Yuval Garini

Yuval GariniPhysics Department & Nanotechnology Institute
Bar-Ilan University,
Ramat Gan 5290002, Israel
Phone: +972-3-531-7433
Fax: +972-3-738-4054
Email

Biography

Yuval Garini acts as an associate professor at the Physics Department and the NanoTechnology Institute. He is acting as the Head of The Institute for nanotechnology in Bar Ilan.

His work is centered in nano-bio-phtonics studies.
Yuval graduated the Technion Institute of Technology in Haifa, Israel (Physics Department) working on optical properties of quantum wells.
After that he was part of a startup company that developed unique spectral imaging systems and its genetics applications, including the development of spectral karyotyping (SKY).
Before coming to Bar-Ilan, he was an assistant professor at the Applied Sciences department in Delft University of Technology, Delft, The Netherlands (2002-2006)

Research Overview

Nano-optics: photon-plasmon interaction and its utilization for high-resolution optical microscopy and single molecule detection.

Structural organization of the genome in the nucleus and cancer pathways studied by high resolution 3D optical microscopy.
The dynamic properties of the nucleus are also studied in living cells by labeling different entities such as the telomeres. In another study, the transcription of RNA is studied on a single gene-copy.

DNA-protein single molecule interaction detection by metallic beads and photonics method. A unique optical system is developed that is based on tethered particle motion and uses the special properties of metal beads.

Publications

  1. A. Vivante, E. Brozgol, I. Bronshtein and Y. Garini, Genome Organization in the Nucleus: From Dynamic Measurements to Functional Model, Methods, published online (2017). http://dx.doi.org/10.1016/j.ymeth.2017.01.008
  2. M. Lindner, Z. Shotan and Y. Garini, Rapid microscopy measurement of very large spectral imagesOptics Express 24, 9511-9527 (2016).
  3. I. Bronshtein, I. Kanter, E. Kepten, M. Lindner, S. Berezin, Y. Shav-Tal and Y. Garini, Exploring chromatin organization mechanisms through its dynamic propertiesNucleus 7, 1-7 (2016). [Download PDF]
  4. E. Kepten, A. Weron, I. Bronshtein, K. Burnecki and Y. Garini, Uniform contraction-expansion description of relative centromere and telomere motion. Biophysical Journal 109, 1454-1462 (2015).
  5. L. Rosenfeld, E. Kepten, S. Yunger, Y. Shav-Tal and Y. Garini, Single-site transcription rates through fitting of ensemble-averaged data from fluorescence recovery after photobleaching: A fat-tailed distribution. Physical Review E 92, 032715 (2015).
  6. I. Bronshtein, E. Kepten, I. Kanter, S. Berezin, M. Lindner, A. B. Redwood, S. Mai, S. Gonzalo, R. Foisner, Y. Shav-Tal and Y. Garini, Loss of lamin A function increases chromatin dynamics in the nuclear interior. Nature Communications, 6, 8044 (2015).
    Related Publications: HaAretz article – October 2015, ScienceDaily September 2015.
  7. S. Grigoryan, M. B. Yee, Y. Glick, D. Gerber, E. Kepten, Y. Garini, In H. Yang, P. R. Kinchington and R. S. Goldstein, Direct transfer of viral and cellular proteins from Varicella-Zoster virus-infected non-neuronal cells to human axons. PLoS One, 10, e0126081 (2015).
  8. K. Burnecki, E. Kepten, Y. Garini, G. Sikora and A. Weron, Estimating the anomalous diffusion exponent for single particle tracking data with measurement errors – An alternative approach. Scientific Reports, 5, 11306 (2015).
  9. E. Kepten, A. Weron, G. Sikora, K. Burnecki, Y. Garini, Guidelines for the fitting of anomalous diffusion mean square displacement graphs from single particle tracking experiments, PLOS One, 10, e0117722 (2015).
  10. S. Berezin, B. S. Kalanoor, H. Taha, Y. Garini and Y. R. Tischler, Multiprobe NSOM fluorescence, Nanophotonics, 3, 117-124 (2014).
