acyl-CoA Binding Protein Folding Revealed by Simulation and Experiment”, J. Am. Chem. Soc.2012, 134,  12565–77. PMID: 22747188. PMCID:PMC 3462454

http://pubs.acs.org/doi/pdf/10.1021/ja302528z

 

131.        Chakraborty, A.; Wang, D.;  Ebright, Y.W.; Korlann, Y.; Kortkhonjia, E.; Kim, T.; Chowdhury, S.; Wigneshweraraj, S.; Irschik, H.; Jansen, R.; Nixon, B.T.; Knight, J.; Weiss, S.; Ebright, R.H.; “Opening and closing of the RNA polymerase clamp”, Science2012, 337, 591-5.  PMID: 22859489.Pub Med Central in process NIHMSID#454816

http://www.sciencemag.org/content/337/6094/591.full.pdf    

 

132.        Lijun Xu, L.; Feng, Z.; Sinha, D.; Ebenstein, Y.; Gauron, C.; Lin, S.; Weiss, S.; Jullien, L.; Vriz, S.; Bensimon, D.; "Spatio-temporal manipulation of retinoic acid activity in zebrafish hindbrain development via photo-isomerization", Development, 2012, 139, 3355-62. PMID: 22874920.

http://dev.biologists.org/content/early/2012/08/08/dev.077776.full.pdf

 

133.        Xu, J.; Ruchala, P.; Ebenstain, Y.; Li, J.J.; Weiss, S.; “Stable, compact, and bright biofunctional Quantum Dots with improved peptide coating”,  J. Phys. Chem. B, 2012, 116, 11370−11378. PMID:22920542 PMCID:PMC3470653

http://pubs.acs.org/doi/pdf/10.1021/jp306453y

 

134.        Park, K.; Deutsch, Z.; Li, J.J.; Oron, D.; Weiss, S.; “Single Molecule Quantum Confined Stark Effect Measurements of Semiconductor Nanoparticles at Room Temperature”, ACS Nano, 2012, 6, 10013–10023. PMCID:PMC3507316.

http://pubs.acs.org/doi/pdf/10.1021/nn303719m

 

135.        Xu, J.; Teslaa, T.; Wu, T.H.; Chiou, P.Y.; Teitell, M.A.; Weiss, S.; “Nanoblade delivery and incorporation of quantum dot conjugates into tubulin networks in live cells”, Nano Letters, 2012, 12 (11), 5669–72. PMID: 23094784; PMCID:PMC 3500567.

http://pubs.acs.org/doi/pdf/10.1021/nl302821g

 

136.        Michalet, X.; Colyer, R.A.; Scalia, G.; Ingargiola, A.; Lin, R.; Millaud, J.E.; Weiss, S.; Siegmund, O.H.W.; Tremsin, A.S.; Vallerga, J.V.; Cheng, A.; Levi, M.; Aharoni, D.; Ariasaka, K.; Villa, F.; Guerrieri, F.; Panzeri, F.; Rech, I.; Gulinatti, A.; Zappa, F.; Ghioni, M.; Cova, S.; “Development of new photon-counting detectors for single-molecule fluorescence microscopy”, Phil. Trans. R. Soc. B. 2013, 368 (1611), 20120035. PMID:23267185; PMCID:PMC3538434.

http://rstb.royalsocietypublishing.org/content/368/1611/20120035.full.pdf+html

 

137.        Robb, N.C.; Cordes, T.; Hwang, L.C.; Gryte, K.; Duchi, D.; Craggs, T.D.; Santoso, Y.; Weiss, S.; Ebright, R.H.; Kapanidis, A.N.; “The transcription bubble of the RNA polymerase-promoter open complex exhibits conformational heterogeneity and millisecond-scale dynamics: implications for transcription start-site selection”, Journal of Molecular Biology, 2013, 425, 875–885. PMID:23274143. http://www.sciencedirect.com/science/article/pii/S0022283612009485

 

