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Ilya J. Finkelstein, Ph.D. - Publications

Affiliations: 
2007 Stanford University, Palo Alto, CA 
Area:
molecular dynamics
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67 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Sang CC, Moore G, Tereshchenko M, Nosella ML, Zhang H, Alderson TR, Dasovich M, Leung A, Finkelstein IJ, Forman-Kay JD, Lee HO. PARP1 condensates differentially partition DNA repair proteins and enhance DNA ligation. Biorxiv : the Preprint Server For Biology. PMID 38328070 DOI: 10.1101/2024.01.20.575817  0.335
2023 Kaur P, Lu X, Xu Q, Irvin EM, Pappas C, Zhang H, Finkelstein IJ, Shi Z, Tao YJ, Yu H, Wang H. High-speed AFM imaging reveals DNA capture and loop extrusion dynamics by cohesin-NIPBL. The Journal of Biological Chemistry. 105296. PMID 37774974 DOI: 10.1016/j.jbc.2023.105296  0.348
2023 Zhang H, Shi Z, Banigan EJ, Kim Y, Yu H, Bai XC, Finkelstein IJ. CTCF and R-loops are boundaries of cohesin-mediated DNA looping. Molecular Cell. PMID 37536339 DOI: 10.1016/j.molcel.2023.07.006  0.332
2022 Soniat MM, Nguyen G, Kuo HC, Finkelstein IJ. The MRN complex and Topoisomerase IIIa-RMI1/2 synchronize DNA resection motor proteins. The Journal of Biological Chemistry. 102802. PMID 36529288 DOI: 10.1016/j.jbc.2022.102802  0.332
2022 Schaub JM, Soniat MM, Finkelstein IJ. Polymerase theta-helicase promotes end joining by stripping single-stranded DNA-binding proteins and bridging DNA ends. Nucleic Acids Research. 50: 3911-3921. PMID 35357490 DOI: 10.1093/nar/gkac119  0.334
2020 Jones SK, Hawkins JA, Johnson NV, Jung C, Hu K, Rybarski JR, Chen JS, Doudna JA, Press WH, Finkelstein IJ. Massively parallel kinetic profiling of natural and engineered CRISPR nucleases. Nature Biotechnology. PMID 32895548 DOI: 10.1038/S41587-020-0646-5  0.337
2020 Press WH, Hawkins JA, Jones SK, Schaub JM, Finkelstein IJ. HEDGES error-correcting code for DNA storage corrects indels and allows sequence constraints. Proceedings of the National Academy of Sciences of the United States of America. PMID 32675237 DOI: 10.1073/Pnas.2004821117  0.344
2020 Zhang H, Schaub JM, Finkelstein IJ. RADX condenses single-stranded DNA to antagonize RAD51 loading. Nucleic Acids Research. PMID 32621611 DOI: 10.1093/Nar/Gkaa559  0.47
2020 Deshpande RA, Myler LR, Soniat MM, Makharashvili N, Lee L, Lees-Miller SP, Finkelstein IJ, Paull TT. DNA-dependent protein kinase promotes DNA end processing by MRN and CtIP. Science Advances. 6: eaay0922. PMID 31934630 DOI: 10.1126/Sciadv.Aay0922  0.441
2019 Kim Y, Shi Z, Zhang H, Finkelstein IJ, Yu H. Human cohesin compacts DNA by loop extrusion. Science (New York, N.Y.). PMID 31780627 DOI: 10.1126/Science.Aaz4475  0.401
2019 Simon AJ, Ellington AD, Finkelstein IJ. Retrons and their applications in genome engineering. Nucleic Acids Research. PMID 31598685 DOI: 10.1093/Nar/Gkz865  0.351
2019 Caron MC, Sharma AK, O'Sullivan J, Myler LR, Ferreira MT, Rodrigue A, Coulombe Y, Ethier C, Gagné JP, Langelier MF, Pascal JM, Finkelstein IJ, Hendzel MJ, Poirier GG, Masson JY. Poly(ADP-ribose) polymerase-1 antagonizes DNA resection at double-strand breaks. Nature Communications. 10: 2954. PMID 31273204 DOI: 10.1038/S41467-019-10741-9  0.401
2019 Soniat MM, Myler LR, Kuo HC, Paull TT, Finkelstein IJ. RPA Phosphorylation Inhibits DNA Resection. Molecular Cell. PMID 31153714 DOI: 10.1016/J.Molcel.2019.05.005  0.411
