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Ilya J Finkelstein
Associate Professor
Molecular BiosciencesDiscovery & Biophysical Studies of Molecular Machines-
Latest publications
Dr. Ilya Finkelstein is an Associate Professor of Molecular Biosciences at the University of Texas at Austin. Prior to his position at UT-Austin, Dr. Finkelstein received a B.S. from the University of California, Berkeley, a Ph.D. in Chemistry from Stanford University, and completed postdoctoral training at Columbia University Medical Center. Dr. Finkelstein’s lab is investigating the molecular mechanisms of genome maintenance, CRISPR biology, and epigenetic inheritance. Since 2019, the Finkelstein lab is also working on pandemic countermeasures with the goal of understanding viral variants and designing better vaccines.
Lab website: https://finkelsteinlab.org/
Prospective students and postdocs are encouraged to reach out via e-mail.
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Latest publications
Finkelstein lab website (with PDFs)
Preprints
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)
BioRxiv.
[PDF] [Supplement] DOI: 10.1101/2022.04.18.488614Yu-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)
BioRxiv.
[PDF] [Supplement] DOI: 10.1101/2021.12.04.471212Kaylee E. Dillard†, Cynthia Terrace, Kamyab Javanmardi, Wantae Kim, Kevin J. Forsberg, and Ilya J. Finkelstein† († co-corresponding)
BioRxiv.
[PDF] [Supplement] DOI: 10.1101/2021.09.15.460536Jule 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: 10.1101/2021.04.07.4388492022
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: 35351518Jeffery M. Schaub†, Michael M. Soniat & Ilya J. Finkelstein†
NAR. 50 (7): 3911-3921
[PDF] [Supplement] DOI: 10.1093/nar/gkac119 PMID: 35357490Behrouz 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) († co-corresponding)
Nat Commun.
[PDF] [Supplement] DOI: 10.1038/s41467-022-28994-2 PMID: 35292641Amanda 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: 350776812021
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: 34919820James 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: 3484502473. Opfi: A Python package for identifying gene clusters in large genomics and metagenomics data setsAlexis 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: 35445164Jeffrey 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: 34611365Molly 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: 34760161Chien-Hui Ma, Kamyab Javanmardi, Ilya J. Finkelstein†, Makkuni Jayaram† († co-corresponding)
eLife.
[PDF] [Supplement] DOI: 10.7554/eLife.65763 PMID: 34435949Randall 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: 34303698William 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. 372 (6546): 1108-1112
[PDF] [Supplement] DOI: 10.1126/science.abg5268 PMID: 33947773Carlos 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: 33729813S. 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: 33741335Isabel 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: 336921022020
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: 33127862Stephen 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: 32895548Corey 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: 32719507Ching-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:
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:
Hongshan Zhang, Jeffrey M. Schaub & Ilya J. Finkelstein
Nucleic Acids Research. 48 (14): 7834-7843
[PDF] [Supplement] DOI: 10.1093/nar/gkaa559 PMID: 32621611Rajashree 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: 31934630Please see https://finkelsteinlab.org/papers/ for all papers
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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)
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BCH339M: Structure and Function of Molecular Machines
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An updated list of current lab members is available on the Finkelstein lab website.
Interested in joining the team?
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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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