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  1. 1.   Translation of HIV-1 unspliced RNA is regulated by 5' untranslated region structure
  2. Cheng,Zetao; Islam,Mohammad Saiful; Kanlong, Joseph G; Sheppard, Madeline; Seo, Heewon; Nikolaitchik,Olga; Kearse, Michael G; Pathak,Vinay; Musier-Forsyth, Karin; Hu,Wei-Shau
  3. Journal of Virology. 2024, Sep 24; e0116024.
  1. 2.   Crystal structure of Escherichia coli thiamine pyrophosphate-sensing riboswitch in the apo state
  2. Lee,Hyun Kyung; Lee,Yun-Tzai; Fan,Lixin; Wilt, Haley M; Conrad, Chelsie E; Yu,Ping; Zhang, Jinwei; Shi,Genbin; Ji,Xinhua; Wang,Yun-Xing; Stagno,Jason
  3. Structure (London, England : 1993). 2023, Jul 7; 31(7): 848-859..
  1. 3.   Structural insights of the conserved "priming loop" of hepatitis B virus pre-genomic RNA
  2. LeBlanc, Regan M; Kasprzak,Wojciech; Longhini, Andrew P; Olenginski, Lukasz T; Abulwerdi, Fardokht; Ginocchio, Stefano; Shields, Brigit; Nyman, Julie; Svirydava, Maryia; Del Vecchio, Claudia; Ivanic,Joseph; Schneekloth,Jay; Shapiro, Bruce A; Dayie, Theodore Kwaku; Le Grice,Stuart
  3. Journal of Biomolecular Structure & Dynamics. 2022, Jun 22; 40(20): 9761-9773.
  1. 4.   Flexible pri-miRNA structures enable tunable production of 5' isomiRs
  2. Bofill De Ros,Xavier; Hong,Zhenyi; Birkenfeld, Ben; Alamo-Ortiz,Sarangelica; Yang,Acong; Dai,Lisheng; Gu,Shuo
  3. RNA Biology. 2022, Jan; 19(1): 279-289.
  1. 5.   Tying the knot in the tetrahydrofolate (THF) riboswitch: A molecular basis for gene regulation
  2. Wilt,Haley; Yu,Ping; Tan, Kemin; Wang, Yun-Xing; Stagno,Jason
  3. Journal of Structural Biology. 2021, Mar; 213(1):
  1. 6.   Using SHAPE-MaP to probe small molecule-RNA interactions
  2. Martin, Sarah; Blankenship, Carson; Rausch,Jason; Sztuba-Solinska, Joanna
  3. Methods (San Diego, Calif.). 2019, SEP 1; 167: 105-116.
  1. 7.   Co-crystal structure of the iMango-III fluorescent RNA aptamer using an X-ray free-electron laser
  2. Trachman, Robert J; Stagno,Jason; Conrad, Chelsie; Jones, Christopher P; Fischer, Pontus; Meents, Alke; Wang, Yun Xing; Ferré-D'Amaré, Adrian R
  3. Acta crystallographica. Section F, Structural biology communications. 2019, Aug 01; 75(Pt 8): 547-551.
  1. 8.   Co-crystal structure of the Fusobacterium ulcerans ZTP riboswitch using an X-ray free-electron laser
  2. Jones, Christopher; Tran, Brandon; Conrad, Chelsie; Stagno,Jason; Trachman, Robert; Fischer, Pontus; Meents, Alke; Ferre-D'Amare, Adrian
  3. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS. 2019, Jul; 75(Part 7): 496-500.
  1. 9.   Structural Differences between Pri-miRNA Paralogs Promote Alternative Drosha Cleavage and Expand Target Repertoires
  2. Bofill De Ros, Xavier; Kasprzak, Wojciech; Bhandari, Yuba; Fan, Lixin; Cavanaugh, Quinn; Jiang, Minjie; Dai, Lisheng; Yang, Acong; Shao, Tie-Juan; Shapiro, Bruce; Wang, Yun-Xing; Gu, Shuo
  3. Cell reports. 2019, Jan 08; 26(2): 447-459.e4.
  1. 10.   The roles of five conserved lentiviral RNA structures in HIV-1 replication
  2. Liu, Yang; Chen, Jianbo; Nikolaitchik, Olga; Desimmie, Belete; Busan, Steven; Pathak, Vinay; Weeks, Kevin M; Hu, Wei-Shau
