Weiss, Shimon

Physical

Short Biography

Shimon received his PhD in Electrical Engineering from the Technion, Israel in 1989. After a year of postdoctoral research in AT&T Bell Laboratories, he was hired by Lawrence Berkeley National Laboratory as a staff Scientist. In 2001 he joined the departments of Chemistry & Biochemistry and Physiology at UCLA

Research Interests

Identifying and cataloging all gene sequences and their corresponding protein high-resolution static 3-dimensional structures is only a prelude to the real challenges of future biological inquiries. We need to understand the dynamic structural changes of isolated macromolecules undergoing biochemical reactions. We need to identify transient interactions between macromolecules. We need to decipher the cell circuitry and its detailed time-dependent responses to various stimuli. We need to decode intracellular and extracellular communication signals and the corresponding molecular-level responses of live cells, tissues and whole organs. Analytical tools will need to be developed in order to identify and measure these molecular conformations and interactions. High-sensitivity fluorescence methods will play a vital role in this endeavor because they offer many advantages for probing isolated molecules and molecules in live cells, tissues and organs. Fluorescence is non-invasive; it provides imaging and sectioning capabilities in three dimensions; it has high sensitivity, down to the single molecule level, and it allows the observation of molecular- and organelle-specific signals. Our group develops and applies ultrahigh-resolution, ultrahigh-sensitivity fluorescence imaging and spectroscopy tools to solving outstanding problems in biology.

Conformational dynamics of biomolecules: Many of the molecular machines that are essential for cell function and survival (transcription, replication, translation, recombination, splicing, protein folding etc.) are asynchronous, have multiple kinetic pathways and intermediates, and are comprised of several interacting components. The ability to watch one molecule at a time helps us obtain unique information on distribution functions of relevant observables, resolve subpopulations in heterogeneous samples, and record asynchronous time trajectories of observables that would otherwise be hidden. For example, dynamic distance changes between two sites on a macromolecule (or between two different molecules) can be measured via single-pair fluorescence resonance energy transfer (spFRET) by following spectral changes in the emission of a single donor-acceptor pair. Orientational changes can be detected via single-molecule fluorescence polarization anisotropy (smFPA) by following changes in the dipole orientation of a rigidly-attached or tethered probe. Our group developed such tools and uses them to study protein folding and transcription on the single-molecule level. We study the folding reaction energy landscape, pathways, conformational distributions and folding intermediates. The same tools are used to answer 25-years-old outstanding questions about the mechanisms of DNA transcription by the enzyme RNA polymerase. We are studying the relative motions between the enzyme and its DNA molecular track, the conformational motions in the enzyme itself, and conformational transitions in the DNA during the various steps of the transcription reaction.

Development of semiconductor nanocrystals as biological probes: Single-molecule experiments are currently performed predominantly in in-vitro environments. The ultimate challenge is to image cellular substructures, determine the relationships and dynamics of vesicles and organelles, describe existing conformational dynamics and biomolecular interactions, and localization all of the above in-vivo with single molecule sensitivity and nanometer-accuracy. This will allow the study of enzymes and multi-component molecular machines in their natural environment, with the signaling and regulation circuitry all wired-up. Towards the accomplishment of this tremendously complex task, we are developing colloidal fluorescent semiconductor nanocrystals (a class of quantum dots) for biological labeling. Nanocrystals posses several properties that make them very attractive as fluorescent probes for in-vivo single-molecule experiments: broad excitation spectra, narrow emission spectra, precise-tunable emission peaks, long fluorescence lifetimes, and negligible photobleaching. We are developing organic coatings, bioconjugation schemes, targeting strategies, and unique instrumentation that take advantage of nanocrystals spectral properties. Recently, we have shown how these distinctive properties increase the resolution of fluorescence microscopy measurements down to the nanometer level using far-field optics. We have also shown that their long fluorescence lifetime can be used to observe molecules and organelles in live cells without interference from autofluorescence background (a pre-requisite for single molecule detectability). We are currently pursuing applications in genomics (physical mapping, genome rearrangement), vesicle trafficking, cargo selection and in-vivo motility assays of molecular motors.

Biomolecular interactions by coincidence detection: Understanding the intricate network of protein interactions that take place within the cell of an organism allows the understanding of the mechanisms that control its growth, maintenance, and disease. Protein-protein interactions are most commonly identified using the yeast two-hybrid (Y2H) assay. However, Y2H has several limitations including complications associated with the use of protein fusions, incorrect protein folding, incorrect post-translational modification, potential for toxicity and incompatibility with DNA binding proteins. We are developing a new method for detecting static and transient macromolecular interactions with ultrahigh sensitivity, based on two-color coincident detection of single molecules in a confocal detection volume. Towards this end, we are developing unique fluorescent reagents, site-directed labeling schemes and novel single-molecule detection and analysis tools for monitoring protein-protein and protein-DNA interactions initially in-vitro and at a later stage in-vivo. We envision applications in cellular signaling and bio-sensing.

Honors & Awards

  • Rothschild Fellowship Rothschild Fellowship
  • Royal College of Physicians, London Rank Prize
  • Michael and Kate Barany Biophysical Society Award
  • Optical Society of America Fellow
  • The Director Outstanding Performance Award, Lawrence Berkeley Laboratory
  • AAAS
  • ACS
  • APS
  • Biophysical Society
  • Fellow, Optical Society of America (1999)

Representative Publications

  • Sternklar, S.; S., W.; Fischer, B., Controlling the self-frequency shift and intensity of oscillations with photorefractive crystals. Appl. Optics 1985, 24, 3121.
