https://yesselmanlab.com/gallery daily 0.75 2026-01-30 https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/1737743361909-TWF8NKVJZQD0812RV7J7/PHOTO-2022-12-03-01-39-42.jpg Gallery https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/1737743361909-TWF8NKVJZQD0812RV7J7/PHOTO-2022-12-03-01-39-42.jpg Gallery https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/1737743370519-59G9VLKN33MPHJ0PJKRQ/IMG_9082.JPG Gallery https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/1737743386594-8OCE4425W7FJQK7TW5P0/088c6e1f-97b1-4f19-a9a3-9fd0725db0c5.jpg Gallery https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/1737743392625-UGFZWOX83RF6MR5SBM7Q/IMG_1223.jpg Gallery https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/1737744673913-7N9VZT6BICNF6AOUSIOU/IMG_4088.jpg Gallery https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/1737744900547-O7OXHZ0EQY7ZUPIZ0XLO/ee32fd7d-fda4-42bb-9ca3-0ca87c476062.JPG Gallery https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/1769811696374-7F6GW2856SMOCOXNNENJ/IMG_5954.jpeg Gallery https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/1769811764618-6WMUQJ8R2S9X3KERY11A/IMG_0456.jpg Gallery https://yesselmanlab.com/work-jasper daily 0.75 2025-05-12 https://yesselmanlab.com/test daily 1.0 2020-01-10 https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/1537927859033-G9ZDMDBYOO0O0R5MDLQC/extended_banner.png Home https://yesselmanlab.com/pagecv daily 0.75 2019-08-21 https://yesselmanlab.com/publications daily 0.75 2025-08-01 https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/1566246451705-XI00MMTY59I1LQ0R5R6J/ribosolve_figure.png Publications - Ribosolve is a computational / experimental pipeline to determine RNA-only structures. Functional insights from Ribosolve models. (A) Overlay of V. cholerae and F. nucleatum glycine riboswitches with glycine. (B) Overlay of both glycine aptamers from the F. nucleatum and V. cholerae structures. (C-D) Structural homology between the SAM-IV riboswitch and SAM-I and SAM-I/IV riboswitches. (C) The SAM-I crystal structure (37), the SAM-I/IV crystal structure (36), and the SAM-IV Ribosolve model, and (D) an overlay of all three structures, with peripheral elements shown as gray transparent cartoons. SAM is shown as transparent red spheres. (E) The computationally designed eterna3D-JR_1 structure (gray) overlaid with the Ribosolve model (purple). (E-G) Comparisons of Ribosolve structures and the computationally designed models for (E) Eterna3D-JR_1, (F) ATP-TTR-3 with and without AMP, and (G) Spinach-TTR-3. https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/1535412618301-ZLOWNJ37SLVXSCUUD0QA/RNAMake_dg_screenshot_2.png Publications - RNAMake-ΔΔG accounts for changes in tertiary RNA assembly affinity in a blind prediction challenge. Scatterplot compares the dependence of the observed changes in ΔΔG (compared to the median) on the RNAMake-ΔΔG model for 1536 chip piece variants (R = 0.84). Red dashed line indicates the best-fit line (slope = 0.54); cyan dotted line indicates the line of slope 1. https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/1535399352516-ZZQTQMN0731NDC3GSXJL/figure_1_v2+copy.png Publications - Problems in RNA nanotechnology solved by RNAMake (a) ‘miniTTRs’ require two strands (green, purple between tetraloop (orange) and tetraloop-receptor (blue); (b) tethered ribosomes require two strands (green, purple) to link the small subunit (orange) to the large subunit (blue). c) ‘Locking’ a small-molecule binding aptamer (cyan; ATP molecule in pink spheres) by designing four strands (green, purple, teal, magenta) to a peripheral tertiary contact(orange, blue). d) Demonstration of RNAMake design algorithm, which builds an RNA path via the successive addition of motifs and helices from a starting base pair to the ending base pair. https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/1535398190134-4EFHTNU021Q1C7ZFT4XS/cell_paper_screenshot.png Publications - High throughput measurements of RNA tertiary structure energetics Characterizing the thermodynamic fingerprints of >1,000 RNA junctions reveals principles for how RNA sequence affects tertiary assembly energetics, highlighting a path toward tertiary folding prediction by integrating static structural and dynamic energetic information. https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/1535397704389-ZC0DGD4WV9FBUDQXMW64/RMDB_screenshoot.png Publications - RMDB simplifies chemical mapping data distribution Screenshot of the new interactive user interface for viewing RMDB entries: An example of an entry. https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/1535393335975-ULE8M3GG3FDYSK2CHKEB/Fig4_FourRNAs_UpdatedForSecondProofs_WEBSITETHUMB.png Publications - M2-seq recovers helices across diverse RNA folds M2-seq recovers the secondary structure of the P4–P6 domain of Tetrahymena ribozyme. Depicts the crystallographic secondary structure and M2-seq data (square graphs) with colored labels (on both display items) marking helices and multihelix