Prof. Shimon Weiss

Prof. Shimon Weiss


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


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.


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




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,



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


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


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.


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. 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


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.


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.;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.


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,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


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  single-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. 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, 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. PMID: 18339751 PMCID:PMC62426651


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


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


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: 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; 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., 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; 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.   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. 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.  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. 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, 22, 397-402. 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, 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,.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,. 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., 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, 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. PMID: 20940780 PMCID: PMC3072111


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


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.


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


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.


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.


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.


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.


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


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


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    


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.


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


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.


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.


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.


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.


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. 


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.


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.


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.



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.


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


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.


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.


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.


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.


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.


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.

 “---”, “Assembling the μs-ALEX Setup”, Cold Spring Harbor Protocols, (protocols), Nov. 2015, 11, 1024-26.

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

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



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.