Preprints
Asgard archaea defense systems and their roles in the origin of immunity in eukaryotes
Pedro Leão†, Mary E. Little, Kathryn E. Appler, Daphne Sahaya, Emily Aguilar-Pine, Kathryn Currie, Ilya J. Finkelstein, Valerie De Anda1, and Brett J. Baker† († co-corresponding)
BioRxiv.
[PDF]    [Supplement]    DOI: 10.1101/2023.09.13.557551    
Unraveling the mechanisms of PAMless DNA interrogation by SpRY Cas9
Grace N. Hibshman*, Jack P. K. Bravo*†, Hongshan Zhang, Tyler L. Dangerfield, Ilya J. Finkelstein, Kenneth A. Johnson, David W. Taylor† (* co-first authors) († co-corresponding)
BioRxiv.
[PDF]    DOI: 10.1101/2023.06.22.546082    
Massively Parallel Profiling of RNA-targeting CRISPR-Cas13d
Hung-Che Kuo†, Joshua Prupes, Chia-Wei Chou, Ilya J. Finkelstein† († co-corresponding)
BioRxiv.
[PDF]    [Supplement]    DOI: 10.1101/2023.03.27.534188    
Distinct horizontal transfer mechanisms for type I and type V CRISPR-associated transposons
Kuang Hu†, Chia-Wei Chou, Claus O. Wilke, Ilya J. Finkelstein† († co-corresponding)
BioRxiv.
[PDF]    [Supplement]    DOI: 10.1101/2023.03.03.531003    
DNA capture and loop extrusion dynamics by cohesin-NIPBL
Parminder Kaur†, Zhubing Shi, Xiaotong Lu, Hongshan Zhang, Ilya J. Finkelstein, Yizhi Jane Tao, Hongtao Yu, Hong Wang† († co-corresponding)
BioRxiv.
[PDF]    DOI: 10.1101/2022.08.18.504320    
Mechanism of broad-spectrum Cas9 inhibition by AcrIIA11
Kaylee E. Dillard†, Cynthia Terrace, Kamyab Javanmardi, Wantae Kim, Kevin J. Forsberg, and Ilya J. Finkelstein† († co-corresponding)
BioRxiv.
[PDF]    [Supplement]    DOI: 10.1101/2021.09.15.460536    
Synthetic repertoires derived from convalescent COVID-19 patients enable discovery of SARS-CoV-2 neutralizing antibodies and a novel quaternary binding modality
Jule Goike*, Ching-Lin Hsieh*, Andrew Horton*, Elizabeth C. Gardner*, Foteini Bartzoka, Nianshuang Wang, Kamyab Javanmardi, Andrew Herbert, Shawn Abbassi, Rebecca Renberg, Michael J. Johanson, Jose A. Cardona, Thomas Segall-Shapiro, Ling Zhou, Ruth H. Nissly, Abhinay Gontu, Michelle Byrom, Andre C. Maranhao, Anna M. Battenhouse, Varun Gejji, Laura Soto-Sierra, Emma R. Foster, Susan L. Woodard, Zivko L. Nikolov, Jason Lavinder, Will N. Voss, Ankur Annapareddy, Gregory C. Ippolito, Andrew D. Ellington, Edward M. Marcotte, Ilya J. Finkelstein, Randall A. Hughes, James M. Musser, Suresh V. Kuchipudi, Vivek Kapur, George Georgiou, John M. Dye, Daniel R. Boutz†, Jason S. McLellan†, & Jimmy D. Gollihar† (* co-first authors) († co-corresponding)
BioRxiv.
[PDF]    [Supplement]    DOI: 10.1101/2021.04.07.438849    
2024
90. Structural Basis for Target Discrimination and Activation by Cas13d.
Chia-Wei Cho;, Selma Sinan;, Hung-Che Kuo;, Carlos Arguello;, Rick Russell, Ilya J. Finkelstein † († co-corresponding)
Submitted.    DOI: 10.1038/s44319-024-00285-5    
89. PARP1 condensates differentially partition DNA repair proteins and enhance DNA ligation
Christopher Chin Sang;, Gaelen Moore;, Maria Tereshchenko;, Hongshan Zhang;, Michael L Nosella;, Morgan Dasovich;, T Reid Alderson;, Anthony K L Leung;, Ilya J Finkelstein;, Julie D Forman-Kay;, and Hyun O Lee † († co-corresponding)
EMBO Rep.
[PDF]    [Supplement]    DOI: 10.1038/s44319-024-00285-5    
88. Kinetic dissection of pre-crRNA binding and processing by CRISPR-Cas12a
Selma Sinan;, Nathan M Appleby;, Chia-Wei Chou ;, Ilya J Finkelstein ;, Rick Russell † († co-corresponding)
RNA. 30 (10): 1345-1355
[PDF]    [Supplement]    DOI: 10.1261/rna.080088.124    
87. Massively Parallel Profiling of RNA-targeting CRISPR-Cas13d
Hung-Che Kuo†, Joshua Prupes;, Chia-Wei Chou;, Ilya J. Finkelstein † († co-corresponding)
Nature Communications.
[PDF]    [Supplement]    DOI: 10.1038/s41467-024-44738-w    
