Room 829, Hamilton Hall
639 N. 12th Street
University of Nebraska-Lincoln
Lincoln, NE 68588
(402) 472 - 2523
jyesselm [at] unl.edu
Education
2008 - 2013
Ph.D., Biophysics, University of Michigan, MI
2003 - 2008
B.S. in Physics, University of Rochester, NY
Professional
2019 - Present
Assistant Professor, Department of Chemistry, University of Nebraska-Lincoln
2013 - 2019
NIH NRSA postdoctoral fellow (with R. Das, Stanford University)
Honors and Awards
2015 - 2017
NIH Ruth L. Kirschstein National Research Service Award Postdoctoral Fellowship
2014 - 2015
Deans Fellowship, Stanford University
2014
Best Poster at RosettaCon
2014
Rackham Travel Grant to attend American Chemical Society, University of Michigan
2012
Rackham Travel Grant to attend Biophysical Society, University of Michigan
2008 – 2009
Biophysics Fellowship, University of Michigan
2007 – 2008
Take Five Scholarship to Study Artificial Intelligence, University of Rochester
2007
Research Experiences for Undergraduates in Physics, University of Rochester
Publications
*Contributed equally
[17] *Kappel K, *Zhang K, Su Z, Kladwang W, Li S, Pintilie G, Topkar VV, Rangan R, Zheludev IN, Watkins AM, Yesselman JD, Chiu W, Das R “Ribosolve: Rapid determination of three-dimensional RNA-only structures”, submitted, Science. (Preprint)
[16] *Yesselman JD, *Denny SK, Bisaria N, Herschlag D, Greenleaf WJ, Das R, “Blind Predictions of RNA Tertiary Assembly Energetics at Chemical Accuracy”, in press, epub available, Proceedings of the National Academy of Sciences U.S.A.
[15] Yesselman JD, Eiler D, Carlson ED, Ooms AN, Kladwang W, Shi X, Costantino D, Herschlag D, Jewett MC, Kieft JS, Das R “Computational Design of Asymmetric Three-dimensional RNA Structures and Function", in press, epub available, Nature Nanotechnology
[14] *Denny SK, *Bisaria N, Yesselman JD, Das R, Herschlag D, Greenleaf WJ (2018) “High-throughput, quantitative characterization of RNA tertiary structure elements”, Cell 174, 1–14
[13] *Yesselman JD, *Tian S, Lui X, Shi L, Li JB, Das R (2017) "Updates to the RNA Mapping Database (RMDB), Version 2", Nucleic Acids Research 46 (D1): D375 - D379
[12] *Cheng CY, *Kladwang W, Yesselman JD, Das R (2017) “Serendipitous high-resolution RNA structural information overlooked in dimethyl sulfate mapping experiments”, Proceedings of the National Academy of Sciences U.S.A. 114 (37) 9876-9881
[11] Wang Y, Yesselman JD, Zhang, Q, Kang M, Feigon J (2016) Structural conservation in the template/pseudoknot domain of vertebrate telomerase RNA from teleost fish to human. Proceedings of the National Academy of Sciences U.S.A. 113(35): 5125–5134
[10] Sengupta RN, Van Schie SNS, Giambasu G, Dai Q, Yesselman JD, York D, Piccirilli JA, Herschlag D (2016) “An active site rearrangement within the Tetrahymena group I ribozyme releases nonproductive interactions”. RNA, 22: 32–48
[9] Yesselman JD and Das R (2016) “Modeling small non-canonical RNA motifs with the Rosetta FARFAR server”, Methods in Molecular Biology, RNA modeling 1490: 187 - 98
[8] Yesselman JD and Das R. (2015) “RNA-Redesign: A web server for fixed-backbone 3D design of RNA” Nucleic Acids Research 43 (W1): W498 - W501
[7] Tian, S, Yesselman JD, Cordero, P and Das, R (2015) “Primerize: automated primer assembly for transcribing non-coding RNA domains” Nucleic Acids Research 43 (W1): W522 – W526
[6] *Yesselman JD, *Horowitz S, Brooks CL III, Trievel RC. Frequent side chain methyl carbon-oxygen hydrogen bonding in proteins revealed by computational and stereochemical analysis of neutron structures. Proteins 83(3):403-10
[5] Horowitz S, Dirk LM, Yesselman JD, Nimtz JS, Adhikari U, Mehl RA, Scheiner S, Houtz RL, Al-Hashimi HM, Trievel RC (2013) "Conservation and functional importance of carbon-oxygen hydrogen bonding in AdoMet-dependent methyltransferases" Journal of the American Chemical Society 135(41):15536-48
[4] *Knight, J. L., *Yesselman, J.D, Brooks, C. L. III (2013) "Assessing the Quality of Absolute Hydration Free Energies Among CHARMM-Compatible Ligand Parameterization Schemes" Journal of Computational Chemistry 34, 983-903
[3] Yesselman, JD, Price, DJ, Knight, JL and Brooks, CL III (2012) "MATCH: An Atom-Typing Toolset for Molecular Mechanics Force Fields" Journal of Computational Chemistry 33: 189–202
[2] Arthur EJ, Yesselman, JD, Brooks CL III (2011) "Predicting extreme pKa shifts in staphylococcal nuclease mutants with constant pH molecular dynamics" Proteins: Structure, Function and Bioinformatics 79(12): 3276–3286
[1] Horowitz S, Yesselman JD, Al-Hashimi HM, Trievel RC (2011) "Direct evidence for methyl group coordination by carbon-oxygen hydrogen bonds in the lysine methyltransferase SET7/9" Journal of Biological Chemistry 27;286(21):18658-63
Conference Presentations
[14] Yesselman JD, Eiler D, Ooms AN, Kladwang W, Shi X, Costantino D, Herschlag D, Kieft JS, Das R, (2017) “Computational Design of Asymmetric Three-dimensional RNA Structures and Machines”, selected to present a poster at RNA Society, Berkley, CA.