  3. Virology. 2018, JAN 15; 514: 1-8.
  1. 11.   Probing the Structures of Viral RNA Regulatory Elements with SHAPE and Related Methodologies
  2. Rausch, Jason; Sztuba-Solinska, Joanna; Legrice, Stuart
  3. Frontiers in Microbiology. 2018, Jan 9; 8: 2634.
  1. 12.   The "Topological Train Ride" of a Viral Long Non-Coding RNA
  2. Sztuba-Solinska, Joanna; Legrice, Stuart
  3. RNA Biology. 2018, Jan 02; 15(1): 13-16.
  1. 13.   Understanding the effects of carbocyclic sugars constrained to north and south conformations on RNA nanodesign
  2. Kim, T.; Barchi, J. J.; Marquez, V. E.; Shapiro, B. A.
  3. Journal of Molecular Graphics & Modelling. 2011, Feb; 29(5): 624-634.
  1. 14.   Solution structure of the cap-independent translational enhancer and ribosome-binding element in the 3 ' UTR of turnip crinkle virus
  2. Zuo, X. B.; Wang, J. B.; Yu, P.; Eyler, D.; Xu, H.; Starich, M. R.; Tiede, D. M.; Simon, A. E.; Kasprzak, W.; Schwieters, C. D.; Shapiro, B. A.; Wang, Y. X.
  3. Proceedings of the National Academy of Sciences of the United States of America. 2010, Jan 26; 107(4): 1385-1390.
  1. 15.   A Method for Helical RNA Global Structure Determination in Solution Using Small-Angle X-Ray Scattering and NMR Measurements
  2. Wang, J. B.; Zuo, X. B.; Yu, P.; Xu, H.; Starich, M. R.; Tiede, D. M.; Shapiro, B. A.; Schwieters, C. D.; Wang, Y. X.
  3. Journal of Molecular Biology. 2009 393(3): 717-734.
  1. 16.   Structural domains within the 3 ' untranslated region of Turnip crinkle virus
  2. McCormack, J. C.; Yuan, X. F.; Yingling, Y. G.; Kasprzak, W.; Zamora, R. E.; Shapiro, B. A.; Simon, A. E.
  3. Journal of Virology. 2008 82(17): 8706-8720.
  1. 17.   Structural differentiation of the HIV-1 poly(A) signals
  2. Gee, A. H.; Kasprzak, W.; Shapiro, B. A.
  3. Journal of Biomolecular Structure & Dynamics. 2006, FEB; 23(4): 417-428.
  1. 18.   Intermediate states of ribonuclease III in complex with double-stranded RNA
  2. Gan, J. H.; Tropea, J. E.; Austin, B. P.; Court, D. L.; Waugh, D. S.; Ji, X. H.
  3. Structure. 2005, OCT; 13(10): 1435-1442.
  1. 19.   ARTS: alignment of RNA tertiary structures
  2. Dror, O.; Nussinov, R.; Wolfson, H.
  3. Bioinformatics. 2005, SEP; 21(Suppl. 2): 47-53.
  1. 20.   Noncatalytic assembly of ribonuclease III with double-stranded RNA
  2. Blaszczyk, J.; Gan, J. H.; Tropea, J. E.; Court, D. L.; Waugh, D. S.; Ji, X. H.
  3. Structure. 2004 12(3): 457-466.
  1. 21.   From base-pair to tertiary interactions: G-A linkers in RNA structures
  2. Xin, Y. R.; Lu, X. J.; Olson, W. K.
  3. Biophysical Journal. 2004 86(1, Part 2 Suppl. S): 144A-144A.
  1. 22.   Prediction of DNA single-strand conformation polymorphism: analysis by capillary electrophoresis and computerized DNA modeling
  2. Atha, D. H.; Kasprzak, W.; O'Connell, C. D.; Shapiro, B. A.
  3. Nucleic Acids Research. 2001 29(22): 4643-4653.
  1. 23.   A new algorithm for computing similarity between RNA structures
  2. Collins, G. D.; Le, S. Y.; Zhang, K. Z.
  3. Information Sciences. 2001 139(1-2): 59-77.
  1. 24.   The human endogenous retrovirus K Rev response element coincides with a predicted RNA folding region
  2. Yang, J.; Bogerd, H.; Le, S. Y.; Cullen, B. R.
  3. Rna-a Publication of the Rna Society. 2000 6(11): 1551-1564.
  1. 25.   Phylogenetic evidence for the improved RNA higher-order structure in internal ribosome entry sequences of HCV and pestiviruses
  2. Le, S. Y.; Liu, W. M.; Maizel, J. V.
  3. Virus Genes. 1998 17(3): 279-295.
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