Papers · Finkelstein Lab

Preprints

Discrete Subdomains Establish Epigenetic Diversity in Subtelomeric Heterochromatin

Agnisrota Mazumder, John Cooper, Can Goksal, Jasbeer S. Khanduja, Richard I. Joh, Johannes J. Groos, Rosario Y.J. Brockhausen, Junko Kanoh, Mo Motamedi, Ilya J. Finkelstein, Bassem Al-Sady†, and Sigurd Braun† († co-corresponding)
bioRxiv.
(

) DOI: 10.1101/2025.09.25.678047

2026

100. Structural basis for target discrimination and activation by Cas13d

Chia-Wei Chou, Selma Sinan, Hung-Che Kuo, You-Chiun Chang, Carlos Arguello, Daphne Sahaya, Rick Russell, and Ilya J. Finkelstein † († corresponding)
Science Advances. 12 (34): eaec4221
(

) [Supplement] DOI: 10.1126/sciadv.aec4221 PMID: 42616864

99. Single-Molecule Visualization of DNase I-Mediated DNA Cleavage by High-Speed Atomic Force Microscopy

Nada Elessawy, Selma Sinan, Hongshan Zhang, Zhenglin Yang, Yi Lu, Ilya J. Finkelstein, and Yi-Chih Lin† († corresponding)
ACS Chemical Biology. 21 (6): 1260-1268
(

) [Supplement] DOI: 10.1021/acschembio.6c00195 PMID: 42246973

98. Phage-encoded factor stimulates DNA degradation by the Hna anti-phage defense system

Matthew M. Hooper, Benjamin T. Hoover, Hongshan Zhang, Adam S. Franco, Ilya J. Finkelstein, and David W. Taylor† († corresponding)
Nature Communications. 17 (1): 6544
(

) [Supplement] DOI: 10.1038/s41467-026-73157-2 PMID: 42151145

2025

97. One-Pot Isothermal Linear Amplification and Cas12a-Based Nucleic Acid Detection

Selma Sinan, Remy M. Kooistra, Karunya Rajaraman, Zeba Islam, Damian Madan, Eric A. Nalefski †, and Ilya J. Finkelstein † († co-corresponding)
ACS Synthetic Biology. 14 (12): 4714-4722
(

) DOI: 10.1021/acssynbio.5c00463 PMID: 41248489

96. Discovery and engineering of retrons for precise genome editing

Jesse D. Buffington*, Hung-Che Kuo*, Kuang Hu*, You-Chiun Chang*, Kamyab Javanmardi*, Brittney Voigt, Yi-Ru Li, Mary E. Little, Sravan K. Devanathan, Blerta Xhemalçe, Ryan S. Gray, and Ilya J. Finkelstein † (* co-first authors) († corresponding)
Nature Biotechnology.
(

) DOI: 10.1038/s41587-025-02879-3 PMID: 41131151

Press:

95. Unleashing high trans-substrate cleavage kinetics of Cas12a for nucleic acid diagnostics

Eric A. Nalefski, Samantha Hedley, Karunya Rajaraman, Remy M. Kooistra, Ishira Parikh, Selma Sinan, Ilya J. Finkelstein, and Damian Madan
Nucleic Acids Research. 53 (14): gkaf712
(

) DOI: 10.1093/nar/gkaf712 PMID: 40716775

94. Mechanism of Cas9 inhibition by AcrIIA11

Kaylee E. Dillard, Hongshan Zhang, Lianne Z. Dubbs, Chia-Wei Chou, Cynthia Terrace, Kamyab Javanmardi, Wantae Kim, Kevin J. Forsberg, and Ilya J. Finkelstein † († corresponding)
Nucleic Acids Research. 53 (8): gkaf318
(

) [Supplement] DOI: 10.1093/nar/gkaf318 PMID: 40277083

93. Room temperature CRISPR diagnostics for low-resource settings

Eric A. Nalefski, Selma Sinan, Jason L. Cantera, Anastasia G. Kim, Remy M. Kooistra, Rafael E. Rivera, Jordyn P. Janshen, Sanchita Bhadra, Joshua D. Bishop, Andrew D. Ellington, Ilya J. Finkelstein, and Damian Madan
Scientific Reports. 15 (1): 3909
(

) DOI: 10.1038/s41598-025-86373-5 PMID: 39890862

2024

92. 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 † († corresponding)
EMBO Reports. 25 (12): 5635-5666
(

) [Supplement] DOI: 10.1038/s44319-024-00285-5 PMID: 39496836

91. Kinetic dissection of pre-crRNA binding and processing by CRISPR-Cas12a

Selma Sinan, Nathan M. Appleby, Chia-Wei Chou, Ilya J. Finkelstein, and Rick Russell † († corresponding)
RNA. 30 (10): 1345-1355
(

) [Supplement] DOI: 10.1261/rna.080088.124 PMID: 39009379

90. Massively Parallel Profiling of RNA-targeting CRISPR-Cas13d

Hung-Che Kuo †, Joshua Prupes, Chia-Wei Chou, and Ilya J. Finkelstein † († co-corresponding)
Nature Communications. 15 (1): 498
(

) [Supplement] DOI: 10.1038/s41467-024-44738-w PMID: 38216559

89. Mammalian Antigen Display for Pandemic Countermeasures

Andrea Quezada, Ankur Annapareddy, Kamyab Javanmardi, John Cooper, and Ilya J. Finkelstein † († corresponding)
Methods in Molecular Biology.
(