2019 Myler LR, Soniat MM, Zhang X, Deshpande RA, Paull TT, Finkelstein IJ. Purification and Biophysical Characterization of the Mre11-Rad50-Nbs1 Complex. Methods in Molecular Biology (Clifton, N.J.). 2004: 269-287. PMID 31147924 DOI: 10.1007/978-1-4939-9520-2_20  0.435
2019 Soniat MM, Myler LR, Finkelstein IJ. Assembling the Human Resectosome on DNA Curtains. Methods in Molecular Biology (Clifton, N.J.). 1999: 225-244. PMID 31127580 DOI: 10.1007/978-1-4939-9500-4_14  0.452
2019 Dillard KE, Schaub JM, Brown MW, Saifuddin FA, Xiao Y, Hernandez E, Dahlhauser SD, Anslyn EV, Ke A, Finkelstein IJ. Sortase-mediated fluorescent labeling of CRISPR complexes. Methods in Enzymology. 616: 43-59. PMID 30691654 DOI: 10.1016/Bs.Mie.2018.10.031  0.377
2018 Kim Y, Furman CM, Manhart CM, Alani E, Finkelstein IJ. Intrinsically disordered regions regulate both catalytic and non-catalytic activities of the MutLα mismatch repair complex. Nucleic Acids Research. PMID 30541127 DOI: 10.1093/Nar/Gky1244  0.405
2018 Bhattacharyya S, Soniat MM, Walker D, Jang S, Finkelstein IJ, Harshey RM. Phage Mu Gam protein promotes NHEJ in concert with ligase. Proceedings of the National Academy of Sciences of the United States of America. PMID 30487222 DOI: 10.1073/Pnas.1816606115  0.45
2018 Dillard KE, Brown MW, Johnson NV, Xiao Y, Dolan A, Hernandez E, Dahlhauser SD, Kim Y, Myler LR, Anslyn EV, Ke A, Finkelstein IJ. Assembly and Translocation of a CRISPR-Cas Primed Acquisition Complex. Cell. PMID 30343903 DOI: 10.1016/J.Cell.2018.09.039  0.383
2018 Strohkendl I, Saifuddin FA, Rybarski JR, Finkelstein IJ, Russell R. Kinetic Basis for DNA Target Specificity of CRISPR-Cas12a. Molecular Cell. PMID 30078724 DOI: 10.1016/J.Molcel.2018.06.043  0.402
2018 Schaub JM, Zhang H, Soniat MM, Finkelstein IJ. Assessing protein dynamics on low complexity single-strand DNA curtains. Langmuir : the Acs Journal of Surfaces and Colloids. PMID 30044093 DOI: 10.1021/Acs.Langmuir.8B01812  0.492
2018 Hawkins JA, Jones SK, Finkelstein IJ, Press WH. Indel-correcting DNA barcodes for high-throughput sequencing. Proceedings of the National Academy of Sciences of the United States of America. PMID 29925596 DOI: 10.1073/Pnas.1802640115  0.33
2018 Seol JH, Holland C, Li X, Kim C, Li F, Medina-Rivera M, Eichmiller R, Gallardo IF, Finkelstein IJ, Hasty P, Shim EY, Surtees JA, Lee SE. Distinct roles of XPF-ERCC1 and Rad1-Rad10-Saw1 in replication-coupled and uncoupled inter-strand crosslink repair. Nature Communications. 9: 2025. PMID 29795289 DOI: 10.1038/S41467-018-04327-0  0.37
2018 Eichmiller R, Medina-Rivera M, DeSanto R, Minca E, Kim C, Holland C, Seol JH, Schmit M, Oramus D, Smith J, Gallardo IF, Finkelstein IJ, Lee SE, Surtees JA. Coordination of Rad1-Rad10 interactions with Msh2-Msh3, Saw1 and RPA is essential for functional 3' non-homologous tail removal. Nucleic Acids Research. PMID 29660012 DOI: 10.1093/Nar/Gky254  0.395
2017 Myler LR, Gallardo IF, Soniat MM, Deshpande RA, Gonzalez XB, Kim Y, Paull TT, Finkelstein IJ. Single-Molecule Imaging Reveals How Mre11-Rad50-Nbs1 Initiates DNA Break Repair. Molecular Cell. PMID 28867292 DOI: 10.1016/J.Molcel.2017.08.002  0.447
2017 Soniat MM, Myler LR, Schaub JM, Kim Y, Gallardo IF, Finkelstein IJ. Next-Generation DNA Curtains for Single-Molecule Studies of Homologous Recombination. Methods in Enzymology. 592: 259-281. PMID 28668123 DOI: 10.1016/Bs.Mie.2017.03.011  0.48