  • Sternklar, S.; S., W.; Fischer, B., Tunable frequency shifts of photorefractive oscillators. Opt. Lett 1986, 11, 165.
  • Fischer, B.; Sternklar, S.; Weiss, S., Photorefractive oscillation with intracavity image and multimode fiber. Applied Physics Letters 1986, 48, (23), 1567-9.
  • Sternklar, S.; Weiss, S.; Segev, M.; Fischer, B., Beam coupling and locking of lasers using photorefractive four-wave mixing. Opt. Lett. 1986, 11, 528.
  • Sternklar, S.; S., W.; Fischer, B., Double phase conjugate mirror: analysis, demonstration, and applications. Opt. Lett. 1986, 12, 114.
  • 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.
  • 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.
  • 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
  • Fischer, B.; S., W.; Sternklar, S., Spatial light modulation and filtering effects in photorefractive wave mixing. Appl. Phys. Lett. 1987, 50, 483.
  • 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.
  • 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.
  • Weiss, S., Segev, M.,Sternklar, S., and Fischer, B., Photorefractive Dynamic Optical Interconnects. Appl. Opt. 1988, 27, 3422.
  • Fischer, B.; Weiss, S., Solvable optimized four-wave mixing configuration with cubic photorefractive crystals. Appl. Phys. Lett. 1988, 53, 257.
  • Fischer, B.; Sternklar. S.; and Weiss, S., Photorefractive Oscillators. IEEE J. Quantum Electron 1989 QE-25, 550.
  • Weiss, S.; Werner, O.; and Fischer, B., Analysis of coupled photorefractive wave-mixing junctions. Opt. Lett. 1989 14, 186.
  • Weiss, S.; Fischer, B., Photorefractive saturable absorptive and dispersive optical bistability. Optics Communications 1989, 70, (6), 515-21.
  • Weiss, S.; Fischer, B., Instabilities and self-pulsation in a ring cavity with a photorefractive wave mixer. Opt. Lett. 1989, 14, (21), 1213-15.
  • 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.
  • Weiss, S.; Fischer, B., Dynamics of photorefractive nonlinear two-beam coupling and feedback effects. Optical and Quantum Electronics 1990, 22, (Spec. Issue), S17-S45.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • Weiss, S.; Ogletree, D. F.; Botkin, D.; Salmeron, M.; Chemla, D. S., Ultrafast scanning probe microscopy. Appl. Phys. Lett. 1993, 63, 2567.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • Sucha, G.; Bolton, S. R.; Weiss, S.; Chemla, D. S., Period doubling and quasiperiodicity in additive pulse modelocked lasers. Opt. Lett. 1995, 20, 1794.
  • 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.
  • 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.
  • 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.
  • 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.
  • 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.
  • Ha, T.; Chemla, D. S.; Enderle, T.; Weiss, S., Single molecule spectroscopy with automated positioning. Appl. Phys. Lett. 1997, 70, 782.
  • Ha, T.; Enderle, T.; Selvin, P. R.; Chemla, D. S.; Weiss, S., Room temperature observation of quantum jumps. Chem. Phys. Lett. 1997, 271,1.
  • Ha, T.; Chemla, D. S.; Enderle, T.; Weiss, S., Strategy for room temperature spectroscopy of single molecules. Bioimaging 1997, 5, 99.
  • Ha, T.; Glass, J.; Chemla, D. S.; Weiss, S., Hindered rotational diffusion and rotational jumps of single molecules. Phys. Rev. Lett. 1998, 80, 2093.
  • Enderle, T.; Ha, T.; Chemla, D. S.; Weiss, S., Near-field fluorescence microscopy of cells. Ultramicroscopy 1998, 71, (1-4), 303-9.
  • Bruchez, M., Jr.; Moronne, M.; Gin, P.; Weiss, S.; Alivisatos, A. P., Semiconductor nanocrystals as fluorescent biological labels. Science 1998, 281, (5385), 2013-6.
  • U. Banin, M. Bruchez, A.P. Alivisatos, T. Ha, S. Weiss and D.S. Chemla, Ha, T.; Weiss, S., Dual- and single-molecule fluorescence spectroscopy: towards kinetic observation of single-molecule reactions. Organic Mesoscopic Chemistry 1999, 61-74.
  • Weiss, S., Fluorescence spectroscopy of single biomolecules. Science 1999, 283, (5408), 1676-83.
  • 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.
  • 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.
  • 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.
  • 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
  • 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.
  • 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
  • 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
  • Weiss, S., Measuring conformational dynamics of biomolecules by single molecule fluorescence spectroscopy. Nat Struct Biol 2000, 7, (9), 724-9. PMID: 10966638
  • 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
  • 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
  • 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.
  • 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
  • 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.
  • 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.
  • Michalet, X.; Weiss, S., Single-molecule spectroscopy and microscopy. Comptes Rendus Physique 2002, 3, (5), 619-644.
  • 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.
  • 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
  • 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
  • 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
  • Baer, R.; Neuhauser, D.; Weiss, S., Enhanced Absorption Induced by a Metallic Nanoshell. Nano Letters 2004, 4, (1), 85-88.
  • 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.
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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.
  • 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
  • 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
  • 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
  • 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.