  11. E. Sendersky, N. Kozer, M. Levi, Y. Garini, Y. Shav-Tal and R. Schwarz, The proteolysis adaptor, NblA, initiates protein pigment degradation by interacting with the cyanobacterial light-harvesting complexes, The Plant Journal, 79, 118-126 (2014).
  12. Y. Heifetz, M. Lindner, Y. Garini and M.F. Wolfner, Mating Regulates Neuromodulator Ensembles at Nerve Termini Innervating the Drosophila Reproductive Tract, Current Biology, 24, 731-737 (2014).
  13. S. Yunger, L. Rosenfeld, Y. Garini and Y. Shav-Tal, Quantifying the transcriptional output of single alleles in single living mammalian cells, Nature Protocols, 8, 393–408 (2013).
  14. E. Kepten, I. Bronshtein and Y. Garini, Improved estimation of anomalous diffusion exponents in single-particle tracking experiments, Physical Review E, 87, 052713 (2013).
  15. M. Lindner, G. Nir, A. Vivante, I. T. Young and Y. Garini, Dynamic analysis of a diffusing particle in a trapping potential, Physical Review E, 87, 022716 (2013).
  16. Y. Garini and E. Tauber, Spectral Imaging: Methods, Design, and Applications in Biomedical Optical Imaging Technologies: Design and Applications, edited by R. Liang (Springer, Heidelberg, 2013).
  17. K. Burnecki, E. Kepten, J. Janczura, I. Bronshtein, Y. Garini and A. Weron, Universal algorithm for identification of fractional Brownian motion. A case of telomere subdiffusion, Biophysical Journal, 103(9), 1839-1847 (2012).
  18. E. Barkai, Y. Garini and R. Metzler, Strange kinetics of single molecules in living cells, Physics Today, 65, 29-35 (2012).
  19. Z. Zalevsky, A. Gur, R. Aharoni, V. G. Kutchoukov, Y. Garini, Y. Beiderman, V. Mico and J. Garcia, Novel approaches for near and far field super-resolved imaging, in 22nd Congress of the International Commission for Optics: Light for the Development of the World. Puebla, Mexico: SPIE.
  20. G. Nir, M. Lindner and Y. Garini, Protein-DNA Interactions Studies with Single Tethered Molecule Techniques, in Protein Interactions, J. Cai and R. E. Wang, Editors. (2012), InTech. p. 369-400.
  21. M. Lindner, G. Nir and Y. Garini, Plasmonic Scattering as an Efficient Tool for a Force-Free Technique to Follow Single DNA Molecules, The Open Optics Journal, 5, 12-16 (2011).
  22. M. Lindner, G. Nir and Y. Garini, Nano-optics methods for studying DNA-protein interactions, in Recent Advances in Nano-Technology, Z. Zalevsky, Editor. (2011), VDM Verlag: Saarbrücken. p. 155-192.
  23. A. Gur, R. Aharoni, Z. Zalevsky, V.G. Kutchoukov, V. Mico, J. Garcia and Y. Garini, Sub-wavelength and non-periodic holes array based fully lensless imager, Optics Communications 284, 3509-3517 (2011).
  24. E. Kepten, I. Bronstein, Y. Garini, Ergodicity convergence test suggests telomere motion obeys fractional dynamics, Physical Review E. 83, 041919-1-5 (2011).
  25. H.R. Christiaan, F. Wiener, C. Taylor-Kashton, J. Harizanova, B.J. Vermolen, Y. Garini, I.T. Young and S. Mai, Translocation frequencies and chromosomal proximities for selected mouse chromosomes in primary B lymphocytes, Cytometry 79A, 276-283 (2011).
  26. L. Klewes, C. Höbsch, N. Katzir, D. Rourke, Y. Garini and S. Mai, Novel automated three-dimensional (3D) genome scanning based on the nuclear architecture of telomeres, Cytometry 79A, 159-166 (2011).
  27. G. Nir, M. Lindner, H.R.C. Dietrich, O. Girshevitz, C.E. Vorgias, and Y. Garini, HU protein induces incoherent DNA persistence length, Biophysical Journal 100, 784-790 (2011).
