CV

 

B400, Beckman Center
279 Campus Drive West
Stanford University School of Medicine
Stanford, CA 94305
Phone (650) 723-7310
jyesselm [at] stanford.edu

Education

2008 - 2013
Ph.D., Biophysics, University of Michigan, MI

2003 - 2008
B.S. in Physics, University of Rochester, NY

Positions and Employment

2013 - Present
Postdoctoral research with Dr. Rhiju Das, Stanford University. Topic: Automated 3D Design of RNA Nanostructures.

2008 - 2013
Graduate research with Drs. Hashim Al-Hashimi and Charles Brooks III, University of Michigan. Topic: Development of automated tools for parameterization of novel molecules, procedures in constructing RNA dynamic ensembles and computational docking software

2007 – 2008
Research with Dr. George Ferguson, University of Rochester, Topic: Development of Artificial Intelligence using Genetic Programming

2005 - 2007
Research with Dr. Frank Wolfs, University of Rochester, Topic: Processing of data from the Brookhaven National Laboratory particle accelerator and development of software to detect WIMPS (Weakly Interacting Massive Particles)

Teaching Experience

2016
Mentor for Medicine Summer Research Program (SIMR)

2012
Graduate Student Instructor for Biophysics of Disease

2011
Graduate Student Instructor for Physics of Body and Mind

2011
Graduate Student Instructor for Biophysical Modeling

2010,  2013
Graduate Student Instructor for Physical and Chemical Principles Behind Biology and Medicine

2006
Teaching Assistant for Technical Programming

2006
Workshop Leader for Introduction to Computer Programming

2005 - 2007
Teaching Assistant for Introduction to Computer Programing

2005
Teaching Assistant for Black Holes, Time Warps and Large Scale Structures in the Universe

Honors and Awards

2018 -
The Center for HIV RNA Studies Collaborative Development Pilot Grant (Conditional on faculty appointment)

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

[16] *Yesselman JD, *Denny SK, Bisaria N, Herschlag D, Greenleaf WJ, Das R, “Blind Predictions of RNA Tertiary Assembly Energetics at Chemical Accuracy”, in preparation (Preprint)

[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 revisions, Nature Nanotechnology (Preprint)

[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, H.M., Brooks C. L. III (2011) "Exploring RNA Drug Binding Using Consistent Charge Models", selected to present a poster presentation at the Biophysical Society meeting, Baltimore, MD.