2017 Jung C, Hawkins JA, Jones SK, Xiao Y, Rybarski JR, Dillard KE, Hussmann J, Saifuddin FA, Savran CA, Ellington AD, Ke A, Press WH, Finkelstein IJ. Massively Parallel Biophysical Analysis of CRISPR-Cas Complexes on Next Generation Sequencing Chips. Cell. 170: 35-47.e13. PMID 28666121 DOI: 10.1016/J.Cell.2017.05.044  0.426
2017 Kim Y, de la Torre A, Leal AA, Finkelstein IJ. Efficient modification of λ-DNA substrates for single-molecule studies. Scientific Reports. 7: 2071. PMID 28522818 DOI: 10.1038/S41598-017-01984-X  0.454
2017 Brown MW, de la Torre A, Finkelstein IJ. Inserting Extrahelical Structures into Long DNA Substrates for Single-Molecule Studies of DNA Mismatch Repair. Methods in Enzymology. 582: 221-238. PMID 28062036 DOI: 10.1016/Bs.Mie.2016.08.006  0.46
2016 Myler LR, Finkelstein IJ. Eukaryotic resectosomes: A single-molecule perspective. Progress in Biophysics and Molecular Biology. PMID 27498169 DOI: 10.1016/J.Pbiomolbio.2016.08.001  0.473
2016 Yu H, Singh Gautam AK, Wilmington SR, Wylie D, Martinez-Fonts K, Kago G, Warburton M, Chavali S, Inobe T, Finkelstein IJ, Babu MM, Matouschek A. Conserved Sequence Preferences Contribute to Substrate Recognition by the Proteasome. The Journal of Biological Chemistry. PMID 27226608 DOI: 10.1074/Jbc.M116.727578  0.312
2016 Myler LR, Gallardo IF, Zhou Y, Gong F, Yang SH, Wold MS, Miller KM, Paull TT, Finkelstein IJ. Single-molecule imaging reveals the mechanism of Exo1 regulation by single-stranded DNA binding proteins. Proceedings of the National Academy of Sciences of the United States of America. PMID 26884156 DOI: 10.1073/Pnas.1516674113  0.47
2016 Brown MW, Kim Y, Williams GM, Huck JD, Surtees JA, Finkelstein IJ. Dynamic DNA binding licenses a repair factor to bypass roadblocks in search of DNA lesions. Nature Communications. 7: 10607. PMID 26837705 DOI: 10.1038/Ncomms10607  0.454
2016 Myler L, Gallardo I, Kim Y, Paull TT, Finkelstein IJ. Visualizing the First Steps of Human Double-Strand Break Repair on a Crowded DNA Track Biophysical Journal. 110: 65a. DOI: 10.1016/J.Bpj.2015.11.416  0.446
2016 Brown MW, Kim Y, Williams GM, Huck JD, Surtees JA, Finkelstein IJ. Dynamic DNA Binding Licenses a Eukaryotic Repair Complex to Bypass Protein Roadblocks in Search of DNA Lesions Biophysical Journal. 110: 223a. DOI: 10.1016/J.Bpj.2015.11.1233  0.483
2015 Gallardo IF, Pasupathy P, Brown M, Manhart CM, Neikirk DP, Alani E, Finkelstein IJ. High-Throughput Universal DNA Curtain Arrays for Single-Molecule Fluorescence Imaging. Langmuir : the Acs Journal of Surfaces and Colloids. 31: 10310-7. PMID 26325477 DOI: 10.1021/Acs.Langmuir.5B02416  0.455
2014 Robison AD, Finkelstein IJ. High-throughput single-molecule studies of protein-DNA interactions. Febs Letters. 588: 3539-46. PMID 24859086 DOI: 10.1016/J.Febslet.2014.05.021  0.404
2014 Lee JY, Finkelstein IJ, Arciszewska LK, Sherratt DJ, Greene EC. Single-molecule imaging of FtsK translocation reveals mechanistic features of protein-protein collisions on DNA. Molecular Cell. 54: 832-43. PMID 24768536 DOI: 10.1016/J.Molcel.2014.03.033  0.692
2014 Robison AD, Finkelstein IJ. Rapid prototyping of multichannel microfluidic devices for single-molecule DNA curtain imaging. Analytical Chemistry. 86: 4157-63. PMID 24734940 DOI: 10.1021/Ac500267V  0.363
2014 Leung JW, Agarwal P, Canny MD, Gong F, Robison AD, Finkelstein IJ, Durocher D, Miller KM. Nucleosome acidic patch promotes RNF168- and RING1B/BMI1-dependent H2AX and H2A ubiquitination and DNA damage signaling. Plos Genetics. 10: e1004178. PMID 24603765 DOI: 10.1371/Journal.Pgen.1004178  0.334