  28. M. Lindner, G. Nir, S. Medalion, H. R. C. Dietrich, Y. Rabin and Y. Garini, Force-free measurements of the conformations of DNA molecules tethered to a wall, Physical Review E, 83, 011916-1-7 (2011).
  29. S. Yunger, L. Rosenfeld, Y. Garini and Y. Shav-Tal, Single-allele analysis of transcription kinetics in living mammalian cells, Nature Methods 7, 631-633 (2010).
    Related links: Ynet article (Hebrew), Natrure Methods news, The Scientist.
  30. M. Lindner, G. Nir, H. R. C. Dietrich, I. T. Young, E. Tauber, I. Bronshtein, L. Altman and Y. Garini, Studies of single molecules at their natural form, Israel Journal of Chemistry 49 283-291 (2009).
  31. S. Buhbut, S. Itzhakov, E. Tauber, M. Shalom, I. Hod, T. Geiger, Y. Garini, D. Oron and A. Zaban, Built-in Quantum Dot Antennas in Dye-Sensitized Solar Cells, ACS Nano 4 1293-1298 (2010).
  32. M. Gadji, D. Fortin, A.-M. Tsanaclis, Y. Garini, N. Katzir, Y. Wienburg, J. Yan, L. Klewes, T. Klonisch, R. Drouin and S. Mai, Three-dimensional nuclear telomere architecture is associated with differential time to progression and overall survival in glioblastoma patients. Neoplasia 12, 183-191 (2010).
  33. H.R.C. Dietrich, F.H. de Groote, B. Rieger, F.G.M. Wiertz, H.A. Heering, I.T. Young and Y. Garini, Tethered particle motion mediated by scattering from gold nanoparticles and darkfield microscopy, Journal of Nanophotonics, 3, 031795 (2009).
  34. I. Bronstein Berger, Y. Israel, E. Kepten, S. Mai, Y. Shav-Tal, E. Barkai and Y. Garini, Transient anomalous diffusion of telomeres in the nucleus of mammalian cells.
    Physical Review Letters 103, 018102 (2009).
  35. S. Ben Dror, I. Bronshtein, Y. Garini, W.G. O’Neal, P.A. Jacobi and B. Ehrenberg, The localization and photosensitization of modified chlorin photosensitizers in artificial membranes, Photochemical & Photobiological Sciences 8, 354-361 (2009).
  36. V. Raz, B.J. Vermolen, Y. Garini, J.J.M. Onderwater, M.A. Mommaas-Kienhuis, A.J. Koster, I.T. Young, H. Tanke and R.W. Dirks, The nuclear lamina promotes telomere aggregation and centromere peripheral localization during senescence of human mesenchymal stem cells, Journal of Cell Science 121, 4018-4028 (2008).
  37. B.J. Vermolen, Y. Garini, I.T. Young, R.W. Dirks, V. Raz, Segmentation and analysis of the three-dimensional redistribution of nuclear components in hMSC, Cytometry 73, 816-824 (2008).
  38. G.O.F Parikesit, A.P. Markesteijn, O.M. Piciu, A. Bossche, J. Westerweel, I.T. Young and Y. Garini, Size-dependent trajectories of DNA macromolecules due to insulative dielectrophoresis in submicrometer-deep fluidic channels, Biomicrofluidics 2, 024103 (2008).
  39. Y. Shav-Tal, Y. Garini and M. Barda-Saad, Observing the biology [Hebrew]. Galileo 112, 32-41 (2007).
  40. M.W. Docter, P.M. van den Berg, P.F.A. Alkemade, V.G. Kutchoukov, O.M. Piciu, A. Bossche, I.T. Young and Y. Garini, Structured illumination microscopy using extraordinary transmission through sub-wavelength hole-arrays, Journal of Nanophotonics, 1, 011665 (2007).
  41. R. Sarkar, A. Guffei, B.J. Vermolen, Y. Garini and S. Mai, Determining centromere positions in nuclei of normal, immortalized, and malignant B cells, Cytometry, 71A, 386-392 (2007).