86. Mammalian Antigen Display for Pandemic Countermeasures
Andrea Quezada *†, Ankur Annapareddy *, Kamyab Javanmardi ;, John Cooper ;, Ilya J Finkelstein †(† co-corresponding)
MIMB.
[PDF]    DOI: 10.1007/978-1-0716-3666-4_12    PMID: 38315367    
2023
85. High-speed AFM imaging reveals DNA capture and loop extrusion dynamics by cohesin-NIPBL
Parminder Kaur†, Xiaotong Lu, Qi Xu, Elizabeth Marie Irvin, Colette Pappas, Hongshan Zhang, Ilya J. Finkelstein, Zhubing Shi, Yizhi Jane Tao, Hongtao Yu, Hong Wang† († co-corresponding)
Journal of Biological Chemistry.
[PDF]    DOI: 10.1016/j.jbc.2023.105296    PMID: 37774974    
84. CTCF and R-loops are boundaries of cohesin-mediated DNA looping
Hongshan Zhang*, Zhubing Shi*, Edward J. Banigan, Yoori Kim, Hongtao Yu†, Xiao-chen Bai†, Ilya J. Finkelstein†(* co-first authors) († co-corresponding)
Molecular Cell. 83 (16): 2856-2871.e8
[PDF]    [Supplement]    DOI: 10.1016/j.molcel.2023.07.006    PMID: 37536339    
83. In Diverse Conditions, Intrinsic Chromatin Condensates Have Liquid-like Material Properties
Bryan A. Gibson, Claudia Blaukopf, Tracy Lou, Lifeng Chen, Lynda K. Doolittle, Ilya J. Finkelstein, Geeta J. Narlikar, Daniel W. Gerlich, and Michael K. Rosen
PNAS.
[PDF]    [Supplement]    DOI: 10.1073/pnas.2218085120    PMID: 37094140    
82. The MRN complex and topoisomerase IIIa–RMI1/2 synchronize DNA resection motor proteins
Michael M. Soniat†, Gioachau Nguyen, Hung-Che Kuo, and Ilya J. Finkelstein† († co-corresponding)
Journal of Biological Chemistry.
[PDF]    [Supplement]    DOI: 10.1016/j.jbc.2022.102802    PMID: 36529288    
2022
81. Massively Parallel Selection of NanoCluster Beacons
Yu-An Kuo, Cheulhee Jung, Yu-An Chen, Hung-Che Kuo, Oliver S. Zhao, Truong D. Nguyen, James R. Rybarski, Soonwoo Hong, Yuan-I Chen, Dennis C. Wylie, John A. Hawkins, Jada N. Walker, Samuel W. Shields, Jennifer S. Brodbelt, Jeffrey T. Petty, Ilya J. Finkelstein, and Hsin-Chih Yeh)
Advanced Materials.
[PDF]    [Supplement]    DOI: 10.1002/adma.202204957    PMID: 35945159    
80. Antibody escape and cryptic cross-domain stabilization in the SARS-CoV-2 Omicron spike protein
Kamyab Javanmardi†, Thomas H. Segall-Shapiro, Chia-Wei Chou, Daniel R. Boutz, Randall J. Olsen, Xuping Xie, Hongjie Xia, Pei-Yong Shi, Charlie D. Johnson, Ankur Annapareddy, Scott Weaver, James M. Musser, Andrew D. Ellington, Ilya J. Finkelstein†, Jimmy D. Gollihar†(† co-corresponding)
Cell Host Microbe. 30 (9): 1242-1254.e6
[PDF]    [Supplement]    DOI: 10.1016/j.chom.2022.07.016    PMID: 35988543    
79. How Glutamate Promotes Liquid-liquid Phase Separation and DNA Binding Cooperativity of E. coli SSB Protein
Alexander G Kozlov, Xian Cheng, Hongshan Zhang, Min Kyung Shinn, Elizabeth Weiland, Binh Nguyen, Irina A Shkel, Emily Zytkiewicz, Ilya J Finkelstein, M Thomas Record Jr., Timothy M. Lohman
J Mol Bio. 434 (9): 167562
[PDF]    [Supplement]    DOI: 10.1016/j.jmb.2022.167562    PMID: 35351518    
78. Polymerase theta-helicase promotes end joining by stripping single-stranded DNA-binding proteins and bridging DNA ends
Jeffery M. Schaub†, Michael M. Soniat, & Ilya J. Finkelstein† († co-corresponding)
NAR. 50 (7): 3911-3921
[PDF]    [Supplement]    DOI: 10.1093/nar/gkac119    PMID: 35357490    
77. A kinetic model predicts SpCas9 activity, improves off-target classification, and reveals the physical basis of targeting fidelity
Behrouz Eslami-Mossallam*, Misha Klein*, Constantijn V. D. Smagt*, Koen V. D. Sanden*, Stephen K. Jones Jr., John A. Hawkins, Ilya J. Finkelstein, and Martin Depken (* co-first authors)
Nat Commun.
[PDF]    [Supplement]    DOI: 10.1038/s41467-022-28994-2    PMID: 35292641    
76. Compartmentalization of telomeres through DNA-scaffolded phase separation