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • 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
  • Michalet, X.; Siegmund, O.H.W.; Vallerga, J.V.; Jelinsky,P.; Millaud, J.E. and Weiss, S, Detectors for ingle -molecule fluorescence imaging and spectroscopy, Journal of Modern Optics, 2007, 54: 239–81.PMID: 2057633 PMCID :PMC2821066
  • 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
  • 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
  • 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
  • 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
  • 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
  • Schipper, M.L.; Cheng, Z.; Lee, S.W.; Keren, S.; Bentolila, L.A.; Sundaresan, G.; Iyer, G.; Gheysens,O.; Ebenstein, Y.; Li, J.; Rao, J.; Chen, X.; Wu, A.M.; Weiss, S.; Gambhir, S.S.; “MicroPET-Based Biodistribution of Quantum Dots in Living Mice”, J. of Nuclear Medicine, 2007; 48, 1511-1518. DOI: http://pubs.acs.org/10.2967/jnumed.107.040071 . PMCID: PMC2299220
  • Kim, Y.; Ho, S.O.; Gassman, N.R.; Korlann, Y.; Landrof, E.V.; Collart, F.; Weiss, S.; “Efficient site-specific labeling of proteins via cysteines”, Bioconjugate Chemistry, 2008, 19 (3), 786–791, DOI: http://pubs.acs.org/10.1021/bc7002499 . PMID: 18275130 PMCID: PMC3085854
  • Hamadani, K.M.; Weiss, S.; “Non-equilibrium Single Molecule Protein Folding in a Co-axial Mixer”, Biophysical Journal, 2008, 95, 352–365, BioFAST: First Published March 13, 2008. DOI: http://pubs.acs.org/10.1529/biophysj.107.127431 .PMID: 18339751 PMCID:PMC62426651
  • Chang, Y.P.; Pinaud, F.; Michalet, X.; Iyer, G.; and Weiss, S.; “Tracking bio-molecules in live cells using quantum dots”, Journal of Biophotonics, 2008, 4, 287–298; DOI: http://pubs.acs.org/10.1002/jbio.200810029 .PMID: 19343652 PMCID: PMC3075916
  • Korlann, Y.; Dertinger, T.; Michalet, X.; Weiss, S.; Enderlein, J.; “Measuring diffusion with polarization-modulation dual-focus Fluorescence Correlation Spectroscopy”, Optics Express, 2008, 16, 14609-16 DOI: http://pubs.acs.org/10.1364/OE.16.014609 . PMID: 18794997 PMCID:PMC 2832597
  • 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
  • Schipper, M.L., Iyer, G., Koh, A.L., Cheng, Z., Ebenstein, Y., Aharoni, A., Keren, S., Bentolila, L.A., Li, J., Rao, J., Chen, X., Banin, U., Wu, A.M., Sinclair, R., Weiss, S., Gambhir, S.S., “Particle Size, Surface Coating, and Pegylation Influence the Biodistribution of Quantum Dots in Living Mice”, Small, 2009, 5, 126–34; DOI: http://dx.doi.org/10.1002/smll.200800003. PMID: 19051182 PMCID: PMC3084659
  • Waldauer, S.; Bakajin, O.; Ball, T.; Chen, Y.; DeCamp, S.; Kopka, M.; Jäger,, M.; Singh, V.R.; Wedemeyer, W.J.; Weiss, S.; Yao, S.; Lapidus, L.J.; “Ruggedness in the Folding Landscape of Protein L”, HFSP J., 2009, 2, 388-395.,  DOI: http://dx.doi.org/10.2976/1.3013702. PMID: 19436489 PMCID: PMC 2645578
  • Gassman, N.R.; Ho, S.O.; Korlann, Y.; Chiang, J.; Wu, Y.; Perry, J.; Kim, Y.; Weiss, S.; “In-vivo assembly and single molecule characterization of the transcription machinery from Shewanella Oneidensis MR-1”, Protein Expression and Purification, 2009, 65, 66–76; DOI: http://dx.doi.org/10.1016/j.pep.2008.11.013. PMID: 19111618 PMCID: PMC3084661
  • Pinaud, F.; Michalet, X.; Iyer, G.; Margeat, E.; Moore, H.P.; Weiss, S.; “Dynamic Partitioning of a GPI-Anchored Protein in Glycosphingolipid-Rich Microdomains of the Cell Membrane”, Traffic, 2009,10, 691-712. DOI: http://dx.doi.org/10.1111/j.1600-0854.2009.00902 PMID:19416475 PMCID:PMC 2766537
  • Antelman, J.; Ebenstein, Y.; Chang, C.W.; Weiss, S.; Michalet, X.; “Nanometer Distance Measurements Between Multicolor Quantum Dots”, Nano Letters, 2009, 9, 2199-2205. DOI: http://dx.doi.org/10.1021/nl901163k .PMID;19374434 PMCID: PMC 2748936
  • Ebenstein, Y.; Gassman, N.R.; Antelman, J.; Kim, Y.; Kim, S.; Ho, S.O.; Samuel, R.; Michalet, X.; Weiss, S.; “Lighting up Individual DNA Binding Proteins with Quantum Dots”, Nano Lett., 2009, 9, 1598–1603. DOI: http://dx.doi.org/10.1021/nl803820b . PMID:1920670 PMCID: PMC 3084662
  • Bentolila, L.A.; Ebenstein, Y.; Weiss, S.; “Quantum Dots for in vivo Small Animal Imaging”, J. of Nuclear Medicine, 2009, 50, 493-6. DOI: http://dx.doi.org/0.2967/jnumed.108.053561 . PMID: 19289434 PMCID:PMC3081879
  • Ebenstein, Y.; Gassman, N.R.; Kim, S.; Antelman, J.; Weiss, S.; “Combining Atomic Force and Fluorescence microscopy For Analysis of Quantum-dot labeled Protein–DNA Complexes”, Journal of Molecular Recognition, 2009, DOI: http://dx.doi.org/10.1002/jmr.956 .PMID:19452448 PMCID: PMC3085854
  • Antelman, J.; Ebenstein, Y.; Michalet, X.; Weiss, S.; “Suppression of quantum dots’ blinking in DTT-doped polymer films”, J. Phys. Chem. C, 2009, 113, 11541-45, DOI: http://dx.doi.org/10.1021/jp811078e PMID: 20161096 PMCID:PMC 2745152
