Publications

 

38. N. Strugo, C. Burstein, Sk S. Hossain, N. Nago, H. Khamis, and A. Kaplan, “Intrinsically disordered regions facilitate Msn2 target search to drive promoter selectivity”. Submitted (2025). bioRxiv 2025.05.23.654710. PDF
37. B. Shirt-Ediss, E. Torelli, S. Navarro, H. Khamis, A. Kaplan, W. Trewby, J. Elezgaray, N. Moradzadeh-Esmaeili, M. Haydell, M. Famulok, and N. Krasnogor, “Optimizing DNA origami assembly through selection of scaffold sequences that minimise off-target interactions”. Submitted (2025). bioRxiv 2025.01.29.635450. PDF
36.  T. Refael, M. Sudman, G. Golan, L. Pnueli, S. Naik, E. Preger-Ben Noon, A. Henn, A. Kaplan & P. Melamed, “An i-motif-regulated enhancer, eRNA and adjacent lncRNA affect Lhb expression through distinct mechanisms in a sex-specific context”, Cellular and Molecular Life Sciences 81, 361 (2024). PDF
35. V. Gaydar, R. Zananiri, L. Saied, O. Dvir, A. Kaplan and A. Henn, “Communication between DNA and nucleotide binding sites facilitates stepping by the RecBCD helicase”, Nucleic Acids Research  52, 3911 (2024). PDF
34. R. Zananiri*, S. Mangapuram Venkata*, V. Gaydar*, D. Yahalom, O. Malik, S. Rudnizky, O. Kleifeld, A. Kaplan and A. Henn, “Auxiliary ATP binding sites support DNA unwinding by RecBCD”, Nature Communications 13, 1806 (2022) PDF
33. H. Khamis, S. Rudnizky, P. Melamed and A. Kaplan, “Single molecule characterization of the binding kinetics of a transcription factor and its modulation by DNA sequence and methylation”, Nucleic Acids Research 49, 10975 (2021) PDF
32. S. Rudnizky, H. Khamis, Y. Ginosar, E. Goren, P. Melamed and A. Kaplan, “Extended and dynamic linker histone-DNA interactions control chromatosome compaction”, Molecular Cell 81, 3410 (2021) PDF
31. B. Bar-Sadeh, S. Rudnizky, L. Pnueli, G. R. Bentley, R. Stöger, A. Kaplan and P. Melamed, “Unravelling the role of epigenetics in reproductive adaptations to early-life environment”, Nature Reviews Endocrinology 16, 519 (2020) PDF
30. S. Rudnizky*, H. Khamis*, O. Malik, P. Melamed, and A. Kaplan, “The base pair-scale diffusion of nucleosomes modulates binding of transcription factors”, PNAS 116, 12161 (2019). PDF
29. R. Kreiserman, O. Malik and A. Kaplan, “Decoupling conservative forces and hydrodynamic interactions between optically trapped spheres”, Phys. Rev. E 99, 012611 (2019). PDF
28. R. Zananiri, O. Malik, S. Rudnizky, V. Gaydar, R. Kreiserman, A. Henn and A. Kaplan, “Synergy between RecBCD subunits is essential for efficient DNA unwinding”, eLife 8, e40836 (2019). PDF
27. B. Zhitomirsky, A. Yunaev, R. Kreiserman, A. Kaplan, M. Stark, and Y. Assaraf, “Lysosomotropic drugs activate TFEB via lysosomal membrane fluidization and consequent inhibition of mTORC1 activity”, Cell Death Dis. 9, 1191 (2018). PDF
26. P. Melamed, M. Haj, Y. Yosefzon, S. Rudnizky, A. Wijeweera, L. Pnueli and A. Kaplan, “Multifaceted targeting of the chromatin mediates GnRH effects on gene expression in the gonadotrope”, Frontiers in Endocrinology 9, 58 (2018). PDF
25. H. Khamis, S. Rudnizky and A. Kaplan, “Mobile nucleosomes and the accessibility of transcription factors to DNA: a modified dynamic equilibrium model”, bioRxiv 187815 (2017).  PDF
24.  S. Rudnizky*, H. Khamis*, O. Malik, A. Squires, A. Meller, P. Melamed and A. Kaplan, “Single-molecule DNA unzipping reveals asymmetric modulation of a transcription factor by its binding site sequence and context”, Nucleic Acids Research 46, 1513 (2018).  PDF
23.  O. Malik*, H. Khamis*, S. Rudnizky and A. Kaplan, “The mechano-chemistry of a monomeric reverse transcriptase”, Nucleic Acids Research 45, 12954 (2017).  PDF
22.  O. Malik*, H. Khamis*, S. Rudnizky, A. Marx and A. Kaplan, “Pausing kinetics dominates strand-displacement polymerization by Reverse Transcriptase”, Nucleic Acids Research 45, 10190 (2017).  PDF
21.  S. Rudnizky, O. Malik, A. Bavly, L. Pnueli, P. Melamed and A. Kaplan, “Nucleosome mobility and the regulation of gene expression: Insights from single-molecule studies“, Protein Science 26, 1266 (2017).  PDF
20. S. Rudnizky, A. Bavly, O. Malik, L. Pnueli, P. Melamed and A. Kaplan, “H2A.Z controls the stability and mobility of nucleosomes to regulate expression of the LH genes”, Nature Communications 7, 12958 (2016).  PDF
19.  T. Liu*, A. Kaplan*, L. Alexander, S. Yan, J-D. Wen, L. Lancaster,  C. Wickersham, K. Fredrick, H. Noller, I. Tinoco and C. Bustamante, “Direct measurement of the mechanical work during translocation by the ribosome”,  eLife 2014;3:e03406 (*) Equal contribution.  PDF
18.  K. Aathavan*, A. T. Politzer*, A. Kaplan*, J. R. Moffitt*, Y. R. Chemla, S. Grimes, P. J. Jardine, D. L. Anderson, and C. Bustamante, “Substrate Interactions and Promiscuity in a Viral DNA Packaging Motor”, Nature 461, 669 (2009). (*) Equal contribution.  PDF
17.  M. F. Andersen, A. Kaplan, T. Grünzweig, and N. Davidson, “Decay of Quantum Correlations in Atom Optics Billiards with Chaotic and Mixed Dynamics”, Phys. Rev. .Lett. 97, 104102 (2006).