  42. A. Caporali, L. Wark, B.J. Vermolen, Y. Garini and S. Mai, Telomeric aggregates and end-to-end chromosomal fusions require myc box II, Oncogene 26, 1398-1406 (2007).
  43. M.W. Docter, I.T. young, O.M. Piciu, A. Bossche, P.F.A. Alkemade, P.M.v.d. Berg, and Y. Garini, Measuring the wavelength-dependent divergence of transmission through sub-wavelength hole-arrays by spectral imaging, Optics Express 14, 9477-9482 (2006).
  44. V. Raz, F. Carlotti, B.J. Vermolen, E.v.d. Poel, W.C.R. Sloos, S. Knaän-Shanzer, A.A.F.d. Vries, R.C. Hoeben, I.T. Young, H.J. Tanke, Y. Garini and R.W. Dirks, Changes in lamina structure are followed by spatial reorganization of heterochromatic regions in Caspase-8-activated human mesenchymal stem cells, Journal of Cell Science 119, 4247-4256 (2006).
  45. Y. Garini, I.T. Young and G. McNamara, Spectral Imaging: Principles and applications, Cytometry 69A, 735-747 (2006).
  46. S. Mai and Y. Garini, The significance of telomeric aggregates in the interphase nuclei of tumor cells, Journal of Cellular Biochemistry 97, 904-915 (2006).
  47. S. Mai and Y. Garini, Oncogenic remodeling of the three-dimensional organization of the interphase nucleus, Cell Cycle 4, 1327-1331 (2005).
  48. B.J. Vermolen, Y. Garini, S. Mai, V. Mougey, T. Fest, T.C.-Y. Chuang, A.Y.-C. Chuang, L. Wark and I.T. Young. Characterizing the three-dimensional organization of telomeres, Cytometry 67A, 144-150 (2005).
  49. G.O.F. Parikesit, A.P. Markesteijn, V.G. Kutchoukov, O. Piciu, A. Bossche, J. Westerweel, Y. Garini and I.T. Young, Electroosmotic flow analysis of a branched U-turn nanofluidic device, Lab on a Chip 5, 1067-1074 (2005).
  50. S.F. Louis, B.J. Vermolen, Y. Garini, I.T. Young, A. Guffei, Z. Lichtensztejn, F. Kuttler, T.C.Y. Chuang, S. Moshir, V. Mougey, A.Y.C. Chuang, P.D. Kerr, T. Fest, P. Boukamp, and S. Mai, c-Myc induces chromosomal rearrangements through telomere and chromosome remodeling in the interphase nucleus, Proceedings of the National Academy of Sciences USA 102, 9613-9618 (2005).
  51. V.G. Kutchoukov, L. Pakula, G.O.F. Parikesit, Y. Garini, L.K. Nanver and A. Bossche, Fabrication of nanofluidic devices in glass with polysilicon electrodes, Sensors and Actuators A, 123-124, 602-607 (2005).
  52. Y. Garini, B.J. Vermolen and I.T. Young, From micro to nano: recent advances in high-resolution microscopy, Current Opinion in Biotechnology 16, 1-10 (2005).
  53. B. J. Vermolen, Y. Garini and I.T. Young, 3D restoration with multiple images acquired by a modified conventional microscope, Microscopy Research and Technique 64, 113-125 (2004).
  54. T. Chih Yuan Chuang, S. Moshir, Y. Garini, A. Ya-Chun Chuang, I. T. Young, B. Vermolen, R. Van Den Doel, V. Mougey, M. Perrin, M. Braun, P. D. Kerr, T. Fest, P. Boukamp, S. Mai, The three-dimensional organization of telomeres in the nucleus of telomeres in the nucleus of mammalian cells, BMC Biology 2:12 (2004).
  55. V. G. Kutchoukov, F. Laugere, W. van der Vlist, L. Pakula, Y. Garini and A. Bossche, Fabrication of nanofluidic devices using glass-to-glass anodic bonding, Sensors and Actuators A 114, 521-527 (2004).