  • Tremsin, A.S.; Siegmund, O.H.W.; Vallerga, J.V.; Raffanti, R.; Weiss, S.; Michalet, X.; “High Speed Multichannel Charge Sensitive Data Acquisition System with Self-Triggered Event Timing”, IEEE Trans. Nucl. Sci., 2009, 56, 1148-52, DOI: http://dx.doi.org/10.1109/TNS.2009.2015302 .PMID: 20174482 PMCID:PMC 2824915
  • Barat, B.; Sirk, S.; McCabe K.; Li, J.; Lepin, Remenyi, R.; E.; Koh, AL.; Olafsen, T.; Gambhir, SS.; Weiss, S.; and Wu, AM.; “Cys-antibody-quantum dot conjugates (immunoQdots) for cancer marker detection”,  Bioconjugate Chemistry, 2009, 20, 1474-8, DOI: http://dx.doi.org/10.1021/bc800421f . PMID: 19642689 PMCID:PMC 2891877
  • 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
  • Liu, C.; Chung, S.; Lee, S.; Weiss, S.; Neuhauser, D.; “Adsorbate induced absorption red-shift in an organic cluster conjugate: electronic effects of surfactants and organic adsorbate on band edge excitations in a methanethiol CdSe conjugate”, J. Chem. Phys, 2009, 131, 174705-1/-8., DOI: http://dx.doi.org/10.1063/1.3251774 PMID: 19895033 PMCID:PMC 2787060
  • Dertinger, T.; Colyer, R.; Iyer, G.; Weiss, S.; Enderlein, J.; “Fast, background-free, 3D superresolution optical fluctuation imaging (SOFI)”, Proc Natl Acad Sci, 2009, 106, 22287-92, DOI: http://dx.doi.org/10.1073/pnas.0907866106 PMID:20018714 PMCID:PMC 2799731
  • Dertinger, T.; Colyer, R.; Vogel, R.; Enderlein, J.; Weiss, S.; “Achieving increased resolution and more pixels with Superresolution Optical Fluctuation Imaging (SOFI)”, Optics Express, 2010, 18. 18875-85.  DOI: http://dx.doi.org/10.1364/OE.18.018875 PMID: 20940780 PMCID: PMC3072111
  • Dertinger, T.; Heilemann, M.; Vogel, R.; Sauer, M.; Weiss, S.; “Superresolution Optical Fluctuation Imaging with Organic Dyes”, accepted, Angew. Chem. 2010, 49, 1–4. DOI: http://dx.doi.org/10.1002/anie.201004138 PMID:21031383 PMCID: PMC 3007670
  • 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 8×1 SPAD array”, Biomedical Optics Express. 2010, 1, 1408-31. DOI: http://dx.doi.org/10.1364/BOE.1.001408 PMID: 21258559 PMCID:PMC 3018120
  • 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, DOI: http://dx.doi.org/10.1038/nmeth.1569 PMID: 212976618 PMCID: PMC 3075913
  • 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., DOI: http://dx.doi.org/10.1021/bc100593
  • 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.
  • 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.
  • 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.
  • 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. PMCID: PMC3807127.
  • 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
  • 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”, Science, 2012, 337, 591-5. PMID: 22859489.
  • 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.
  • 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
  • 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.
  • 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.
  • 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.
  • 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.
  • 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. PMCID: PMC 3855418
  • 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. PMCID: PMC 3747630
  • 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”, Reports on Progress in Physics. Rep. Prog. Phys., 2013, 76, 072601, 1-21. PMCID: PMC 3736146
  • 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, 2138−46. PMCID: PMC 3733402
  • 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. PMCID: PMC3981610.
  • Aberle, C.; Li, J.J.; Weiss, S.; Winslow, L.; “Optical Properties of Quantum-Dot-Doped Liquid Scintillators”, Journal of Instrumentation. 2013, 8, P10015. PMCID: PMC 4225632
  • 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. PMCID: PMC 4022788
  • 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. PMCID: PMC 3918773
  • 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, 20, 3804420. PMCID: PMC 4190971
  • 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. PMCID: PMC 4788496
  • 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. PMID: 26235127 NIHMSID 881006
  • 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. PMID: 26527772
  • Ingargiola, A.; Laurence, T.; Weiss, S.; Michalet, X.; “Photon-HDF5: an open file format for single-molecule fluorescence experiments using photon-counting detectors”, Biophysical Journal 2016, 110, 26–33. PMCID: PMC 4805879
  • Lerner, E.; Ploetz, E.; Hohlbein, J.; Cordes, T.; Weiss, S., “A Quantitative Theoretical Framework For Protein-Induced Fluorescence Enhancement−Förster-Type Resonance Energy Transfer (PIFE-FRET)”, J Phys Chem B, 2016, 120, 6401–10. PMCID# PMC4939467.
