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FINKELSTEIN, ILYA J
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Ilya J Finkelstein

Associate Professor
Molecular Biosciences

Lorene Morrow Kelley Endowed Faculty Fellowship Fund

Biophysical Studies of Molecular Machines

ifinkelstein@cm.utexas.edu

Phone: 512-471-1394

Office Location
MBB 3.422

Postal Address
2500 SPEEDWAY
AUSTIN, TX 78712
  • B.S., in Chemistry - UC Berkeley (2001)
  • Ph.D., in Chemistry - Stanford University (2007)
  • Postdoctoral Training in Molecular Biophysics - Columbia University Medical Center (2012)

 

Research Interests

We develop biophysical tools to understand how molecular machines edit and repair our genomes. Current focus areas include the biology and applications of CRISPR adaptive immunity, mammalian gene editing, and the mechanisms of genome maintenance. Our interdisciplinary research program combines single-molecule biophysics, hihgh-throughput assays and micro-/nano-scale engineering to understand how organisms are able to maintain and edit their genomic integrity. 

Prospective students and postdocs are encouraged to reach out via e-mail.

 

Latest publications

Google Scholar

Finkelstein lab website (with PDFs)

2021

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, Dnaiel 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 Dye, Andrew Herbert, Ilya J. Finkelstein, Ralph S. Baric, Jason S. McLellan, George Georgiou, Jason L. Lavinder†, Gregory C. Ippolito† († co-corresponding)
Science.    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. 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.  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  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    
 
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.  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.    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.   DOI: 10.1126/science.abd0826    PMID: 32703906    
 
 
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.   DOI: 10.1073/pnas.2004821117    PMID: 32675237    
 
59. RADX condenses single-stranded DNA to antagonize RAD51 loading
Hongshan Zhang, Jeffrey M. Schaub & Ilya J. Finkelstein
Nucleic Acids Research. 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  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. 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  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 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.  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 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  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    

2018- 

Older publications 

Awards

2021                      Norman Hackerman Award in Chemical Sciences, Welch Foundation

2018                      Fellow, William H. Tonn Professorial Fund

2015                      National Science Foundation CAREER Award                    

2014                      American Federation of Aging Research Junior Fellow

2013                      Emerging Investigator, Molecular BioSystems

2013                      Protege, The Academy of Medicine, Engineering and Science of Texas

2012                      CPRIT Fellow in Cancer Research                           

2011                      Pathway to Independence Award (NIH K99/R00)                                        

2007                      NRSA Postdoctoral Fellow (NIH F32)

BCH339M: Structure and Function of Molecular Machines

An updated list of current Finkelstein lab website is available on the Finkelstein lab website.

Interested in joining the team?

The Finkelstein group is an interdisciplinary team of biophysicists seeking to discover how molecular machines maintain and edit our genetic information. We combine molecular biology with high-throughput approaches and single-molecule biophysics. We are especially interested in scientists that are at the interface of biophysics, bioinformatics, and molecular biology. For specific job openings, see below:

Postdoc Openings

Applicants with a strong background in bioinformatics, molecular (bio)physics, biomedical engineering, or computer science are strongly encouraged to apply. However, enthusiasm and a strong work ethic in your graduate career are the only requirements. Please email Ilya a CV and a cover letter that explains why you are interested in the lab.

Graduate Students

Prospective graduate students that are interested in molecular biophysics, bioinformatics, or biomedical engineering can join the lab by applying to a number of graduate programs at UT Austin. Possibilities include:

Undergraduate Students

The laboratory strives to include exceptional undergraduates with prior research experience in the life of the lab. To get started in research, please apply to these or related Freshman Research Initiative streams:

Students that are interested in joining the lab are encouraged to e-mail Ilya a short (one-page) summary of their prior research project. Unfortunately, I cannot consider applications without a one-page research summary.

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