  56. Y. Garini, V. G. Kutchoukov, A. Bossche, P. F. A. Alkemade, M. W. Docter, P. W. Verbeek, L. J. van Vliet and Ian T. Young, Toward the development of a three-dimensional mid-field microscope, Proceedings of SPIE 5327, 115-122 (2004).
  57. I. T. Young, Y. Garini, H. R. C. Dietrich, W. van Oel and G. L. Lung, LEDs for fluorescence microscopy, Proceedings of SPIE 5324, 208-215 (2004).
  58. U. Huth, A. Wieschollek, Y. Garini, R. Schubert1, R. Peschka-S&uumlss, Fourier transformed spectral bio-imaging for studying the intracellular fate of liposomes, Cytometry 57A, 10-21 (2004).
  59. V. G. Kutchoukov, F. Laugere, W. van der Vlist, L. Pakula, Y. Garini, P. F. A. Alkemade and A. Bossche, Fabrication of nanochannels using glass to glass anodic bonding, in Transducers ‘03, Proc. The 12th International Conference on Solid State Sensors, Actuators and Microsystems. (Boston 2003) pp. 1327-1330.
  60. V. G. Kutchoukov, L. Pakula, Y. Garini, J. R. Mollinger and A. Bossche, Fabrication technology for nanofluidic channel devices for biochemical applications, in MME 2003, Proc. 14th Micromechanics Europe Workshop. (Delft, 2003) pp. 167-170.
  61. M.V. Macville, J.A. Van Der Laak, E.J. Speel, N. Katzir, Y. Garini, D. Soenksen, G. McNamara, P.C. de Wilde, A.G. Hanselaar, A.H. Hopman, and T. Ried, Spectral imaging of multi-color chromogenic dyes in pathological specimens, Analytical Cellular Pathology 22, 133-142 (2001).
  62. Y. Garini, A. Gil, I. Bar-Am, D. Cabib and N. Katzir, Signal to noise analysis of multiple color fluorescence imaging microscopy, Cytometry 35, 214-226 (1999).
  63. M. Lavi, U. Milman, D. Cabib, Y. Garini, A. Gil, T. Juta and M. Adel, A new compact design interferometer based spectral imaging system for bio-medical applications, SPIE Proceedings 3261 (1998).
  64. E. Schröck, Y. Garini, M.  Köhler and T. Ried, Spectral karyotyping in clinical and tumor cytogenetics in Diagnostic Cytogenetics, edited by R. Wegner (Springer Verlag, Heidelberg, 1998).
  65. D. Cabib, R. A. Buckwald, Y. Garini and D. G. Soenksen, Spectrally Resolved Fourier Transform spectroscopy (Spectral Imaging): a powerful tool for quantitative analytical microscopy, SPIE Proceedings 2678 (1996).
  66. Y. Garini, N. Katzir, D. Cabib, R. A. Buckwald, D. G. Soenksen and Z. Malik, Spectral Bio-Imaging in Fluorescence Imaging Spectroscopy and Microscopy, edited by X. F. Wang and B. Herman (John Wiley and Sons, 1996), Vol. 137, p. 87-124.
  67. Y. Garini, M. Macville, S. du Manoir, R. A. Buckwald, M. Lavi, N. Katzir, D. Wine, I. Bar-Am, E. Schröck, D. Cabib and T. Ried, Spectral karyotyping, Bioimaging 4, 65-72 (1996).
  68. Z. Malik, M. Dishi and Y. Garini, Fourier transform multipixel spectroscopy and spectral imaging of protoporphyrin in single melanoma cells, Photochem Photobiol 63, 608-614 (1996).
  69. D. G. Soenksen, T. J. Sick and Y. Garini, Use of a novel spectral bio-imaging system as an imaging oximeter in intact rat brain, SPIE Proceedings 2679 (1996).
  70. D. G. Soenksen, Y. Garini and I. Bar-Am, Multicolor FISH using a novel spectral bio-imaging system, SPIE Proceedings 2678 (1996).