  • Ingargiola, A.; Lerner, E.; Chung, S.; Weiss, S.; Michalet, X.; “FRETBursts: An Open Source Toolkit for Analysis of Freely-Diffusing Single-Molecule FRET”, PLOS One, 2016, 1-27. PMCID: PMC 4988647.
  • Boutelle, R.; Neuhauser, D.; Weiss, S.; “Far-field Superresolution Detection of Plasmonic Near-fields”, accepted to ACS Nano. ACS Nano, 2016, 10, 7955–62. PMID: 27501216 NIHMSID 864100
  • Ploetz, E.; Lerner, E.; Florence Husada, F.; Roelfs, M.; Chung, S.; Hohlbein, J.; Weiss, S.; Cordes, T.; “Fluorescence resonance energy transfer and protein-induced fluorescence enhancement as synergetic multi-scale molecular rulers”, Scientific Reports, 2016, 6, Article number: 33257. PMCID: PMC 5027553.
  • Lerner, E.; Chung S.; Allen, B.L.; Wang, S.; Lee, J.J; Lu, W.S.; Grimaud, W.L.; Ingargiola, A.; Michalet, X.; Elhadid Y.; Borukhov, S.; Strick, T.; Taatjes J.D.; Weiss, S.; “Backtracked and paused transcription initiation intermediate of Escherichia coli RNA polymerase”,
  •  PNAS, 2016, 113, E6562–E6571, PMCID: PMC 5087071. doi: 10.1073/pnas.1605038113
  • Park, K.; Weiss, S.; “Performance Predictions and Design Rules for Membrane-Embedded Semiconducting Voltage-Sensing Nanoparticles”, Biophysical Journal, 2017, 112, 703–13. PMCID: PMC 5340176.
  • Alhadid, Y.; Chung S.; Lerner, E.; Taatjes, D.J.; Borukhov, S.; Weiss, S.; “Studying transcription initiation by Escherichia coli RNA polymerase with diffusion-based single molecule fluorescence”, Protein Science 2017, 26, 1278–1290. NIHMSID 880999
  • Lerner, E.; Ingargiola, A.; Lee, J.J.; Borukhov, S.; Michalet, X.; Weiss, S.; “Different types of pausing modes during transcription initiation”, Transcription. 2017, 0, 1–12. NIHMSID 8811001
  • Ingargiola, A.; Lerner, E.; Chung, S.; Panzeri, F.; Gulinatti, A.; Rech, I.; Ghioni, M.; Weiss, S.; Michalet, X.; “Multispot single-molecule FRET: towards high-throughput analysis of freely diffusing molecules”, accepted, PLOS ONE, 2017, 12(4): e0175766. NIHMSID 881002
  • Feng, Z.; Suzy Nam, S.; Hamouri, F.; Ducos, B.; Vriz, S.; Volovitch, M. Jullien, L.; Lin, S.; Weiss, S.; Bensimon, D.; “Optical control of tumor induction in the zebrafish”, Scientific Reports, 2017, 7: 9195, 1-12.
  • Chio, U.; Chung, S.; Weiss, S.; Shan, S.; “A protean clamp guides membrane targeting of tail-anchored proteins”, PNAS, October 2017, 114 no. 41 E8585-E8594. doi: 10.1073/pnas.1708731114
  • Ingargiola, A.; Segal, M.; Gulinatti, A.; Rech, I.; Labanca, I.; Maccagnani, P.; Ghioni, M.; Weiss, S.; Michalet, X.; “48-spot single-molecule FRET setup with periodic acceptor excitation”, Journal of Chemical Physics, 2018, 148, 123304-1-15.
  • Lerner, E.; Weiss, S.; “Characterizing highly dynamic conformational states: the transcription bubble in RNAP-promoter open complex as an example”, Journal of Chemical Physics, 2018, 148 , 123315-1-9.
  • 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”, Science Advances, 2018, 4: e1601453, 1-10, 12 January 2018.
  • Lerner, E.; Cordes, T.; Ingargiola, A.; Alhadid, Y.; Chung, S.; Michalet, X.; Weiss, S.; “Towards dynamic structural biology: “Two decades of single-molecule Förster resonance energy transfer”, Science, 2018, 359, 288 1-12, 19 January 2018.