2013 Finkelstein IJ, Greene EC. Molecular traffic jams on DNA. Annual Review of Biophysics. 42: 241-63. PMID 23451891 DOI: 10.1146/Annurev-Biophys-083012-130304  0.67
2013 Wang F, Redding S, Finkelstein IJ, Gorman J, Reichman DR, Greene EC. The promoter-search mechanism of Escherichia coli RNA polymerase is dominated by three-dimensional diffusion. Nature Structural & Molecular Biology. 20: 174-81. PMID 23262491 DOI: 10.1038/Nsmb.2472  0.618
2013 Lee JY, Finkelstein IJ, Crozat E, Sherratt DJ, Greene EC. Single-Molecule DNA Curtains Reveals the Details of KOPS Targeting, Translocation, and Collision with Protein Roadblocks of DNA Translocase FtsK Biophysical Journal. 104: 173a. DOI: 10.1016/J.Bpj.2012.11.977  0.672
2013 Wang F, Redding S, Finkelstein I, Gorman J, Reichman D, Greene E. E. Coli RNA Polymerase Searches for Promoters through 3D Diffusion Biophysical Journal. 104: 541a. DOI: 10.1016/J.Bpj.2012.11.2997  0.632
2012 Gibb B, Silverstein TD, Finkelstein IJ, Greene EC. Single-stranded DNA curtains for real-time single-molecule visualization of protein-nucleic acid interactions. Analytical Chemistry. 84: 7607-12. PMID 22950646 DOI: 10.1021/Ac302117Z  0.664
2012 Lee JY, Finkelstein IJ, Crozat E, Sherratt DJ, Greene EC. Single-molecule imaging of DNA curtains reveals mechanisms of KOPS sequence targeting by the DNA translocase FtsK. Proceedings of the National Academy of Sciences of the United States of America. 109: 6531-6. PMID 22493241 DOI: 10.1073/Pnas.1201613109  0.655
2012 Finkelstein IJ, Yil Lee J, Crozat E, Sherratt DJ, Greene EC. Single-Molecule Imaging Reveals Mechanisms of Roadblock Clearance by DNA Motor Enzymes Biophysical Journal. 102: 610a-611a. DOI: 10.1016/J.Bpj.2011.11.3329  0.672
2011 Finkelstein IJ, Greene EC. Supported lipid bilayers and DNA curtains for high-throughput single-molecule studies. Methods in Molecular Biology (Clifton, N.J.). 745: 447-61. PMID 21660710 DOI: 10.1007/978-1-61779-129-1_26  0.675
2010 Finkelstein IJ, Visnapuu ML, Greene EC. Single-molecule imaging reveals mechanisms of protein disruption by a DNA translocase. Nature. 468: 983-7. PMID 21107319 DOI: 10.1038/Nature09561  0.684
2010 Wang F, Finkelstein I, Greene E. Single Molecule Study of Promoter Search By E Coli RNAP Biophysical Journal. 98: 69a. DOI: 10.1016/J.Bpj.2009.12.393  0.628
2010 Finkelstein IJ, Greene EC. Molecular Traffic Jams on DNA Highways: Single Molecule Observation of Collisions Between RecBCD Helicase and DNA Binding Proteins Biophysical Journal. 98: 61a-62a. DOI: 10.1016/J.Bpj.2009.12.352  0.686
2009 Finkelstein IJ, Greene EC. XPD helicase speeds through a molecular traffic jam. Molecular Cell. 35: 549-50. PMID 19748351 DOI: 10.1016/J.Molcel.2009.08.012  0.654
2009 Ishikawa H, Kim S, Finkelstein IJ, Fayer MD. Ultrafast 2D-IR vibration echo spectroscopy of proteins Advances in Biomedical Spectroscopy. 2: 79-103. DOI: 10.3233/978-1-60750-045-2-79  0.504
2008 Finkelstein IJ, Greene EC. Single molecule studies of homologous recombination. Molecular Biosystems. 4: 1094-104. PMID 18931785 DOI: 10.1039/B811681B  0.651
2007 Ishikawa H, Finkelstein IJ, Kim S, Kwak K, Chung JK, Wakasugi K, Massari AM, Fayer MD. Neuroglobin dynamics observed with ultrafast 2D-IR vibrational echo spectroscopy. Proceedings of the National Academy of Sciences of the United States of America. 104: 16116-21. PMID 17916624 DOI: 10.1073/Pnas.0707718104  0.77