  71. Z. Malik, D. Cabib, R. A. Buckwald, A. Talmi, Y. Garini and S. G. Lipson, Fourier transform multi-pixel spectroscopy for quantitative cytology, Journal of Microscopy 182, 133-140 (1996).
  72. E. Schröck, S. du Manoir, T. Veldman, B. Schoell, J. Wienberg, M. A. Ferguson-Smith, Y. Ning, D. H. Ledbetter, I. Bar-Am, D. Soenksen, Y. Garini and T. Ried, Multicolor spectral karyotyping of human chromosomes, Science 273, 494-497 (1996).
  73. D. L. Farkas, B. T. Ballou, G. W. Fisher, D. Fishman, Y. Garini, W. Niu and E. S. Wachman, Microscopic and mesoscopic spectral bio-imaging, Proc. Soc. Photo-Optical Instr. Eng. 2678, 200-206 (1996).
  74. Y. Garini, M. Katz, E. Cohen, E. Ehrenfruend, D. Gershoni, A. Ron and L. N. Pfeiffer, Photoinduced Intersubband Absorption by Excitons, Electrons and Holes in GaAs/AlAs Mixed Type I–Type II Superlattices, In The 22nd International Conference on the Physics of Semiconductors, edited by D. J. Lockwood (World Scientific Publishing Co., Vancouver, Canada, 1994), Vol. 2, p. 1153-1156.
  75. Z. Malik, D. Cabib, R. A. Buckwald, Y. Garini and D. Soenksen, A novel spectral imaging system combining spectroscopy with imaging – applications for biology, Proceedings of Optical and Imaging Techniques in Biomedicine 2329, 180 (1994).
  76. Y. Garini, E. Linder, E. Cohen, D. Gershoni, E. Ehrenfruend, A. Ron and L. N. Pfeiffer, Interband and Intersubband Transitions in Photoexcited Mixed Type I and Type II GaAs/AlAs Superlattices, Journal De Physique IV 3, 241-244 (1993).
  77. J. Oiknine-Schlesinger, Y. Garini, E. Cohen, E. Ehrenfreund, D. Gershoni, A. Ron, E. Linder, L. N. Pfeiffer, K.-K. Law, J. L. Merz and A. C. Gossard, The Interaction of Photoexcited e-h Pairs with a Two Dimensional Electron Gas Studied by Intersubband Spectroscopy, In Quantum Well Intersubband Transition Physics and Devices, edited by H. C. Liu and B. Levine (Nato ASI Series, Kluwer, 1993).
  78. Y. Garini, E. Ehrenfreund, E. Cohen, A. Ron, K. K. Law, J. L. Merz and A. C. Gossard, Optically induced intersubband absorption in the presence of a two-dimensional electron gas in quantum wells, Physical Review B 48, 4456-4459 (1993).
  79. Y. Garini, H. Tuffigo, I. Brener, E. Cohen, N. Magnea and H. Mariette, Resonant Raman scattering mediated by excitons in CdTe/CdZnTe multiple quantum wells, Journal of Luminescence 53, 348 (1992).
  80. Y. Garini, E. Cohen, E. Ehrenfreund, A. Ron, K.-K. Law, J. L. Merz and A. C. Gossard, Photoinduced intersubband absorption in n-type well- and barrier-doped quantum wells, Surface Science 263, 562 (1992).
  81. A. Frommer, Y. Garini, A. Ron and E. Cohen, Resonant Raman scattering within an inhomogeneously broadened exciton band in semiconductors, Journal of Luminescence 45, 9 (1990).
  82. Y. Garini, M. Olszakier, E. Cohen, E. Ehrenfreund, A. Ron, K.-K. Law, J. L. Merz and A. C. Gossard, Photoinduced intersubband absorption in barrier doped multi-quantum-wells, Superlattices and Microstructures 7, 287-290 (1990).
  83. Y. Garini, E. Cohen, A. Ron and H. Shtrikman, Exciton states and LO-phonon resonant Raman scattering in CdTe/ZnTe superlaticces, Journal of Crystal growth 101, 783 (1990).
  84. More than 14 issued patents.