domains automatically identified by M2-net analysis (A neural network). https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/1503617531064-6AB4QLF8KUVFSDEMUIZX/F6.medium.gif Publications - Structural comparison between medaka and human telemerase pseudoknot Comparison of minimal mdPK and hPK (PDB ID code 2K95) structures. Secondary structure elements are P2b (red), P3 (blue), J2a/3 (green), and J2b/3 (gold). https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/1503523673784-FQRDFGU04VX30J6J38SN/F5.medium.gif Publications - Model of active state transition in Tetrahymena ribozyme Models for active site interactions within (E•S•G)O and (E•S•G)C.. The black arrows highlight changes in the positions of active site residues in going from (E•S•G)C to (E•S•G)O. https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/1503523352903-YCST4VEXU7FC1IHG0WXD/screenshot.png Publications - FARFAR RNA 3D prediction accuracy A) GCAA tetraloop (1ZIH), RNA Denovo lowest energy models displays a high level of convergence. B) Pseudoknot (1L2X), less converged then tetraloop but also larger, still within 3Å heavy-atom rmsd for top model. C) 4x4 internal loop solved by NMR at PDB ID 2L8F, converges despite presenting 4 non-canonical base pairs. https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/1503522845850-9GJGXQ46ML7JDY26CRCA/gkv465fig1.png Publications - Accessing accurate RNA 3D Rosetta modeling RP domain IV RNA (PDB ID: 1LNT) contains highly conserved AC base pairs that RNA-Redesign mutates to stabilize the RNA https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/1502763387331-W6S2J49PSJH35HZFQ307/gkv538fig1.png Publications - Schematic and runtime of the primerize algorithm Schematic of the Primerize algorithm. Tm (STEP 1) and misprime matrices (STEP 2) are pre-calculated for the dynamic programming assembly. https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/1502762922391-0TI18BDVVP9950HSBUEL/image-asset.png Publications - Survey of C---OH hydrogen bonds in proteins Depiction of angles and distances measured. B: Methyl hydrogen donor to acceptor distances in which the acceptor is oxygen (solid line) or carbon (dashed line). Dashed-dot line is the difference of the latter curves. C: Elevation angles of methyl CH···O hydrogen bonds. D: Methyl CH···X angles in which X is oxygen (solid line) or carbon (dashed line). https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/1502761751111-VO61D5IP91G13PT9P22X/image-asset.jpeg Publications - Six classes of adomet-dependent methyltransferases The hydrogen-bond donor and methyl C···O interaction distances are labeled in each enzyme. https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/1502761256162-EARVBNTYSLCK3W0K7GHJ/image-asset.jpeg Publications - Chemical classes requiring additional refinement Average unsigned errors of hydration free energies for specific chemical classes for (top panel) CGENFF molecules and (bottom panel) non-CGENFF compounds. https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/1502749087094-XOC4ICU3JR1G197HTFVE/image-asset.jpeg Publications - Quality of the minimized MATCH-typed molecules PubChem drug-like molecules that were successfully processed using the CGENFF libraries within MATCH to generate their respective topology and parameter files. RMSD was computed by comparing conformations found in the PubChem database to the ones after minimization. https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/1502748495565-5Y5Q5QVX43JDHDVSZD4E/titrating_residues_.png Publications - Locations of ionizable residues in Δ+PHS Δ+PHS staphylococcal nuclease is shown here with all ionizing residues highlighted. Glutamic acid is cyan, and aspartic acid is orange https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/1503616448089-YC6775EHRUL97PK7R5YD/F2.large.jpg Publications - Optimized active site with bound adomet Truncated AdoMet and the protein are depicted with green and gray carbon atoms, respectively. Residues labeled in red designate CH O acceptors. H O distances from methyl protons to nearest oxygen atom for optimized and broken geometry are shown in magenta and cyan, respectively. https://yesselmanlab.com/contact daily 0.75 2019-08-19 https://yesselmanlab.com/research daily 0.75 2019-08-21 https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/1535736288467-SQTAEOC1JSR6R1XVXHKH/image-asset.png Research Figure 1: a-c) Examples of RNAMake building new RNA segments. a) A simple nanostructure b) A tether between ribosome subunits c) A scaffold to 'lock' an RNA small-molecule binding motif. d) An example build-up of a RNAMake design. https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/1566255114495-G0V9MOBR3U23DA190OMD/stablization_figure.jpg Research Figure 2: a) 'locking' RNA aptamers to improve sensitivity b) RNAMake-stabilized aptamers are more over 10x more sensitive to ATP then aptamer alone. c-d) RNAMake-stabilized spinach aptamers are brighter then original spinach aptamer. e) Improved aptamers survive over 10x longer in cell