) DOI: 10.1007/978-1-0716-3666-4_12 PMID: 38315367

2023

88. 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, and Hong Wang † († co-corresponding)
Journal of Biological Chemistry. 299 (11): 105296
(

) DOI: 10.1016/j.jbc.2023.105296 PMID: 37774974

87. Asgard archaea defense systems and their roles in the origin of eukaryotic immunity

Pedro Leão, Mary E. Little, Kathryn E. Appler, Daphne Sahaya, Emily Aguilar-Pine, Kathryn Currie, Ilya J. Finkelstein, Valerie De Anda, and Brett J. Baker † († corresponding)
Nature Communications. 15 (1): 6386
(

) [Supplement] DOI: 10.1038/s41467-024-50195-2 PMID: 39085212

86. 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
(

) [Supplement] DOI: 10.1016/j.molcel.2023.07.006 PMID: 37536339

85. Unraveling the mechanisms of PAMless DNA interrogation by SpRY-Cas9

Grace N. Hibshman*, Jack P. K. Bravo*, Matthew M. Hooper, Tyler L. Dangerfield, Hongshan Zhang, Ilya J. Finkelstein, Kenneth A. Johnson, and David W. Taylor † (* co-first authors) († corresponding)
Nature Communications. 15 (1): 3663
(

) DOI: 10.1038/s41467-024-47830-3 PMID: 38688943

84. 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. 120 (18): e2218085120
(

) [Supplement] DOI: 10.1073/pnas.2218085120 PMID: 37094140

83. Distinct horizontal transfer mechanisms for type I and type V CRISPR-associated transposons

Kuang Hu, Chia-Wei Chou, Claus O. Wilke, and Ilya J. Finkelstein † († corresponding)
Nature Communications. 15 (1): 6653
(

) [Supplement] DOI: 10.1038/s41467-024-50816-w PMID: 39103341

82. The MRN complex and topoisomerase IIIa–RMI1/2 synchronize DNA resection motor proteins

Michael M. Soniat †, Giaochau Nguyen, Hung-Che Kuo, and Ilya J. Finkelstein † († co-corresponding)
Journal of Biological Chemistry. 299 (2): 102802
(

) [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. 34 (41): e2204957
(

) [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
(

) [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
(

) [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
(

) [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)
Nature Communications. 13 (1): 1367
(

) [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
(

) [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
(

) [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
(

) [Supplement] DOI: 10.1073/pnas.2112279118 PMID: 34845024

Press:

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.
(

) 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)
Nature Protocols. 16 (11): 5339-5356
(

) 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
(

) [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.
(

) [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
(

) 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
(

) [Supplement] DOI: 10.1126/science.abg5268 PMID: 33947773

Press:

Our Immune Systems Blanket the SARS-CoV-2 Spike Protein with Antibodies (UT News) (md | pdf)

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
(

) [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
(

) 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
(

) [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
(

) DOI: 10.1128/mBio.02707-20 PMID: 33127862

Press:

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. 39 (1): 84-93
(

) [Supplement] DOI: 10.1038/s41587-020-0646-5 PMID: 32895548

Press:

Matching CRISPR to the Job (UT News) (md | pdf)

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. 5 (11): 1374-1389
(

) 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
(

) [Supplement] DOI: 10.1126/science.abd0826 PMID: 32703906

Press:

60. HEDGES error-correcting code for DNA storage corrects indels and allows 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
(

) [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
(

) [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
(

) [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
(

) [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
(

) [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
(

) [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.
(

) [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
(

) [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
(

) [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.
(

) 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.
(

) 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.
(

) DOI: 10.1016/bs.mie.2018.10.031 PMID: 30691654

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. 47 (4): 1823-1835
(

) [Supplement] DOI: 10.1093/nar/gky1244 PMID: 30541127

2018

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
(

) [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 (4): 934-946.e15
(

) [Supplement] DOI: 10.1016/j.cell.2018.09.039 PMID: 30343903

Press:

Two Studies Shed Light on Complex CRISPR Systems (UT CNS) (md | pdf)

45. Assessing Protein Dynamics on Low-Complexity Single-Stranded DNA Curtains.

Jeffrey M. Schaub, Hongshan Zhang, Michael M. Soniat, Ilya J. Finkelstein
Langmuir. 34 (49): 14882-14890
(

) [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. 71 (5): 816-824.e3
(

) [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.
(

) [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
(

) [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
(

) [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
(

) [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
(

) 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
(

) [Supplement] DOI: 10.1016/j.molcel.2017.08.002 PMID: 28867292

Highlights:

F1000 recommended

37. Eukaryotic resectosomes: A single-molecule perspective.

Logan R. Myler and Ilya J. Finkelstein
Progress in Biophysics and Molecular Biology.
(

) 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
(

) [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
(

) [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.
(

) [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.
(

) 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.
(

) 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
(

) [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
(

) [Supplement] DOI: 10.1073/pnas.1516674113 PMID: 26884156

Press:

The Daily Texan (md | pdf)
UT College of Natural Sciences (md | pdf)

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.
(

) [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
(

) [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
(

) 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
(

) [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
(

) 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
(

) [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
(

) [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.
(

) 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.
(

) 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
(

) [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
(

) 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
(

) [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.
(

) 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
(

) [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
(

) 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
(

) 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
(

) 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
(

) 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
(

) [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
(

) 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
(

) 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
(

) [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
(

) [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
(

) [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
(

) 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
(

) 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
(

) 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
(

) 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
(

) [Supplement] DOI: 10.1021/ja035654x PMID: 14599220

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