16.  N. Davidson, A. Kaplan, M. F. Andersen, and T. Grunzweig, “Classical and quantum dynamics with ultra cold atoms in billiards”, in “Quantum Computer, Algorithms and Chaos”, Volume 162 International School of Physics Enrico Fermi, Edited by: G. Casati, D.L. Shepelyansky, P. Zoller and G. Benenti ( IOS Press, Amsterdam 2006).
15.  A. Kaplan, M. F. Andersen, T. Grünzweig, and N. Davidson, “Hyperfine spectroscopy of optically trapped atoms”, J. Opt. B: Quant. Semiclass. Opt. 7, R103 (2005).
14.  M.F. Andersen, T. Grünzweig, A. Kaplan, and N. Davidson, “Revivals of Coherence in Chaotic Atom Optics Billiards”, Phys. Rev. A 69, 063413 (2004).
13.  M. F. Andersen, A. Kaplan, T. Grünzweig, and N. Davidson, “Supression of Dephasing of Optically Trapped Atoms”, Phys. Rev. A 70, 013405 (2004).
12. A. Kaplan, N. Friedman, M. Andersen, and N. Davidson, “Stable regions and singular trajectories in chaotic soft wall billiards”, Physics D 187, 136 (2004).
11.  A. Kaplan, M. Andersen, N. Friedman and N. Davidson, “Atom optics billiards”, in Chaotic dynamics and transport in classical and quantum systems, Editors: P. Collet, M. Courbage, S. Metens, A. Neishtast and G. Zaslavsky, NATO science series II, vol. 182 (Springer, 2004).
10.  M. F. Andersen, A. Kaplan, T. Grünzweig, and N. Davidson, “Echo spectroscopy and Atom Optics Billiards”, Communications in Nonlinear science and numerical simulation 8, 289 (2003).
9.  M. F. Andersen, A. Kaplan, and N. Davidson, “Echo spectroscopy and quantum stability of trapped atoms”, Phys. Rev. Lett. 90, 023001 (2003).
8.  A. Kaplan, N. Friedman, N. Davidson, “Optimized single-beam dark optical trap”, J. Opt. Soc. Am B 19, 1233 (2002).
 7.  A. Kaplan, M. F. Andersen, and N. Davidson, “Suppression of inhomogeneous broadening in rf spectroscopy of optically trapped atoms”, Phys. Rev. A 66, 045401 (2002).
6. M. F. Andersen, A. Kaplan, N. Friedman and N. Davidson, “Stable islands in chaotic atom- optics billiards, caused by curved trajectories”, J. Phys. B: At. Mol. Opt. Phys. 35, 2183 (2002).
5. N. Friedman, A. Kaplan, N. Davidson, “Dark Optical Traps for Cold Atoms”, Adv. At. Mol. Opt. Phys. 48, 99 (2002).
4. A. Kaplan, N. Friedman, and N. Davidson, “Acousto-optic lens with very fast focus scanning”, Opt. Lett. 26, 1078 (2001).
3. A. Kaplan, N. Friedman, M. Andersen, and N. Davidson, “Observation of Islands of Stability in Soft Wall Atom-Optics Billiards”, Phys. Rev. Lett. 87, 274101 (2001).
2. N. Friedman, A. Kaplan, D. Carasso, and N. Davidson, “Observation of chaotic and regular dynamics in atom-optics billiards”, Phys. Rev. Lett. 86, 1518 (2001).
1. N. Friedman, A. Kaplan, and N. Davidson, “Acousto-optic scanning system with very fast nonlinear scans”, Opt. Lett. 25, 1762 (2000).