  • Zhang, W.; Hamouri, F.; Feng, Z.; Aujard, I.; Ducos, B.; Ye, S.; Weiss, S.; Volovitch, M.; Vriz, S.; Jullien, L.; Bensimon, D.; “Control of protein activity and gene expression by cyclofen-OH uncaging”, ChemBioChem,. 10.1002/cbic.201700630
  • Lee, J.H.; Chandrasekar, S.; Chung, S.Y.; Fu, Y.H.; Liu, D.; Weiss, S.; Shan, S.O.; “Sequential activation of human signal recognition particle by the ribosome and signal sequence drives efficient protein targeting”, PNAS,. 2018 DOI:10.1073/pnas.1802252115. http://www.pnas.org/content/pnas/early/2018/05/29/1802252115.full.pdf
  • Bar-Elli, O.; Steinitz, D.; Yang, G.; Tenne, R.; Ludwig, A.; Kuo, Y.; Triller, A.; Weiss, S.; Oron, D.; “Rapid voltage sensing with single nanorods via the quantum confined Stark Effect”, ACS Photonics, 2018, 2860–2867. DOI:10.1021/acsphotonics.8b00206. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6053642/pdf/ph8b00206.pdf
  • Schidorsky, S.; Yi, X.; Razvag, Y.; Sajman, J.; Weiss, S.; Sherman, E.; “Synergizing superresolution optical fluctuation imaging with single molecule localization microscopy”,  Methods of Applied Fluorescence,2018, 6, 045008. http://iopscience.iop.org/article/10.1088/2050-6120/aadc2b/pdf
  • Ingargiola, A.; Segal, M.; Gulinatti, A.; Rech, I.; Labanca, I.; Maccagnani, P.; Ghioni, M.; Weiss, S.; Michalet, X.; “Optical crosstalk in SPAD arrays for high-throughput single-molecule fluorescence spectroscopy”, Nuclear Instruments and Methods in Physics Research A. 2018, 912, 255-258.  https://doi.org/10.1016/j.nima.2017.11.070
  • Ingargiola A.; Weiss, S.; Lerner, E.;, “Monte-Carlo Diffusion-Enhanced Photon Interence: Distance Distributions and COnformational Dynamics in single-molecule FRET”, J. Phys. Chem. B 2018, 122, 11598−11615. https://doi.org/10.1021/acs.jpcb.8b07608
  • Kuo, Y.; Li, J.J.; Michalet, X.; Meir, N.; Bar-Elli, O.; Chan, E.; Oron, D.; Weiss, S.; “Characterizing the Quantum Confined Stark Effect in Nanorods for Single-Molecule Electrophysiology”,  ACS Photonics, 2018, 5, 4788-4800. https://doi.org/10.1021/acsphotonics.8b00617 
  • Ulku, A.C.; Bruschini, C.; Antolovic, I.M.; Kuo, Y.; Park, J.; Weiss, S.; Michalet, X.; Charbon, E.; “A 512×512 SPAD Image Sensor with Integrated Gating for Widefield FLIM”, accepted, IEEE Journal of Selected Topics in Quantum Electronics (JSTQE) special issue on Biophotonics., 2019, 25, 6801212. https://doi.org/10.1109/JSTQE.2018.2867439
  • Chung, S.; Lerner, E.; Jin, Y.; Kim, S.; Elhadid Y.; W.S.; Grimaud, Zhang, I.X.; Knobler, C.M.; Gelbart, W.M., Weiss, S.; “The effect of macromolecular crowding on single-round transcription by E. coli RNA polymerase”, Nucleic Acids Research, 2019 , 47, 1440–1450. https://doi.org/10.1093/nar/gky1277
  • Chio, U.S.; Chung, S.Y.; Weiss, S.; Shan, S.O.; “A chaperone lid ensures efficient and privileged client transfer during tail-anchored protein targeting”, Cell Reports, 2019, 26, 37–44. https://doi.org/10.1016/j.celrep.2018.12.035
  • Ghosh, S.; Chizhik, A.M.; Wang, G.; Gregor, I.; Oron, D.; Weiss, S.; Enderlein, J.; Chizhik, A.I.; “Excitation and emission transition dipoles of type-II semiconductor nanorods”, Nano Letters, 2019, 19, 1695-1700. https://pubs.acs.org/doi/pdf/10.1021/acs.nanolett.8b04695
  • Yi, X.; Son., S.; Weiss, S.; “Moments reconstruction and local dynamic range compression of high order Superresolution Optical Fluctuation Imaging”, Biomedical Optics Express, 2019, 10, 2430-45. https://doi.org/10.1364/BOE.10.002430 
  • Park, J.; Yung Kuo, Y.; Li, J.J.; Chen, E.; Weiss, S.; “Improved surface functionalization and characterization of membrane targeted semiconductor voltage nanosensors”, Journal of Physical Chemistry Letters, 2019,10, 3906−3913. https://doi.org/10.1021/acs.jpclett.9b01258 
  • Segal, M.; Ingargiola, A.; Lerner, E.; Chung, S.; White, J.; Streets, A.; Weiss, S.; Michalet, X.; “High-throughput smFRET analysis of freely diffusing nucleic acid molecules and associated proteins”, Methods, 2019. https://www.sciencedirect.com/science/article/pii/S1046202318304432
  • Yudovich, S.; Steinitz, D.; Grupi, A.; Oron, D.; S.; Weiss, S.; “Ratiometric Widefield Imaging with Spectrally Balanced Detection”, Biomedical Optics Express, 2019, 10, 5385-94.https://www.osapublishing.org/boe/viewmedia.cfm?uri=boe-10-10-5385&seq=0
  • Grupi, A.; Ashur, I.; Marzouqe, A.; Morgenstein, L.; Yudovich, S.; Yatzkan-Shapira, Z.; Degani-Katzav, N.; Weiss, S.; “Interfacing the cell with ‘biomimetic membrane proteins’ ”, Small, 2019, 1903006 https://doi.org/10.1002/smll.201903006
  • Ankri, R.; Basu, A.; Ulku, A.C.; Charbon, E.; Weiss, S.; Michalet, X.; “Single Photon, Time-Gated, Phasor-based Fluorescence Lifetime Imaging Through Highly Scattering Medium”, ACS Photonics, 2019, 7 (1), 68-79.