Amanda Jack*, Yoonji Kim*, Amy R. Strom *, Daniel S.W. Lee, Byron Williams, Jeffrey M. Schaub, Elizabeth H. Kellogg, Ilya J. Finkelstein, Luke S. Ferro† Ahmet Yildiz†, and Clifford P. Brangwynne† (* co-first authors) († co-corresponding)
Dev Cell. 57 (2): 277-290.e9
[PDF]    [Supplement]    DOI: 10.1016/j.devcel.2021.12.017    PMID: 35077681    
2021
75. Rapid characterization of spike variants via mammalian cell surface display
Kamyab Javanmardi†, Chia-Wei Chou, Cynthia Terrace, Ankur Annapareddy, Tamer S. Kaoud, Qingqing Guo, Josh Lutgens, Hayley Zorkic, Andrew P. Horton, Elizabeth C. Gardner, Giaochau Nguyen, Daniel R. Boutz, Jule Goike, Will N. Voss, Hung-Che Kuo, Kevin N. Dalby, Jimmy D. Gollihar & Ilya J. Finkelstein† († co-corresponding)
Mol Cell. 81 (24): 5099-5111.e8
[PDF]    [Supplement]    DOI: 10.1016/j.molcel.2021.11.024    PMID: 34919820    
74. Metagenomic Discovery of CRISPR-Associated Transposons
James R. Rybarski*, Kuang Hu*, Alexis M. Hill*, Claus O. Wilke, Ilya J. Finkelstein (* co-first authors)
PNAS. 118 (49): e2112279118
[PDF]    [Supplement]    DOI: 10.1073/pnas.2112279118    PMID: 34845024    
73. Opfi: A Python package for identifying gene clusters in large genomics and metagenomics data sets
Alexis M. Hill*, James R. Rybarski*, Kuang Hu, Ilya J. Finkelstein, and Claus O. Wilke(* co-first authors)
Journal of Open Source Software.
[PDF]    DOI: 10.21105/joss.03678    PMID: 35445164    
72. Expression and characterization of SARS-CoV-2 Spike Proteins
Jeffrey M. Schaub*, Chia-Wei Chou*, Hung-Che Kuo*, Kamyab Javanmardi*, Ching-Lin Hsieh, Jory Goldsmith, Andrea M. DiVenere, Kevin C. Le, Daniel Wrapp, Patrick O. Byrne, Christy K. Hjorth, Nicole V. Johnson, John Ludes-Meyers, Annalee W. Nguyen, Nianshuang Wang, Jason J. Lavinder, Gregory C. Ippolito, Jennifer A. Maynard, Jason S. McLellan, and Ilya J. Finkelstein (* co-first authors)
Nat Protoc.
[PDF]    DOI: 10.1038/s41596-021-00623-0    PMID: 34611365    
71. Characterization of the T4 gp32-ssDNA complex by native, cross-linking, and ultraviolet photodissociation mass spectrometry
Molly S. Blevins, Jada N. Walker, Jeffrey M. Schaub, Ilya J. Finkelstein and Jennifer S. Brodbelt
Chem Sci. 12 (41): 13764-13776
[PDF]    [Supplement]    DOI: 10.1039/d1sc02861h    PMID: 34760161    
70. Disintegration promotes proto-spacer integration by the Cas1-Cas2 complex
Chien-Hui Ma, Kamyab Javanmardi, Ilya J. Finkelstein†, Makkuni Jayaram† († co-corresponding)
eLife.
[PDF]    [Supplement]    DOI: 10.7554/eLife.65763    PMID: 34435949    
69. Trajectory of Growth of SARS-CoV-2 Variants in Houston, Texas, January through May 2021 Based on 12,476 Genome Sequences
Randall J. Olsen, Paul A. Christensen*, S. Wesley Long*, Sishir Subedi*, Parsa Hodjat, Robert Olson, Marcus Nguyen, James J. Davis, Prasanti Yerramilli, Matthew Odeja Saavedra, Lanye Pruitt, Kristina Reppond, Madison N. Shyer, Jessica Cambric, Ryan Gaad, Rashi M. Thakur, Akanksha Batajoo, Ilya J. Finkelstein, Jimmy Gollihar, and James M. Musser (* co-authors)
American Journal of Pathology. 191 (10): 1754-1773
[PDF]    DOI: 10.1016/j.ajpath.2021.07.002    PMID: 34303698    
68. Prevalent, protective, and convergent IgG recognition of SARS-CoV-2 non-RBD spike epitopes
William N. Voss, Yixuan J. Hou*, Nicole V. Johnson*, George Delidakis, Jin Eyun Kim, Kamyab Javanmardi, Andrew P. Horton, Foteini Bartzoka, Chelsea J. Paresi, Yuri Tanno, Chia-Wei Chou, Shawn A. Abbasi, Whitney Pickens, Katia George, Daniel R. Boutz, Dalton M. Towers, Jonathan R. McDaniel, Daniel Billick, Jule Goike, Lori Rowe, Dhwani Batra, Jan Pohl, Justin Lee, Shivaprakash Gangappa, Suryaprakash Sambhara, Michelle Gadush, Nianshuang Wang, Maria D. Person, Brent L. Iverson, Jimmy D. Gollihar, John M. Dye, Andrew S. Herbert, Ilya J. Finkelstein, Ralph S. Baric, Jason S. McLellan, George Georgiou, Jason L. Lavinder†, Gregory C. Ippolito† (* co-first authors) († co-corresponding)