138.        Gallina, M.E.; Xu, J.; Dertinger, T.; Aizer, A.; Shav-Tal, Y.; Weiss, S.;  “ Resolving the spatial relationship between intracellular components by dual color super resolution optical fluctuations imaging (SOFI)”, Optical Nanoscopy. 2013, 2, 2. NIHMSID# 455154.

http://www.optnano.com/content/pdf/2192-2853-2-2.pdf 

 

139.        Dertinger, T.; Pallaoro, A.; Braun, G.; Ly, S.; Laurence, T.A.; Weiss, S.; “Advances in Superresolution Optical Fluctuation Imaging (SOFI)”, Quarterly Reviews of Biophysics, 2013, 1-12. NIHMSID# 496894.

http://journals.cambridge.org/download.php?file=%2FQRB%2FS0033583513000036a.pdf&code=02a56c7a4893cb92f111c69b82140018

 

140.        Feng, Z.; Zhang, W.; Xu, J.;  Gauron, C.; Ducos, B.; Vriz, S.; Volovitch, M.; Jullien, L.; Weiss, S.; Bensimon, D.;  “Optical control and study of biological processes at the single cell level in a live organism”, accepted, Reports on Progress in Physics. Rep. Prog. Phys., 2013, 76, 072601, 1-21. NIHMSID# 496896.

http://iopscience.iop.org/0034-4885/76/7/072601/pdf/0034-4885_76_7_072601.pdf

 

141.        Xu, J.; Chang, J.; Yan, Q.; Dertinger, T.; Bruchez, M.; Weiss, S.; “Labeling cytosolic targets in live cells with blinking probes”, J. Phys. Chem. Lett., 2013, 4, 213846. PMCID in process.

                http://pubs.acs.org/doi/pdf/10.1021/jz400682m

 

142.        Jung, M.E.; Trzoss, M.; Tsay, J.M.; Weiss, S.; “A Bis-Phosphine Modified Peptide Ligand for Stable and Luminescent Quantum Dots”, Synthesis 2013, 45, A–E.

https://www.thieme-connect.com/ejournals/pdf/10.1055/s-0033-1339340.pdf

 

143.        Aberle, C.; Li, J.J.; Weiss, S.; Winslow, L.; “Optical Properties of Quantum-Dot-Doped Liquid Scintillators”, Journal of Instrumentation. 2013, 8, P10015.

http://iopscience.iop.org/1748-0221/8/10/P10015/pdf/1748-0221_8_10_P10015.pdf

 

144.        Levy-Sakin, M.; Grunwald, A.; Kim, S.; Gassman, N.; Antelman, J.; Kim, Y.; Ho, S.; Samuel, R.; Michalet, X.; Gottfried, A.; Lin, R.R.; Dertinger, T.; Kim, A.S.; Chung, S.; Colyer, R.A.; Weinhold, E.; Weiss, S.; Ebenstein, Y.; “Towards single-molecule optical mapping of the epigenome”, ACS Nano, 2014, 8, 14–26.

http://pubs.acs.org/doi/pdf/10.1021/nn4050694

 

145.        Weitz, S.; Gong, M.; Barr, I.; Weiss, S.; Guo, F.; “Processing of microRNA primary transcripts requires heme in mammalian cells”, PNAS, 2014, 111, 1861-6.

http://www.pnas.org/content/early/2014/01/17/1309915111.long

 

146.        Michalet, X.; Ingargiola, A.; Colyer, R.A.; Scalia, G.; Weiss, S.; Maccagnani, P.; Gulinatti, A.; Rech, I.; Ghioni, M.; “Silicon photon counting avalanche diodes for single-molecule fluorescence spectroscopy”,  Journal of Selected Topics in Quantum Electronics  2014, Volume PP, Issue99.

http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=6861975

 

147.        Barr, I.; Weitz, S.H.; Atkin, T.; Hsu, P.; Karayiorgou, M.; Gogos, J.A.; Weiss, S.; Guo, F.; “Cobalt (III) protoporphyrin activates the DGCR8 protein and can compensate microRNA processing deficiency”, Chemistry and Biology 2015, 22, 793–802.