lysate then control. f) comparison between the RNAMake model of stabilized aptamer (left) and the solved structure via cryo-EM (right), both structures are within the cryo-EM determined density in gray. https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/1566257810579-HQMVQZUY6SR7G652ZFK1/tecto_figure.png Research Figure 3: A) tectoRNA model system. B) tectoRNA formation is measured via fluorescence C) Computational model of tectoRNA formation, each series of base-pairs is modeled as an ensemble of states. D) TectoRNA formation is predicted by running 1 million Monte Carlo steps, tallying how often the complex is ‘bound’. E) Results of blind predictions of our model (RNAMake-ΔΔG), demonstrating high accuracy. https://yesselmanlab.com/preprint daily 0.75 2017-09-29 https://yesselmanlab.com/people daily 0.75 2026-01-30 https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/ec1f3dcb-7656-4c86-8bcf-541306bb5828/220215_Yesselman_011%5B89%5D+copy.png People - Joe Yesselman Principal Investigator jyesselm@unl.edu Curriculum Vitae https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/ef4d467b-27f4-4e29-bed1-7acef46b4249/IMG_2658.jpg People - Gage Kircher Lab Manager bkircherii2@unl.edu https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/8258546e-69ad-4d07-800b-e79b15eeb475/20210315_104719.jpg People - Sanduni Deenalattha Graduate Student sdeenalattha2@huskers.unl.edu Sanduni is from Sri Lanka. Her research focuses on characterizing 3D RNA structural features using chemical probing methods. Outside the lab, she enjoys cooking, experimenting with different cuisines, and watching TV shows. A fun fact about Sanduni is that she knows almost every restaurant in Lincoln, making her a go-to guide for food recommendations. https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/e2508dfb-74d9-4d3b-8f8d-933166ed47ce/IMG_0556.png People - Sakshi Jain Graduate Student sjain5@huskers.unl.edu Sakshi was born and raised in Delhi, India. She studies the thermodynamics and stability of RNA kissing loops using chemical probing. When she’s not in the lab, she enjoys a bit of doom-scrolling on shopping websites. Fun fact: she can do both a headstand and a handstand. https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/61245aa6-ea4b-4bbe-8095-d7728df5b7a7/erikprofessional.jpg People - Erik Whiting Graduate Student ewhiting4@huskers.unl.edu https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/d2f2bafe-fdb5-4eef-a86d-a83e3a4a4c83/IMG_2357.jpg People - Alabi Oladeji John Graduate Student oalabi2@huskers.unl.edu https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/c0faf8dc-baaa-43f7-a590-5def6fd66d17/WhatsApp+Image+2024-01-14+at+7.58.55+PM.jpeg People - Danushi Pathirage Graduate Student dpathirage2@huskers.unl.edu https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/d9e08231-38c8-4246-829c-0dc107014b18/IMG_9580.jpg People - Nusfa Mohamed Lafir Graduate Student fmohamedlafir2@huskers.unl.edu https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/33073bb4-77d4-45bd-8a1a-a8d87abe4d51/IMG_7128.jpg People - Kamshinen Dewan Graduate Student kdewan2@huskers.unl.edu https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/49ecb0e4-7d3d-4c83-bbfb-20cde28af642/IMG_9676+copy.png People - Beau Stearns Undergraduate Student jstearns4@huskers.unl.edu https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/c4ca36fa-028f-434f-8a4c-62d59042863d/_DSC0080.jpg People - Elliott Conway Undergraduate Student econway2@huskers.unl.edu https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/372f264f-81ae-4b88-9c3a-525f907a3933/Headshot3.jpg People - Daniel Linford https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/4643734c-b250-42ce-89c3-31263f56f34e/image.png People - David Deibert https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/2318e3bf-d83b-470b-a9bc-1bfdbf593220/Screen+Shot+2023-04-02+at+1.36.51+PM.png People - Chris Jurich https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/6392d0f7-697f-40ee-98da-61346acd2a1f/Darren.jpeg People - Darren Armstrong https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/552d23b5-87aa-41fa-b0ec-96a3e75c2870/IMG_3874.png People - Bret Lange https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/f3a1ad4a-c8de-4c86-86e2-d13d702dd193/IMG_3083.JPG People - Gavin Anderson https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/cabf39a1-1525-4747-b1b8-bfa513165379/IMG_1690.jpeg People - Sarah Brady https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/79ba454c-4a50-4f25-becc-9137872b8d0d/Image.jpeg People - Skylar Mosby https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/7bfcdd8f-ba4f-41c4-b9d2-e7480d0e01d1/Screenshot_20221110-160000_Gallery.jpg People - Ricardo Gato Gil https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/ee2c75ad-be43-486b-8f14-779a91bcb249/2022-11-08+11_55_07.226-0600.jpg People - Jasur Iskandarov https://images.squarespace-cdn.com/content/v1/598baa9c15d5db7e604bd32f/a2c45f5e-6db9-4eb0-9566-9483d7256918/image+%281%29.png People - Cristian Gonzalez