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Joseph Yesselman - Publications

Affiliations: 
2014 Biophysics University of Michigan, Ann Arbor, Ann Arbor, MI 
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27 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2024 Lange B, Gil RG, Anderson GS, Yesselman JD. High-throughput determination of RNA tertiary contact thermodynamics by quantitative DMS chemical mapping. Nucleic Acids Research. PMID 39082277 DOI: 10.1093/nar/gkae633  0.325
2023 Camara MB, Lange B, Yesselman JD, Eichhorn CD. Visualizing a two-state conformational ensemble in stem-loop 3 of the transcriptional regulator 7SK RNA. Nucleic Acids Research. PMID 38084902 DOI: 10.1093/nar/gkad1159  0.75
2023 Camara MB, Lange B, Yesselman JD, Eichhorn CD. Visualizing a two-state conformational ensemble in stem-loop 3 of the transcriptional regulator 7SK RNA. Biorxiv : the Preprint Server For Biology. PMID 37609139 DOI: 10.1101/2023.08.09.552709  0.75
2023 Jurich CP, Yesselman JD. Automated 3D Design and Evaluation of RNA Nanostructures with RNAMake. Methods in Molecular Biology (Clifton, N.J.). 2586: 251-261. PMID 36705909 DOI: 10.1007/978-1-0716-2768-6_15  0.457
2022 Jurich CP, Brivanlou A, Rouskin S, Yesselman JD. Web-based platform for analysis of RNA folding from high throughput chemical probing data. Nucleic Acids Research. PMID 35657086 DOI: 10.1093/nar/gkac435  0.478
2022 Van Damme R, Li K, Zhang M, Bai J, Lee WH, Yesselman JD, Lu Z, Velema WA. Chemical reversible crosslinking enables measurement of RNA 3D distances and alternative conformations in cells. Nature Communications. 13: 911. PMID 35177610 DOI: 10.1038/s41467-022-28602-3  0.512
2021 Zafferani M, Haddad C, Luo L, Davila-Calderon J, Chiu LY, Mugisha CS, Monaghan AG, Kennedy AA, Yesselman JD, Gifford RJ, Tai AW, Kutluay SB, Li ML, Brewer G, Tolbert BS, et al. Amilorides inhibit SARS-CoV-2 replication in vitro by targeting RNA structures. Science Advances. 7: eabl6096. PMID 34826236 DOI: 10.1126/sciadv.abl6096  0.382
2020 Zafferani M, Haddad C, Luo L, Davila-Calderon J, Yuan-Chiu L, Shema Mugisha C, Monaghan AG, Kennedy AA, Yesselman JD, Gifford RR, Tai AW, Kutluay SB, Li ML, Brewer G, Tolbert BS, et al. Amilorides inhibit SARS-CoV-2 replication in vitro by targeting RNA structures. Biorxiv : the Preprint Server For Biology. PMID 33299997 DOI: 10.1101/2020.12.05.409821  0.446
2020 Shi H, Rangadurai A, Abou Assi H, Roy R, Case DA, Herschlag D, Yesselman JD, Al-Hashimi HM. Rapid and accurate determination of atomistic RNA dynamic ensemble models using NMR and structure prediction. Nature Communications. 11: 5531. PMID 33139729 DOI: 10.1038/s41467-020-19371-y  0.554
2020 Kappel K, Zhang K, Su Z, Watkins AM, Kladwang W, Li S, Pintilie G, Topkar VV, Rangan R, Zheludev IN, Yesselman JD, Chiu W, Das R. Accelerated cryo-EM-guided determination of three-dimensional RNA-only structures. Nature Methods. 17: 699-707. PMID 32616928 DOI: 10.1038/S41592-020-0878-9  0.512
2020 Miao Z, Adamiak RW, Antczak M, Boniecki MJ, Bujnicki JM, Chen SJ, Cheng CY, Cheng Y, Chou FC, Das R, Dokholyan NV, Ding F, Geniesse C, Jiang Y, Joshi A, ... ... Yesselman JD, et al. RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers. Rna (New York, N.Y.). PMID 32371455 DOI: 10.1261/Rna.075341.120  0.577
2019 Yesselman JD, Eiler D, Carlson ED, Gotrik MR, d'Aquino AE, Ooms AN, Kladwang W, Carlson PD, Shi X, Costantino DA, Herschlag D, Lucks JB, Jewett MC, Kieft JS, Das R. Computational design of three-dimensional RNA structure and function. Nature Nanotechnology. PMID 31427748 DOI: 10.1038/S41565-019-0517-8  0.48