http://www.cell.com/chemistry-biology/pdf/S1074-5521(15)00199-4.pdf

 

148.        Kisley, L.; Brunetti, R.; Tauzin, L.J.; Shuang, B.; Yi, X.; Kirkeminde, A.W.; Higgins, D.A.; Weiss, S.; Landes, C.F.; “Characterization of porous materials by fcsSOFI”, ACS Nano. 2015, 9, 9158-66.

http://pubs.acs.org/doi/pdf/10.1021/acsnano.5b03430

 

149.        Kapanidis, A.; Majumdar, D.; Heilemann, M.; Nir, E.; Weiss, S.; “Alternating Laser Excitation for Solution-Based Single-Molecule FRET”, Cold Spring Harbor Protocols (topic introduction), Nov. 2015, 11, 979-87. http://cshprotocols.cshlp.org/content/2015/11/pdb.top086405.full.pdf+html

 “---”, “Assembling the μs-ALEX Setup”, Cold Spring Harbor Protocols, (protocols), Nov. 2015, 11, 1024-26. http://cshprotocols.cshlp.org/content/2015/11/pdb.prot086413.full.pdf+html

 “---”, “Aligning the μs-ALEX Setup”, Cold Spring Harbor Protocols, (protocols), Nov. 2015, 11, 1027-28.

http://cshprotocols.cshlp.org/content/2015/11/pdb.prot086421.full.pdf+html

 “---”,  “Sample Preparation and Data Acquisition for μs-ALEX”, Cold Spring Harbor Protocols, (protocols), Nov. 2015, 11, 1029-31.

http://cshprotocols.cshlp.org/content/2015/11/pdb.prot086439.full.pdf+html

 

 

2) Accepted

150.        Ingargiola, A.; Laurence, T.; Weiss, S.; Michalet, X.; “Photon-HDF5: an open file format for single-molecule fluorescence experiments using photon-counting detectors”, accepted, Biophysical Journal.

 

 

                3) Submitted

151.        Weitz, S.H.; Quick-Cleveland, J.; Jacob, J.P.; Barr, I.; Senturia, R.; Weiss, S.; Guo, F.; “The pool of available Fe(III) heme in mammalian cells”, submitted to Cell Metabolism.

 

152.        Park, K.; Kuo, Y.; Shvadchak, V.; Ingargiola, A.; Dai, X.; Hsiung, L.; Kim, W.; Zhou, Z.H.; Zou, P.; Levine, A.J.; Li, J.J.; Weiss, S.;  “Membrane insertion of- and membrane potential sensing by-semiconductor voltage nanosensors: feasibility demonstration”, submitted to Nature Communications.

 

153.        Park, K.; Weiss, S.; “Performance Predictions and Design Rules for Membrane-Embedded Semiconducting Voltage-Sensing Nanoparticles”, submitted to Physical Review X.

 

 

                3) In preparation

154.        Yi, Xiyu; Weiss, S.;  “Dynamic range compression for high order SOFI: a sliding-window based tone-mapping approach with self-calibration”, under preparations.

 

155.        Lerner, E.; Ingargiola, A.; Chung, S.; Elhadid, Y.; Michalet, X.; Weiss, S.; “20 years of single molecule FRET – mechanistic examination of gene expression”, under preparations.

 

156.        Lerner, E.; Chung S.;  Elhadid Y.;  Ingargiola A.; Shijia, W.L.; Primaud, L.W.; Allen B.; Lee, J.J; Wang, S.; Strick, T.; Taatjes J.D.; Borukhov, S.; Weiss, S.; “Pausing in Escherichia Coli transcription initiation”,  under preparations.

 

 

c]  Non refereed papers, commentaries, perspectives

1.             Kelley, A. M.; Michalet, X.; Weiss, S., Perspectives: Chemical physics: Single-molecule spectroscopy comes of age. Science (Washington, DC, United States) 2001, 292, (5522), 1671-1672, Perspectives..