2007 Kwak K, Park S, Finkelstein IJ, Fayer MD. Frequency-frequency correlation functions and apodization in two-dimensional infrared vibrational echo spectroscopy: a new approach. The Journal of Chemical Physics. 127: 124503. PMID 17902917 DOI: 10.1063/1.2772269  0.545
2007 Finkelstein IJ, Massari AM, Fayer MD. Viscosity-dependent protein dynamics. Biophysical Journal. 92: 3652-62. PMID 17446536 DOI: 10.1529/Biophysj.106.093708  0.736
2007 Finkelstein IJ, Zheng J, Ishikawa H, Kim S, Kwak K, Fayer MD. Probing dynamics of complex molecular systems with ultrafast 2D IR vibrational echo spectroscopy. Physical Chemistry Chemical Physics : Pccp. 9: 1533-49. PMID 17429547 DOI: 10.1039/B618158A  0.68
2007 Finkelstein IJ, Ishikawa H, Kim S, Massari AM, Fayer MD. Substrate binding and protein conformational dynamics measured by 2D-IR vibrational echo spectroscopy. Proceedings of the National Academy of Sciences of the United States of America. 104: 2637-42. PMID 17296942 DOI: 10.1073/Pnas.0610027104  0.735
2006 Massari AM, McClain BL, Finkelstein IJ, Lee AP, Reynolds HL, Bren KL, Fayer MD. Cytochrome c552 mutants: structure and dynamics at the active site probed by multidimensional NMR and vibration echo spectroscopy. The Journal of Physical Chemistry. B. 110: 18803-10. PMID 16986870 DOI: 10.1021/Jp054959Q  0.701
2006 Massari AM, Finkelstein IJ, Fayer MD. Dynamics of proteins encapsulated in silica sol-gel glasses studied with IR vibrational echo spectroscopy. Journal of the American Chemical Society. 128: 3990-7. PMID 16551107 DOI: 10.1021/Ja058745Y  0.743
2005 Finkelstein IJ, Goj A, McClain BL, Massari AM, Merchant KA, Loring RF, Fayer MD. Ultrafast dynamics of myoglobin without the distal histidine: stimulated vibrational echo experiments and molecular dynamics simulations. The Journal of Physical Chemistry. B. 109: 16959-66. PMID 16853158 DOI: 10.1021/Jp0517201  0.762
2005 Massari AM, Finkelstein IJ, McClain BL, Goj A, Wen X, Bren KL, Loring RF, Fayer MD. The influence of aqueous versus glassy solvents on protein dynamics: vibrational echo experiments and molecular dynamics simulations. Journal of the American Chemical Society. 127: 14279-89. PMID 16218622 DOI: 10.1021/Ja053627W  0.784
2004 McClain BL, Finkelstein IJ, Fayer MD. Dynamics of hemoglobin in human erythrocytes and in solution: influence of viscosity studied by ultrafast vibrational echo experiments. Journal of the American Chemical Society. 126: 15702-10. PMID 15571392 DOI: 10.1021/Ja0454790  0.554
2004 Finkelstein IJ, McClain BL, Fayer MD. Fifth-order contributions to ultrafast spectrally resolved vibrational echoes: heme-CO proteins. The Journal of Chemical Physics. 121: 877-85. PMID 15260618 DOI: 10.1063/1.1758940  0.524
2004 McClain BL, Finkelstein IJ, Fayer MD. Vibrational echo experiments on red blood cells: Comparison of the dynamics of cytoplasmic and aqueous hemoglobin Chemical Physics Letters. 392: 324-329. DOI: 10.1016/J.Cplett.2004.05.080  0.555
2003 Merchant KA, Noid WG, Akiyama R, Finkelstein IJ, Goun A, McClain BL, Loring RF, Fayer MD. Myoglobin-CO substate structures and dynamics: multidimensional vibrational echoes and molecular dynamics simulations. Journal of the American Chemical Society. 125: 13804-18. PMID 14599220 DOI: 10.1021/Ja035654X  0.769
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