  • JH Lee, SY Chung, YHH Fu, R Qian, X Sun, S Weiss, S Shan, “Receptor compaction and GTPase movements drive cotranslational protein translocation”, bioRxiv, 2020.
  • Yi, X.; Weiss, S.; “Cusp-artifacts in high order Super-resolution Optical Fluctuation Imaging”, Biomedical Optics Express, 2020, 11 (2), 554-570.
  • Arin Ulku, Andrei Ardelean, Michel Antolovic, Shimon Weiss, Edoardo Charbon, Claudio Bruschini, Xavier Michalet, “Wide-field time-gated SPAD imager for phasor-based FLIM applications”, Methods and Applications in Fluorescence, 2020, 8 (2), 024002.
  • A Ludwig, P Serna, Ln Morgenstein, G Yang, O Bar-Elli, G Ortiz, E Miller, D Oron, A Grupi, S Weiss, A Triller, “Development of lipid-coated semiconductor nanosensors for recording of membrane potential in neurons”, ACS Photonics, 2020, 7 (5), 1141-1152.
  • E Lerner, B Ambrose, A Barth, V Birkedal, S C Blanchard, R Borner, T Cordes, T D Craggs, T Ha, G Haran, T Hugel, A Ingargiola, A Kapanidis,   D C Lamb, T Laurence, E A Lemke, E Margeat, J Michaelis, X Michalet, D Nettels, T-Otavio Peulen, B Schuler, C AM Seidel, H So-leimaninejad, S Weiss, “The FRET-based structural dynamics challenge–community contributions to consistent and open science practices”, arXiv preprint, 2020, arXiv:2006.03091.
  • A Basu, M K Paul, M Alioscha-Perez, A Grosberg, H Sahli, S Dubinett, S Weiss, “Quantitative Analysis of Actin Cytoskeleton’s Morphological Changes during EMT in Lung Cancer and Pre-Cancer Cell Lines”, Biophysical Journal, 2021, 120 (3), 346a.
  • E Lerner, A Barth, J Hendrix, B Ambrose, V Birkedal, S C Blanchard, R Börner, H Sung Chung, T Cordes, T D Craggs, A A Deniz, J Diao, J Fei,   R L Gonzalez, I V Gopich, T Ha, C A Hanke, G Haran, N S Hatzakis, S Hohng, S-Cheol Hong, T Hugel, A Ingargiola, C Joo, A N Kapanidis, H D Kim, T Laurence, N Ki Lee, Tae-Hee Lee, E A Lemke, E Margeat, J Michaelis, X Michalet, S Myong, D Nettels, T-Otavio Peulen, E Ploetz, Y Razvag, N C Robb, B Schuler, H Soleimaninejad, C Tang, R Vafabakhsh, D C Lamb, C AM Seidel, S Weiss, “FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices”, Elife, 2021, 10, e60416.
  • D Adler, Z Shapira, S Weiss, A Shainberg, A Katz, “Weak Electromagnetic Fields Accelerate Fusion of Myoblasts”, International Journal of Molecular Sciences, 2021, 22 (9), 4407.
  • J Lee, A Jomaa, S Chung, Yu-Hsien Hwang Fu, Ruilin Qian, Xuemeng Sun, Hao-Hsuan Hsieh, Sowmya Chandrasekar, Xiaotian Bi, Simone Mattei, Daniel Boehringer, Shimon Weiss, Nenad Ban, Shu-ou Shan, “Receptor compaction and GTPase rearrangement drive SRP-mediated cotranslational protein translocation into the ER”, Science Advances, 2021, 7 (21), eabg0942.
  • Soma Ghosh, Nishanth Belugali Nataraj, Ashish Noronha, Sushant Patkar, Arunachalam Sekar, Saptaparna Mukherjee, Sabina Winograd-Katz, Lior Kramarski, Aakanksha Verma, Moshit Lindzen, Diana Drago Garcia, Joseph Green, Galit Eisenberg, Hava Gil-Henn, Arkaprabha Basu, Yan Lender, Shimon Weiss, Moshe Oren, Michal Lotem, Benjamin Geiger, Eytan Ruppin, Yosef Yarden, “PD-L1 recruits phospholipase C and enhances tumorigenicity of lung tumors harboring mutant forms of EGFR”, Cell Reports, 2021, 35 (8), 109181.
  • A Grupi, Z Shapira, S Yudovich, N Degani-Katzav, S Weiss, “Point-localized, site-specific membrane potential optical recording by single fluorescent nanodiscs”, Biophysical Reports, 2021, 1 (1), 100007.
  • US Chio, Y Liu, SY Chung, WJ Shim, S Chandrasekar, S Weiss, S Shan, “Subunit cooperation in the Get1/2 receptor promotes tail-anchored membrane protein insertion”, Journal of Cell Biology, 2021, 220 (11), e202103079.
  • Z Shapira, N Degani-Katzav, S Yudovich, A Grupi, S Weiss, “Optical probing of local membrane potential with fluorescent polystyrene beads”, Biophysical Reports, 2021, 1 (2), 100030.
  • S Sehayek, X Yi, S Weiss, PW Wiseman, “Rapid ensemble measurement of protein diffusion and probe blinking dynamics in cells”, Biophysical Reports, 2021, 1 (2), 100015.
  • Arkaprabha Basu, Manash K Paul, Mitchel Alioscha-Perez, Grosberg Anna, Hichem Sahli, Steven M Dubinett, Shimon Weiss, “Statistical Parametrization of Cell Cytoskeleton (SPOCC) reveals novel lung cancer cytoskeletal phenotype with partial EMT signature”, Communications Biology, 2022, 5 (407).