 

2.             Weiss, S., Shattering the diffraction limit of light: A revolution in fluorescence microscopy. PNAS 2001, 97, 8747-8749, Commentary.

 

3.             Bentolila, L. A.; Weiss, S., Biological quantum dots go live, Physics World 2003, 16, 23-24, Commentary.

 

4.             Laurence, T. A.; Weiss, S. How to Detect Weak Pairs, Science 2003, 299, 667-668, Perspectives.

 

5.             Soper, S. A.; Trottier, C.; Davies, M.; Dautet, H.; Wabuyele, M.; Kapanidis, A. N.; Lacoste, T.; Weiss, S., Single Photon-Counting Technology for Single-Molecule Detection Applications in Biotechnology, PharmaGenomics 2004, February, 24-34.

 

6.             Bentolila, L.A.; Michalet, X.; Pinaud, F.; Tsay, J.M.; Doose, S.; Li, J.J.; Sundaresan, G.; Wu, A.M.; S.S. Gambhir, S.S.; and Weiss, S., Quantum dots for molecular imaging and cancer medicine, Discovery Medicine 2005, 5 (26), 213-218.

 

7.             Siegmund, O.H.W.; Michalet, X.; Vallerga, J.V.; Jelinsky, P.; Weiss, S.; Cross Delay Line Detectors for High Time Resolution Astronomical Polarimetry and Biological Fluorescence Imaging,  IEEE Nuclear Science Symposium Conference Record, 2005, N14-55: 448-452.

 

8.             Michalet, X, Weiss, S, Using photon statistics to boost microscopy resolution”, PNAS, 2006, 103 (13): 4797-4798, Commentary.

 

9.             Iyer, G.; Li, J.J.; Pinaud, F.; Tsay, J.M.; Bentolila, L.A.; Michalet, X.; Weiss, S., Near-infrared peptide-coated quantum dots for small animal imaging, Proceedings of SPIE, 2006, 6096: 60960B

 

10.          Ohnukia, T.; Michalet, X.; Tripathia, A.; Weiss, S.; Arisaka, K., Development of an Ultra-fast Single-Photon Counting Imager for Single-Molecule Imaging, Proceedings of SPIE, 2006, 6092: 60920P.

 

11.          Michalet, X.; Siegmund, O.H.W.; Vallerga, J.V.; Jelinsky, P.; Millaud, J.E.; Weiss, S., A space- and time-resolved single-photon counting detector for fluorescence microscopy and spectroscopy Proceedings of SPIE, 2006, 6092: 60920M.

 

12.          Michalet, X.; Siegmund, O.H.W.; Vallerga, J.V.; Jelinsky, P.; Pinaud, F.; Millaud, J.E.; Weiss, S.; Fluorescence lifetime microscopy with a time- and space-resolved single-photon counting detector, Proceedings of SPIE , 2006, 6372: 63720E.

 

13.          Michalet, X.; Siegmund, O.H.W.,; Vallerga, J.V.; Jelinsky, P.; Millaud, J.E.; Arisaka, K.; Weiss, S.; “Detectors fpr Microscopy: Next-generation 3-D detector improves single-molecule imaging”, Laser Focus World 2007, 43: 97-101.

 

14.          Michalet, X.; Cheng, A.; Antelman, J.; Suyama, M.; Arisaka, K.; Weiss, S.; “Hybrid photodetector for single-molecule spectroscopy and microscopy”, Proceedings of SPIE , 2008

 

15.          Hamadani, K.M.; Weiss, S.; “Single molecule protein folding kinetics in a co-axial microfluidic mixer”, Proceedings of SPIE , 2008

 

16.          Shank, C.V.; Weiss, S.; Zyss, J.;  “Daniel Chemla, Obituary”, Nature Materials, 2008, 7, 433.

 

17.          Colyer, R.; Siegmund, O.; Tremsin, A.; Vallerga, J.;  Weiss, S.; Michalet, X.; “Phasor-based single-molecule fluorescence lifetime imaging using a wide-field photon-counting detector”, Proceedings of SPIE, 2009, 7185, 71850T/1-10.