2019 Yesselman JD, Denny SK, Bisaria N, Herschlag D, Greenleaf WJ, Das R. Sequence-dependent RNA helix conformational preferences predictably impact tertiary structure formation. Proceedings of the National Academy of Sciences of the United States of America. PMID 31375637 DOI: 10.1073/Pnas.1901530116  0.529
2018 Yesselman JD, Tian S, Liu X, Shi L, Li JB, Das R. Updates to the RNA mapping database (RMDB), version 2. Nucleic Acids Research. 46: D375-D379. PMID 30053264 DOI: 10.1093/Nar/Gkx873  0.426
2018 Denny SK, Bisaria N, Yesselman JD, Das R, Herschlag D, Greenleaf WJ. High-Throughput Investigation of Diverse Junction Elements in RNA Tertiary Folding. Cell. PMID 29961580 DOI: 10.1016/J.Cell.2018.05.038  0.544
2017 Cheng CY, Kladwang W, Yesselman JD, Das R. RNA structure inference through chemical mapping after accidental or intentional mutations. Proceedings of the National Academy of Sciences of the United States of America. PMID 28851837 DOI: 10.1073/Pnas.1619897114  0.4
2016 Yesselman JD, Das R. Modeling Small Noncanonical RNA Motifs with the Rosetta FARFAR Server. Methods in Molecular Biology (Clifton, N.J.). 1490: 187-198. PMID 27665600 DOI: 10.1007/978-1-4939-6433-8_12  0.53
2016 Wang Y, Yesselman JD, Zhang Q, Kang M, Feigon J. Structural conservation in the template/pseudoknot domain of vertebrate telomerase RNA from teleost fish to human. Proceedings of the National Academy of Sciences of the United States of America. PMID 27531956 DOI: 10.1073/Pnas.1607411113  0.447
2016 Denny S, Bisaria N, Yesselman J, Das R, Herschlag D, Greenleaf W. High Throughput Characterization of RNA Tertiary Elements Biophysical Journal. 110: 363a. DOI: 10.1016/J.Bpj.2015.11.1957  0.604
2015 Sengupta RN, van Schie SN, Giambaşu G, Dai Q, Yesselman JD, York D, Piccirilli JA, Herschlag D. An active site rearrangement within the Tetrahymena group I ribozyme releases nonproductive interactions and allows formation of catalytic interactions. Rna (New York, N.Y.). PMID 26567314 DOI: 10.1261/Rna.053710.115  0.353
2015 Tian S, Yesselman JD, Cordero P, Das R. Primerize: automated primer assembly for transcribing non-coding RNA domains. Nucleic Acids Research. 43: W522-6. PMID 25999345 DOI: 10.1093/Nar/Gkv538  0.387
2015 Yesselman JD, Das R. RNA-Redesign: a web server for fixed-backbone 3D design of RNA. Nucleic Acids Research. 43: W498-501. PMID 25964298 DOI: 10.1093/Nar/Gkv465  0.412
2015 Yesselman JD, Horowitz S, Brooks CL, Trievel RC. Frequent side chain methyl carbon-oxygen hydrogen bonding in proteins revealed by computational and stereochemical analysis of neutron structures. Proteins. 83: 403-10. PMID 25401519 DOI: 10.1002/Prot.24724  0.659
2015 Yesselman JD, Horowitz S, Brooks CL, Trievel RC. Frequent side chain methyl carbon-oxygen hydrogen bonding in proteins revealed by computational and stereochemical analysis of neutron structures Proteins: Structure, Function and Bioinformatics. 83: 403-410. DOI: 10.1002/prot.24724  0.65
2013 Horowitz S, Dirk LM, Yesselman JD, Nimtz JS, Adhikari U, Mehl RA, Scheiner S, Houtz RL, Al-Hashimi HM, Trievel RC. Conservation and functional importance of carbon-oxygen hydrogen bonding in AdoMet-dependent methyltransferases. Journal of the American Chemical Society. 135: 15536-48. PMID 24093804 DOI: 10.1021/Ja407140K  0.701
2011 Horowitz S, Yesselman JD, Al-Hashimi HM, Trievel RC. Direct evidence for methyl group coordination by carbon-oxygen hydrogen bonds in the lysine methyltransferase SET7/9. The Journal of Biological Chemistry. 286: 18658-63. PMID 21454678 DOI: 10.1074/Jbc.M111.232876  0.69
2011 Yesselman JD, Al-Hashimi HM, Brooks CL. Exploring RNA Drug Binding Using Consistent Charge Models Biophysical Journal. 100: 159a. DOI: 10.1016/J.Bpj.2010.12.1085  0.634
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