  • A Marzouq, L Morgenstein, S Yudovich, A Atkins, A Grupi, S Weiss, “Long chain lipids facilitate insertion of large nanoparticles into membranes of small unilamellar vesicles”, Biophysical Journal, 2022, 121 (3), 73a.
  • Jason T Smith, Alena Rudkouskaya, Shan Gao, Arin Ulku, Claudio Bruschini, Edoardo Charbon, Shimon Weiss, Margarida MR Barroso, Xavier Intes, Xavier Michalet, “Characterization of a large gated SPAD array for widefield NIR fluorescence lifetime imaging in vitro and in vivo”, Biophysical Journal, 2022, 121 (3), 415a.
  • Benjamin Ambrose, Victoria E Hill, Robert A Shaw, Tristan Johnston-Wood, Matthew Willmott, Callum Johnston, Rebecca Mächtel, Thorben Cordes, Eitan Lerner, JG Hill, Shimon Weiss, Timothy D Craggs, “A novel single molecule fluorescence quenching technique for measuring distances below 3 nm”, Biophysical Journal, 2022, 121 (3), 431a.
  • D Roy, X Michalet, EW Miller, RP Gunsalus, RT Clubb, S Weiss, “Bacterial resting membrane potential: a case study with Bacillus subtilis”, Biophysical Journal, 2022, 121 (3), 139a.
  • SY Chung, Y Alhadid, M Segal, J Lee, S Borukhov, S Weiss, “Single molecule activity assay for SARS-CoV-2 RNA dependent RNA polymerase”, Biophysical Journal, 2022, 121 (3), 359a-360a.
  • L Morgenstein, M Tsubary, A Atkins, A Grupi, S Weiss, “Controlled membrane interactions by lipid coated quantum dots”, Biophysical Journal, 2022, 121 (3), 73a.
  • PD Harris, A Narducci, C Gebhardt, T Cordes, S Weiss, E Lerner, “Multi-parameter photon-by-photon hidden Markov modeling”, Nature Communications, 2022, 13 (1), 1-12.
  • D Roy, Z Shapira, S Weiss, “Membrane potential sensing: Material design and method development for single particle optical electrophysiology”, The Journal of Chemical Physics, 2022, 156 (8), 084201.
  • D Ferschweiler, M Segal, S Weiss, X Michalet, A user-friendly tool to convert photon counting data to the open-source Photon-HDF5 file format”, Single Molecule Spectroscopy and Superresolution Imaging, 2022, XV 11967, 7-15.
  • X Michalet, A Ulku, JT Smith, C Bruschini, S Weiss, E Charbon, X Intes, “NIR fluorescence lifetime macroscopic imaging with a time-gated SPAD camera”, Multiphoton Microscopy in the Biomedical Sciences, 2022, XXII 11965, 29-37.
  • Jason T Smith, Alena Rudkouskaya, Shan Gao, Arin Ulku, Claudio Bruschini, Edoardo Charbon, Shimon Weiss, Margarida Barroso, Xavier Intes, Xavier Michalet, “Characterization of a large gated SPAD array for in vivo fluorescence lifetime imaging of drug target engagement”, Imaging, Manipulation, and Analysis of Biomolecules, Cells, and Tissues XX, 2022, PC1196408.
  • Jason T Smith, Juhi M Gupta, Alena Rudkouskaya, Shan Gao, Arin Ulku, Claudio Bruschini, Edoardo Charbon, Shimon Weiss, Margarida Barroso, Xavier Intes, Xavier Michalet, “Characterization of a large Gated SPAD camera for in vivo Macroscopic Fluorescence Lifetime Imaging”, Clinical and Translational Biophotonics, 2022, TW4B. 5.
  • Arkaprabha Basu, Manash K Paul, Mitchel Alioscha-Perez, Anna Grosberg, Hichem Sahli, Steven M Dubinett, Shimon Weiss, “Statistical parametrization of cell cytoskeleton reveals lung cancer cytoskeletal phenotype with partial EMT signature”, Communications Biology, 2022, 5 (1), 1-11.
  • Yuting Miao, Robert C Boutelle, Anastasia Blake, Vigneshwaran Chandrasekaran, Chris J Sheehan, Jennifer Hollingsworth, Daniel Neuhauser, Shimon Weiss, “Super-resolution Imaging of Plasmonic Near-Fields: Overcoming Emitter Mislocalizations”, The Journal of Physical Chemistry Letters, 2022, 13, 4520-4529.
  • Jason T Smith, Alena Rudkouskaya, Shan Gao, Juhi M Gupta, Arin Ulku, Claudio Bruschini, Edoardo Charbon, Shimon Weiss, Margarida Barroso, Xavier Intes, Xavier Michalet, “In vitro and in vivo NIR fluorescence lifetime imaging with a time-gated SPAD camera”, Optica, 2022, 9 (5), 532-544.
  • Shimon Yudovich, Adan Marzouqe, Joseph Kantorovitsch, Eti Teblum, Tao Chen, Jörg Enderlein, Evan W Miller, Shimon Weiss, “Electrically Controlling and Optically Observing the Membrane Potential of Supported Lipid Bilayers”, Biophysical Journal, 2022.
  • Y Miao, S Weiss, X Yi, “PySOFI: an open source Python package for SOFI”, Biophysical Reports, 2022, 2 (2), 100052.