 

18.          Colyer, R.A.; Scalia, G.; Rech, I.; Resnatic, D.; Marangonic, S.; Ghionic, M.; Cova, S.; Weiss, S.; Michalet, X.; “High-throughput multispot single-molecule spectroscopy”, Proceedings of SPIE , 2010 , 7571: 75710G

 

19.          Michalet, X.; Colyer, R.A.; Scalia, G.; Kim, T.; Levic, M.; Aharoni, D.; Cheng, A.; Guerrierid, F.; Arisaka, K.; Millaud, J.; Rech, I.; Resnatid, D.; Marangonid, S.; Gulinattid, A.; Ghionid, M.; Tisa, S.; Zappa, F.; Cova, S.; Weiss, S.; “High-throughput single-molecule fluorescence spectroscopy using parallel detection”, Proceedings of SPIE , 2010 , 7608: 76082D

 

20.          Michalet, X.; Colyer, R.A.; Weiss, S.; “New photon-counting cameras and multipixel photon-counting detector arrays are transforming single-molecule observational approaches”, SPIE Newsroom, Biomedical Optics & Medical Imaging, Single-molecule fluorescence spectroscopy and imaging, 2010,   DOI: 10.1117/2.1201009.003163.

 

21.          Colyer, R.A.; Scalia, G.; Villa, F.A.; Guerrieri, F.; Tisa, S.;Zappa, F.; Cova, S.; Weiss, S.; Michalet, X.; “Ultra high-throughput single molecule spectroscopy with a 1024 pixel SPAD”, Proceedings of SPIE, 2011.

 

22.          Michalet, X.; Colyer, R.A.; Scalia, G.; Weiss, S.; Siegmund, O.H.W.; Tremsin, A.S.; Vallerga, J.V.; Villa, F.; Guerrieri, F.; Rech, I.; Gulinatti, A.; Tisa, S.; Zappa, F.; Ghioni, M.; Cova, S.; “New photon-counting detectors for single-molecule fluorescence spectroscopy and imaging”, Proceedings of SPIE, 2011.

 

23.          Siegmund, O.H.W.; Vallerga, J.V.; Tremsin, A.S.; Michalet, X.; Colyer, R.A.; Weiss, S.; “Microchannel Plate Imaging Photon Counters for Ultraviolet through NIR Detection with High Time Resolution”,  Proceedings of SPIE, 2011.

 

24.          Ingargiola, A.; Colyer, R.A.; Kim, D.; Panzeri, F.; Lin, R.; Gulinatti, A.; Rech, I.; Ghioni, M.; Weiss, S.; Michalet, X.; “ ”,  Proceedings of SPIE, 2012, Vol. 8228, 82280B-1.

 

25.          Park, K.; Deutsch, Z.; Li, J.J.; Oron, D.; Weiss, S.; “Single molecule quantum-confined Stark effect measurements of semiconductor nanoparticles at room temperature”, Proceedings of SPIE, 2013, 8595, 859518-2.

 

26.          Ingargiola,A.; Panzeri, F.; Sarkosh, N.; Gulinatti, A.; Rech, I.; Ghioni, M.; Weiss. S.; Michalet, X.; “8-spot smFRET analysis using two 8-pixel SPAD arrays”, Proceedings of SPIE, 2013, 8590, 85900E-2.

 

27.          Panzeri, F.; Ingargiola,A.; Lin, R.R.; Sarkosh, N.; Gulinatti, A.; Rech, I.; Ghioni, M.; Cova, S.; Weiss. S.; Michalet, X.; “Single-molecule FRET experiments with a red-enhanced custom technology SPAD”, Proceedings of SPIE, 2013, 8590, 85900D-2.

 

28.          Qin, J.; Yi, X.; Weiss, S.; Osher, S.; “Shearlet-TGV Based Fluorescence Microscopy Image Deconvolution”, UCLA CAM Report: 14-32, 2014.