[13] Yesselman JD, Eiler D, Ooms AN, Kladwang W, Shi X, Costantino D, Herschlag D, Kieft JS, Das R, (2017) “Computational Design of Asymmetric Three-dimensional RNA Structures and Machines”, selected to present a poster at Biochemistry Research Conference, Santa Cruz, CA.
[12] Yesselman JD, Eiler D, Ooms AN, Kladwang W, Shi X, Costantino D, Herschlag D, Kieft JS, Das R, INVITED, (2017) “Automated Design of Three-Dimensional Asymmetric RNA Structures at Near-Atomic Accuracy”, Invited to give an oral presentation at Foundations of Nanoscience: Self-assembled Architectures and Devices, Snowbird, UT.
[11] Yesselman JD, Eiler D, Ooms AN, Kladwang W, Shi X, Costantino D, Herschlag D, Kieft JS, Das R, (2017) “Automated Design of Three-Dimensional Asymmetric RNA Structures at Near-Atomic Accuracy”, selected to present a poster at Gordon Research Conference: RNA Nanotechnology, Ventura, CA.
[10] Yesselman JD, Denny SK, Bisaria N, Herschlag D, Greenleaf WJ, Das R (2016) “Surprisingly Accurate Energetic Modeling Deconvolves Big Data on RNA 3D Folding”, selected to give an oral presentation at the RNA Society, Kyoto, Japan.
[9] Yesselman JD, Eiler D, Ooms AN, Kladwang W, Shi X, Costantino D, Herschlag D, Kieft JS, Das R, (2016) “Automated Design of Three-Dimensional Asymmetric RNA Structures at Near-Atomic Accuracy”, selected to present an oral presentation at Biochemistry Research Conference, Santa Cruz, CA.
[8] Yesselman JD, Denny SK, Bisaria N, Herschlag D, Greenleaf WJ, Das R (2016) “Towards Accurate Energetic Modeling of RNA 3D Folding: Testing Simple Models with Lots of Data”, selected to present a poster at RosettaCon, Leavenworth, WA.
[7] Yesselman JD, Denny SK, Bisaria N, Herschlag D, Greenleaf WJ, Das R (2015) “A Massively Parallel Approach to RNA Folding and Dynamics”, selected to present an oral presentation at Biochemistry Research Conference, Santa Cruz, CA.
[6] Yesselman JD, Kladwang W, Das R (2015) “RNAMake: an Automated Design Toolkit for RNA 3D Structure”, selected to present a poster at the RNA Society, Madison, WA.
[5] Yesselman JD, Das R (2014) Toward Automated Design of RNA 3D Structure, selected to present a poster at Rosettacon, Leavenworth, WA. Selected for Best Poster.
[4] Yesselman JD, Das R (2014) "Toward Automated Design of RNA 3D Structure", selected to present a poster at the RNA Society, Quebec City, Canada.
[3] Yesselman JD, Das R (2014) "Toward Automated Design of RNA 3D Structure", selected to present a poster at the UCSC symposium RNA Biology/RNA Therapeutics, San Francisco, CA.
[2] Yesselman JD, Knight, JL, Al-Hashimi, HM, Brooks CL III (2012) "An Atom-Typing Toolset for CHARMM", selected to present an oral presentation at the American Chemical Society meeting, San Diego, CA.
[1] Yesselman JD, Al-Hashimi HM, Brooks CL III (2011) "Exploring RNA Drug Binding Using Consistent Charge Models", selected to present a poster presentation at the Biophysical Society meeting, Baltimore, MD.