Science. 372 (6546): 1108-1112
[PDF]    [Supplement]    DOI: 10.1126/science.abg5268    PMID: 33947773    
67. CRISPR-guided programmable self-assembly of artificial virus-like nucleocapsids
Carlos Calcines-Cruz, Ilya J. Finkelstein† & Armando Hernandez-Garcia† († co-corresponding)
Nano Letters. 21 (7): 2752-2757
[PDF]    [Supplement]    DOI: 10.1021/acs.nanolett.0c04640    PMID: 33729813    
66. Sequence Analysis of 20,453 Severe Acute Respiratory Syndrome Coronavirus 2 Genomes from the Houston Metropolitan Area Identifies the Emergence and Widespread Distribution of Multiple Isolates of All Major Variants of Concern
S. Wesley Long, Randall J. Olsen, Paul A. Christensen, Sishir Subedi, Robert Olson, James J. Davis, Matthew Ojeda Saavedra, Prasanti Yerramilli, Layne Pruitt, Kristina Reppond, Madison N. Shyer, Jessica Cambric, Ilya J. Finkelstein, Jimmy Gollihar, James M. Musser(* co-first authors) († co-corresponding)
American Journal of Pathology. 191 (6): 983-992
[PDF]    DOI: 10.1016/j.ajpath.2021.03.004    PMID: 33741335    
65. Inhibition of CRISPR-Cas12a DNA Targeting by Nucleosomes and Chromatin
Isabel Strohkendl, Fatema A. Saifuddin, Bryan A. Gibson, Michael K. Rosen, Rick Russell† & Ilya J. Finkelstein† († co-corresponding)
Science Advances. 7 (11): eabd6030
[PDF]    [Supplement]    DOI: 10.1126/sciadv.abd6030    PMID: 33692102    
2020
64. Molecular Architecture of Early Dissemination and Massive Second Wave of the SARS-CoV-2 Virus in a Major Metropolitan Area
Scott Wesley Long*, Randall J. Olsen*, Paul A. Christensen*, David W. Bernard, James J. Davis, Maulik Shukla, Marcus Nguyen, Matthew Ojeda Saavedra, Prasanti Yerramilli, Layne Pruitt, Sishir Subedi, Hung-Che Kuo, Heather Hendrickson, Ghazaleh Eskandari, Hoang A.T. Nguyen, J. Hunter Long, Muthiah Kumaraswami, Jule Goike, Daniel Boutz, Jimmy Gollihar, Jason S. McLellan, Chia-Wei Chou, Kamyab Javanmardi, Ilya J. Finkelstein & James Musser (* co-first authors)
mBio. 11 (6): e02707-20
[PDF]    DOI: 10.1128/mBio.02707-20    PMID: 33127862    
63. Massively parallel kinetic profiling of natural and engineered CRISPR nucleases
Stephen K. Jones Jr.*, John A. Hawkins*, Nicole V. Johnson, Cheulhee Jung, Kuang Hu, James R. Rybarski, Janice S. Chen, Jennifer A. Doudna, William H. Press & Ilya J. Finkelstein; (* co-first authors)
Nature Biotechnology.
[PDF]    [Supplement]    DOI: 10.1038/s41587-020-0646-5    PMID: 32895548    
62. Epigenetic cell fate in Candida albicans is controlled by transcription factor condensates acting at super-enhancer-like elements
Corey Frazer*, Mae I. Staples*, Yoori Kim, Matthew Hirakawa, Maureen A. Dowell, Nicole V. Johnson, Aaron D. Hernday, Veronica H. Ryan, Nicolas L. Fawzi, Ilya J. Finkelstein & Richard J. Bennett (* co-first authors)
Nature Microbiology.
[PDF]    DOI: 10.1038/s41564-020-0760-7    PMID: 32719507    
61. Structure-based Design of Prefusion-stabilized SARS-CoV-2 Spikes
Ching-Lin Hsieh, Jory A. Goldsmith, Jeffrey M. Schaub, Andrea M. DiVenere, Hung-Che Kuo, Kamyab Javanmardi, Kevin C. Le, Daniel Wrapp, Alison Gene-Wei Lee, Yutong Liu, Chia-Wei Chou, Patrick O. Byrne, Christy K. Hjorth, Nicole V. Johnson, John Ludes-Meyers, Annalee W. Nguyen, Juyeon Park, Nianshuang Wang, Dzifa Amengor, Jason J. Lavinder, Gregory C. Ippolito, Jennifer A. Maynard†, Ilya J. Finkelstein† & Jason S. McLellan† († co-corresponding)
Science. 369 (6510): 1501-1505
[PDF]    [Supplement]    DOI: 10.1126/science.abd0826    PMID: 32703906    

Press:

60. HEDGES error-correcting code for DNA storage corrects indels and allow sequence constraints
William H. Press, John A. Hawkins, Stephen K. Jones Jr., Jeffrey M. Schaub, Ilya J. Finkelstein
Proc Natl Acad Sci USA. 117 (31): 18489-18496
[PDF]    [Supplement]    DOI: 10.1073/pnas.2004821117    PMID: 32675237    

Press:

59. RADX condenses single-stranded DNA to antagonize RAD51 loading
Hongshan Zhang, Jeffrey M. Schaub & Ilya J. Finkelstein
Nucleic Acids Research. 48 (14): 7834-7843
[PDF]    [Supplement]    DOI: 10.1093/nar/gkaa559    PMID: 32621611    
58. DNA-dependent Protein Kinase Promotes DNA End Processing by MRN and CtIP
Rajashree Deshpande, Logan Myler, Michael Soniat, Nodar Makharashvili, Linda Lee, Susan Lees-Miller, Ilya Finkelstein & Tanya Paull
Science Advances. 6 (2): eaay0922
[PDF]    [Supplement]    DOI: 10.1126/sciadv.aay0922    PMID: 31934630    
2019
57. Human cohesin compacts DNA by loop extrusion
Yoori Kim*, Zhubing Shi*, Hongshan Zhang, Ilya J. Finkelstein† & Hongtao Yu† (* co-first authors) († co-corresponding)
Science. 366 (6471): 1345-1349
[PDF]    [Supplement]    DOI: 10.1126/science.aaz4475    PMID: 31780627    
56. Systematic discovery of endogenous human ribonucleoprotein complexes
Anna L Mallam*, Wisath Sae-Lee, Jeffrey M Schaub, Fan Tu, Anna Battenhouse, Yu Jin Jang, Jonghwan Kim, John B. Wallingford, Ilya J Finkelstein, Edward M Marcotte† & Kevin Drew*† (* co-first authors) († co-corresponding)
Cell Reports. 29 (5): 1351-1368
[PDF]    [Supplement]    DOI: 10.1016/j.celrep.2019.09.060    PMID: 31665645    
55. Retrons and their applications in genome engineering
Anna J. Simon, Andrew D. Ellington & Ilya J. Finkelstein
Nucleic Acids Research. 47 (21): 11007-11019
[PDF]    [Supplement]    DOI: 10.1093/nar/gkz865    PMID: 31598685    
54. Functional metagenomics-guided discovery of potent Cas9 inhibitors in the human microbiome
Kevin J Forsberg, Ishan V Bhatt, Danica T. Schmidtke, Kamyab Javanmardi, Kaylee E Dillard, Barry L Stoddard, Ilya J Finkelstein, Brett K Kaiser & Harmit S Malik
eLife.
[PDF]    [Supplement]    DOI: 10.7554/eLife.46540    PMID: 31502535    
53. RPA phosphorylation inhibits DNA resection
Michael M. Soniat, Logan R. Myler, Hung-Che Kuo, Tanya T. Paull & Ilya J. Finkelstein
Molecular Cell. 75 (1): 145-153
[PDF]    [Supplement]    DOI: 10.1016/j.molcel.2019.05.005    PMID: 31153714    
52. Poly(ADP-ribose) polymerase-1 antagonizes DNA resection at double-strand breaks
Marie-Christine Caron*, Ajit K. Sharma*, Julia O’Sullivan, Logan R. Myler, Maria Tedim Ferreira, Amélie Rodrigue, Yan Coulombe, Chantal Ethier, Jean-Philippe Gagné, Marie-France Langelier, John M. Pascal, Ilya J. Finkelstein, Michael J. Hendzel†, Guy G. Poirier† & Jean-Yves Masson† (* co-first authors) († co-corresponding)
Nature Communications. 10 (1): 2954
[PDF]    [Supplement]    DOI: 10.1038/s41467-019-10741-9    PMID: 31273204    
51. Purification and Biophysical Characterization of the Mre11-Rad50-Nbs1 Complex.
Logan R. Myler, Michael M. Soniat, Xiaoming Zhang, Rajashree A. Deshpande, Tanya T. Paull & Ilya J. Finkelstein
Methods Mol Biol.
[PDF]    DOI: 10.1007/978-1-4939-9520-2_20    PMID: 31147924    
50. Assembling the Human Resectosome on DNA Curtains.
Michael M. Soniat, Logan R. Myler & Ilya J. Finkelstein
Methods Mol Biol.
[PDF]    DOI: 10.1007/978-1-4939-9500-4_14    PMID: 31127580    
49. Sortase-mediated fluorescent labeling of CRISPR complexes
Kaylee E. Dillard, Jeffrey M. Schaub, Maxwell W. Brown, Fatema A. Saifuddin, Yibei Xiao, Erik Hernandez, Samuel D. Dahlhauser, Eric v. Anslyn, Ailong Ke, Ilya J. Finkelstein
Methods in Enzymology.
[PDF]    DOI: 10.1016/bs.mie.2018.10.031    PMID: 30691654    
2018
48. Intrinsically disordered regions regulate both catalytic and noncatalytic activities of the MutLα mismatch repair complex.
Yoori Kim*, Christopher M. Furman*, Carol M. Manhart, Eric Alani†, and Ilya J. Finkelstein† (* co-first authors) († co-corresponding)
Nucleic Acids Research.
[PDF]    [Supplement]    DOI: 10.1093/nar/gky1244    PMID: 30541127    
47. Phage Mu Gam protein promotes NHEJ in concert with Escherichia coli ligase
Sudipta Bhattacharyyaa, Michael M. Soniat, David Walker, Sooin Jang, Ilya J. Finkelstein†, & Rasika M. Harshey† († co-corresponding)
Proc Natl Acad Sci USA. 115 (50): E11614-E11622
[PDF]    [Supplement]    DOI: 10.1073/pnas.1816606115    PMID: 30487222    
46. Assembly and Translocation of a CRISPR-Cas Primed Acquisition Complex.
Kaylee E. Dillard*, Maxwell W. Brown*, Nicole V. Johnson, Yibei Xiao, Adam Dolan, Erik Hernandez, Samuel Dahlhauser, Yoori Kim, Logan R. Myler, Eric Anslyn, Ailong Ke, and Ilya J. Finkelstein (* co-first authors)
Cell. 175 (1): 1-13
[PDF]    [Supplement]    DOI: 10.1016/j.cell.2018.09.039    PMID: 30343903    

Press:

45. Assessing Protein Dynamics on Low-Complexity Single-Stranded DNA Curtains.
Jeffrey M. Schaub, Hongshan Zhang, Michael M. Soniat, Ilya J. Finkelstein
Langmuir.
[PDF]    [Supplement]    DOI: 10.1021/acs.langmuir.8b01812    PMID: 30044093    
44. Kinetic Basis for DNA Target Specificity of CRISPR-Cas12a.
Isabel Strohkendl, Fatema A. Saifuddin, James R. Rybarski, Ilya J. Finkelstein, Rick Russell
Mol Cell.
[PDF]    [Supplement]    DOI: 10.1016/j.molcel.2018.06.043    PMID: 30078724    

Press:

43. Noncoding RNA-nucleated heterochromatin spreading is intrinsically labile and requires accessory elements for epigenetic stability.
R A Greenstein, Stephen K Jones, Eric C Spivey, James R Rybarski, Ilya J Finkelstein, Bassem Al-Sady
eLife.
[PDF]    [Supplement]    DOI: 10.7554/eLife.32948    PMID: 30020075    
42. Indel-correcting DNA barcodes for high-throughput sequencing.
John A. Hawkins, Stephen K. Jones Jr., Ilya J. Finkelstein†, and William H. Press† († co-corresponding)
Proc Natl Acad Sci USA. 115 (27): E6217-26
[PDF]    [Supplement]    DOI: 10.1073/pnas.1802640115    PMID: 29925596    

Press:

41. Coordination of Rad1-Rad10 interactions with Msh2-Msh3, Saw1 and RPA is essential for functional 3' non-homologous tail removal.
Robin Eichmiller*, Melisa Medina-Rivera*, Rachel DeSanto, Eugen Minca, Christopher Kim, Cory Holland, Ja-Hwan Seol, Megan Schmit, Diane Oramus, Jessica Smith, Ignacio F Gallardo, Ilya J Finkelstein, Sang Eun Lee & Jennifer A Surtees (* co-first authors)
Nucleic Acids Research. 46 (10): 5075-5096
[PDF]    [Supplement]    DOI: 10.1093/nar/gky254    PMID: 29660012    
40. Distinct roles of XPF-ERCC1 and Rad1-Rad10-Saw1 in replication-coupled and uncoupled inter-strand crosslink repair.
Ja-Hwan Seol*, Cory Holland*, Xiaolei Li*, Christopher Kim, Fuyang Li, Melisa Medina-Rivera, Robin Eichmiller, Ignacio F. Gallardo, Ilya J. Finkelstein, Paul Hasty, Eun Yong Shim, Jennifer A. Surtees & Sang Eun Lee (* co-first authors)
Nature Communications. 9 (1): 2025
[PDF]    [Supplement]    DOI: 10.1038/s41467-018-04327-0    PMID: 29795289    
39. A Microfluidic Device for Massively Parallel, Whole-lifespan Imaging of Single Fission Yeast Cells.
Stephen K Jones Jr, Eric C Spivey, James R Rybarski, and Ilya J Finkelstein
Bio-protocol. 8 (7): e2783
[PDF]    DOI: 10.21769/BioProtoc.2783    PMID: 29770351    
2017
38. Single-molecule imaging reveals how Mre11-Rad50-Nbs1 initiates DNA break repair
Logan R. Myler*, Ignacio F. Gallardo*, Michael M. Soniat, Rajashree A. Deshpande, Xenia B. Gonzalez, Yoori Kim, Tanya T. Paull & Ilya J. Finkelstein (* co-first authors)
Molecular Cell. 67 (5): 891-898
[PDF]    [Supplement]    DOI: 10.1016/j.molcel.2017.08.002    PMID: 28867292    

Highlights:

37. Eukaryotic resectosomes: A single-molecule perspective.
Logan R. Myler and Ilya J. Finkelstein
Progress in Biophysics and Molecular Biology.
[PDF]    DOI: 10.1016/j.pbiomolbio.2016.08.001    PMID: 27498169    
36. Massively Parallel Biophysical Analysis of CRISPR-Cas Complexes on Next Generation Sequencing Chips
Cheulhee Jung*, John A. Hawkins*, Stephen K. Jones, Jr.*, Yibei Xiao, James R. Rybarski, Kaylee E. Dillard, Jeffrey Hussmann, Fatema A. Saifuddin, Cagri A. Savran, Andrew D. Ellington, Ailong Ke, William H. Press, Ilya J. Finkelstein (* co-first authors)
Cell. 170 (1): 35-47.e13
[PDF]    [Supplement]    DOI: 10.1016/j.cell.2017.05.044    PMID: 28666121    

Press:

35. Efficient modification of λ-DNA substrates for single-molecule studies.
Yoori Kim, Armando de la Torre, Andrew A. Leal & Ilya J. Finkelstein
Sci Rep. 7 (1): 2071
[PDF]    [Supplement]    DOI: 10.1038/s41598-017-01984-x    PMID: 28522818    
34. An aging-independent replicative lifespan in a symmetrically dividing eukaryote.
Eric C. Spivey*, Stephen K. Jones*, James R. Rybarski, Fatema A. Saifuddin & Ilya J. Finkelstein (* co-first authors)
eLife.
[PDF]    [Supplement]    DOI: 10.7554/eLife.20340    PMID: 28139976    
33. Next-Generation DNA Curtains for Single-Molecule Studies of Homologous Recombination.
Michael M. Soniat, Logan R. Myler, Jeffrey M. Schaub, Yoori Kim, Ignacio F. Gallardo, Ilya J. Finkelstein
Methods in Enzymololgy.
[PDF]    DOI: 10.1016/bs.mie.2017.03.011    PMID: 28668123    
32. Inserting Extrahelical Structures into Long DNA Substrates for Single-Molecule Studies of DNA Mismatch Repair.
Maxwell W. Brown, Armando de la Torre, and Ilya J. Finkelstein
Methods in Enzymology.
[PDF]    DOI: 10.1016/bs.mie.2016.08.006    PMID: 28062036    
2016
31. Conserved Sequence Preferences Contribute to Substrate Recognition by the Proteasome.
Houqing Yu, Amit K. Singh Gautam, Shameika R. Wilmington, Dennis Wylie, Kirby Martinez-Fonts, Grace Kago, Marie Warburton, Sreenivas Chavali, Tomonao Inobe, Ilya J. Finkelstein, M. Madan Babu and Andreas Matouschek
J Biol Chem. 291 (28): 14526-39
[PDF]    [Supplement]    DOI: 10.1074/jbc.M116.727578    PMID: 27226608    
30. Single-molecule imaging reveals the mechanism of Exo1 regulation by single-stranded DNA binding proteins.
Logan R. Myler*, Ignacio F. Gallardo*, Yi Zhou, Fade Gong, Soo-Hyun Yang, Marc S. Wold, Kyle M. Miller, Tanya T. Paull† & Ilya J. Finkelstein† (* co-first authors) († co-corresponding)
Proc Natl Acad Sci USA. 113 (9): E1170-9
[PDF]    [Supplement]    DOI: 10.1073/pnas.1516674113    PMID: 26884156    

Press:

29. Dynamic DNA binding licenses a repair factor to bypass roadblocks in search of DNA lesions.
Maxwell W. Brown, Yoori Kim, Gregory M. Williams, John D. Huck, Jennifer A. Surtees & Ilya J. Finkelstein
Nature Communications.
[PDF]    [Supplement]    DOI: 10.1038/ncomms10607    PMID: 26837705    
2015
28. High-Throughput Universal DNA Curtain Arrays for Single-Molecule Fluorescence Imaging.
Ignacio F. Gallardo, Praveenkumar Pasupathy, Maxwell Brown, Carol M. Manhart, Dean P. Neikirk, Eric Alani, and Ilya J. Finkelstein.
Langmuir. 31 (37): 10310-7
[PDF]    [Supplement]    DOI: 10.1021/acs.langmuir.5b02416    PMID: 26325477    
2014
27. High-throughput single-molecule studies of protein-DNA interactions.
Aaron D. Robison and Ilya J. Finkelstein
FEBS Lett. 588 (19): 3539-46
[PDF]    DOI: 10.1016/j.febslet.2014.05.021    PMID: 24859086    
26. 3D-printed microfluidic microdissector for high-throughput studies of cellular aging.
Eric C. Spivey, Blerta Xhemalce, Jason B. Shear, and Ilya J. Finkelstein
Anal Chem. 86 (15): 7406-12
[PDF]    [Supplement]    DOI: 10.1021/ac500893a    PMID: 24992972    
25. From cradle to grave: high-throughput studies of aging in model organisms.
Eric C. Spivey and Ilya J. Finkelstein
Mol Biosyst. 10 (7): 1658-67
[PDF]    DOI: 10.1039/c3mb70604d    PMID: 24535099    
24. Single-molecule imaging of FtsK translocation reveals mechanistic features of protein-protein collisions on DNA.
Ja YilLee, Ilya J.Finkelstein, Lidia K.Arciszewska, David J.Sherratt, Eric C.Greene
Mol Cell. 54 (5): 832-43
[PDF]    [Supplement]    DOI: 10.1016/j.molcel.2014.03.033    PMID: 24768536    
23. Rapid prototyping of multichannel microfluidic devices for single-molecule DNA curtain imaging.
Aaron D. Robison and Ilya J. Finkelstein
Anal Chem. 86 (9): 4157-63
[PDF]    [Supplement]    DOI: 10.1021/ac500267v    PMID: 24734940    
22. Nucleosome acidic patch promotes RNF168- and RING1B/BMI1-dependent H2AX and H2A ubiquitination and DNA damage signaling.
Justin W. Leung*, Poonam Agarwal*, Marella D. Canny, Fade Gong, Aaron D. Robison, Ilya J. Finkelstein, Daniel Durocher & Kyle M. Miller (* co-first authors)
PLoS Genet.
[PDF]    DOI: 10.1371/journal.pgen.1004178    PMID: 24603765    
2013
21. Molecular traffic jams on DNA.
Ilya J. Finkelstein and Eric C. Greene
Annu Rev Biophys.
[PDF]    DOI: 10.1146/annurev-biophys-083012-130304    PMID: 23451891    
20. The promoter-search mechanism of Escherichia coli RNA polymerase is dominated by three-dimensional diffusion.
Feng Wang*, Sy Redding*, Ilya J Finkelstein, Jason Gorman, David R Reichman & Eric C Greene (* co-first authors)
Nat Struct Mol Biol. 20 (2): 174-81
[PDF]    [Supplement]    DOI: 10.1038/nsmb.2472    PMID: 23262491    
2012
19. Single-stranded DNA curtains for real-time single-molecule visualization of protein-nucleic acid interactions.
Bryan Gibb, Tim D. Silverstein, Ilya J. Finkelstein, and Eric C. Greene
Anal Chem. 84 (18): 7607-12
[PDF]    DOI: 10.1021/ac302117z    PMID: 22950646    
18. Single-molecule imaging of DNA curtains reveals mechanisms of KOPS sequence targeting by the DNA translocase FtsK.
Ja Yil Lee*, Ilya J. Finkelstein*, Estelle Crozat, David J. Sherratt, and Eric C. Greene (* co-first authors)
Proc Natl Acad Sci USA. 109 (17): 6531-6
[PDF]    [Supplement]    DOI: 10.1073/pnas.1201613109    PMID: 22493241    
2011
17. Supported lipid bilayers and DNA curtains for high-throughput single-molecule studies.
Ilya J. Finkelstein and Eric C. Greene
Methods Mol Biol.
[PDF]    DOI: 10.1007/978-1-61779-129-1_26    PMID: 21660710    
2010
16. Single-molecule imaging reveals mechanisms of protein disruption by a DNA translocase.
Ilya J. Finkelstein, Mari-Liis Visnapuu, and Eric C. Greene
Nature. 468 (7326): 983-7
[PDF]    [Supplement]    DOI: 10.1038/nature09561    PMID: 21107319    
2009
15. XPD helicase speeds through a molecular traffic jam.
Ilya J. Finkelstein and Eric C. Greene
Mol Cell. 35 (5): 549-50
[PDF]    DOI: 10.1016/j.molcel.2009.08.012    PMID: 19748351    
2008
14. Single molecule studies of homologous recombination.
Ilya J. Finkelstein and Eric C. Greene
Mol Biosyst. 4 (11): 1094-104
[PDF]    DOI: 10.1039/b811681b    PMID: 18931785    
2007
13. Neuroglobin dynamics observed with ultrafast 2D-IR vibrational echo spectroscopy.
Haruto Ishikawa, Ilya J. Finkelstein, Seongheun Kim, Kyungwon Kwak, Jean K. Chung, Keisuke Wakasugi, Aaron M. Massari, and Michael D. Fayer
Proc Natl Acad Sci USA. 2007 (104): 41
[PDF]    DOI: 10.1073/pnas.0707718104    PMID: 17916624    
12. Frequency-frequency correlation functions and apodization in two-dimensional infrared vibrational echo spectroscopy: a new approach.
Kyungwon Kwak, Sungnam Park, Ilya J. Finkelstein, and M. D. Fayer
J Chem Phys. 127 (12): 124503
[PDF]    DOI: 10.1063/1.2772269    PMID: 17902917    
11. Viscosity-Dependent Protein Dynamics
Ilya J. Finkelstein, Aaron M. Massari, M.D. Fayer
Biophys J. 92 (10): 3652-62
[PDF]    [Supplement]    DOI: 10.1529/biophysj.106.093708    PMID: 17446536    
10. Probing dynamics of complex molecular systems with ultrafast 2D IR vibrational echo spectroscopy.
Ilya J. Finkelstein, Junrong Zheng, Haruto Ishikawa, Seongheun Kim, Kyungwon Kwaka and Michael D. Fayer
Phys Chem Chem Phys. 9 (13): 1533-49
[PDF]    DOI: 10.1039/b618158a    PMID: 17429547    
9. Substrate binding and protein conformational dynamics measured by 2D-IR vibrational echo spectroscopy.
Ilya J. Finkelstein, Haruto Ishikawa, Seongheun Kim, Aaron M. Massari, and M. D. Fayer
Proc Natl Acad Sci USA. 104 (8): 2637-42
[PDF]    DOI: 10.1073/pnas.0610027104    PMID: 17296942    
2006
8. Cytochrome c552 mutants: structure and dynamics at the active site probed by multidimensional NMR and vibration echo spectroscopy.
Aaron M. Massari, Brian L. McClain, Ilya J. Finkelstein, Andrew P. Lee, Heather L. Reynolds, Kara L. Bren, and Michael D. Fayer
J Phys Chem B. 110 (38): 18803-10
[PDF]    [Supplement]    DOI: 10.1021/jp054959q    PMID: 16986870    
7. Dynamics of proteins encapsulated in silica sol-gel glasses studied with IR vibrational echo spectroscopy.
Aaron M. Massari, Ilya J. Finkelstein, and Michael D. Fayer
J Am Chem Soc. 128 (12): 3990-7
[PDF]    [Supplement]    DOI: 10.1021/ja058745y    PMID: 16551107    
2005
6. The influence of aqueous versus glassy solvents on protein dynamics: vibrational echo experiments and molecular dynamics simulations.
Aaron M. Massari, Ilya J. Finkelstein, Brian L. McClain, Anne Goj, Xin Wen, Kara L. Bren, Roger F. Loring, and Michael D. Fayer
J Am Chem Soc. 127 (41): 14279-89
[PDF]    [Supplement]    DOI: 10.1021/ja053627w    PMID: 16218622    
5. Ultrafast dynamics of myoglobin without the distal histidine: stimulated vibrational echo experiments and molecular dynamics simulations.
Ilya J. Finkelstein, Anne Goj, Brian L. McClain, Aaron M. Massari, Kusai A. Merchant, Roger F. Loring, and M. D. Fayer
J Phys Chem B. 109 (35): 16959-66
[PDF]    DOI: 10.1021/jp0517201    PMID: 16853158    
2004
4. Dynamics of hemoglobin in human erythrocytes and in solution: influence of viscosity studied by ultrafast vibrational echo experiments.
Brian L. McClain, Ilya J. Finkelstein, and M. D. Fayer
J Am Chem Soc. 126 (48): 15702-10
[PDF]    DOI: 10.1021/ja0454790    PMID: 15571392    
3. Fifth-order contributions to ultrafast spectrally resolved vibrational echoes: heme-CO proteins.
Ilya J. Finkelstein, Brian L. McClain, and M. D. Fayer
J Chem Phys. 121 (2): 877-85
[PDF]    DOI: 10.1063/1.1758940    PMID: 15260618    
2. Vibrational echo experiments on red blood cells: Comparison of the dynamics of cytoplasmic and aqueous hemoglobin.
Brian L. McClain, Ilya J. Finkelstein, M.D. Fayer
Chem Phys Lett. 392 (4-6): 324-329
[PDF]    DOI: 10.1016/j.cplett.2004.05.080    
2003
1. Myoglobin-CO substate structures and dynamics: multidimensional vibrational echoes and molecular dynamics simulations.
Kusai A. Merchant, W. G. Noid, Ryo Akiyama, Ilya J. Finkelstein, Alexei Goun, Brian L. McClain, Roger F. Loring, and M. D. Fayer
J Am Chem Soc. 125 (45): 13804-18
[PDF]    [Supplement]    DOI: 10.1021/ja035654x    PMID: 14599220