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  1. 1.   Modeling ligand docking to RNA in the design of RNA-based nanostructures
  2. Kasprzak,Wojciech; Ahmed, Nour Ali; Shapiro,Bruce
  3. Current opinion in biotechnology. 2020, JUN; 63: 16-25.
  1. 2.   Folding behavior of a T-shaped, ribosome-binding translation enhancer implicated in a wide-spread conformational switch
  2. Le, My-Tra; Kasprzak, Wojciech; Kim, Taejin; Gao, Feng; Young, Megan Y. L.; Yuan, Xuefeng; Shapiro, Bruce; Seog, Joonil; Simon, Anne E.
  3. ELIFE. 2017, Feb 13; 6: e22883.
  1. 3.   Growth rate regulation in Escherichia coli
  2. Jin, D. J.; Cagliero, C.; Zhou, Y. N.
  3. FEMS Microbiology Reviews. 2012, Mar; 36(2): 269-287.
  1. 4.   Novel Substrate-Based Inhibitors of Human Glutamate Carboxypeptidase II with Enhanced Lipophilicity
  2. Plechanovova, A.; Byun, Y.; Alquicer, G.; Skultetyova, L.; Mlcochova, P.; Nemcova, A.; Kim, H. J.; Navratil, M.; Mease, R.; Lubkowski, J.; Pomper, M.; Konvalinka, J.; Rulisek, L.; Barinka, C.
  3. Journal of Medicinal Chemistry. 2011, Nov; 54(21): 7535-7546.
  1. 5.   A One-Step Miniprep for the Isolation of Plasmid DNA and Lambda Phage Particles
  2. Lezin, G.; Kosaka, Y.; Yost, H. J.; Kuehn, M. R.; Brunelli, L.
  3. Plos One. 2011, Aug; 6(8):
  1. 6.   The Role of Response Elements Organization in Transcription Factor Selectivity: The IFN-beta Enhanceosome Example
  2. Pan, Y. P.; Nussinov, R.
  3. Plos Computational Biology. 2011, Jun; 7(6): 14.
  1. 7.   Solvent-Induced Shifts in Electronic Spectra of Uracil
  2. DeFusco, A.; Ivanic, J.; Schmidt, M. W.; Gordon, M. S.
  3. Journal of Physical Chemistry A. 2011, May; 115(18): 4574-4582.
  1. 8.   A Boost for the Emerging Field of RNA Nanotechnology Report on the First International conference on RNA Nanotechnology
  2. Shukla, G. C.; Hague, F.; Tor, Y.; Wilhelmsson, L. M.; Toulme, J. J.; Isambert, H.; Guo, P. X.; Rossi, J. J.; Tenenbaum, S. A.; Shapiro, B. A.
  3. Acs Nano. 2011, May; 5(5): 3405-3418.
  1. 9.   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. 10.   Initiation complex dynamics direct the transitions between distinct phases of early HIV reverse transcription
  2. Liu, S. X.; Harada, B. T.; Miller, J. T.; Le Grice, S. F. J.; Zhuang, X. W.
  3. Nature Structural & Molecular Biology. 2010, Dec; 17(12): 1453-U83.
  1. 11.   The mechanism responsible for the supraphysiologic gonadotropin surge in females treated with gonadotropin-releasing hormone (GnRH) agonist and primed with GnRH antagonist
  2. Taylor, J. E.; Miller, B. T.; Gray, K. D.; Scott, R. T.; Catherino, W. H.; Segars, J. H.
  3. Fertility and Sterility. 2010, Mar; 93(5): 1668-1675.
  1. 12.   Assembly Properties of Human Immunodeficiency Virus Type 1 Gag-Leucine Zipper Chimeras: Implications for Retrovirus Assembly
  2. Crist, R. M.; Datta, S.; Stephen, A. G.; Soheilian, F.; Mirro, J.; Fisher, R. J.; Nagashima, K.; Rein, A.
  3. Journal of Virology. 2009 83(5): 2216-2225.
  1. 13.   Mechanism of sequence-specific pausing of bacterial RNA polymerase
  2. Kireeva, M. L.; Kashlev, M.
  3. Proceedings of the National Academy of Sciences of the United States of America. 2009 106(22): 8900-8905.
  1. 14.   Conformationally rigid nucleoside probes help understand the role of sugar pucker and nucleobase orientation in the thrombin-binding aptamer
  2. Saneyoshi, H.; Mazzini, S.; Avino, A.; Portella, G.; Gonzalez, C.; Orozco, M.; Marquez, V. E.; Eritja, R.
  3. Nucleic Acids Research. 2009 37(17): 5589-5601.
  1. 15.   Identifying and Characterizing a Functional HIV-1 Reverse Transcriptase-binding Site on Integrase
  2. Wilkinson, T. A.; Januszyk, K.; Phillips, M. L.; Tekeste, S. S.; Zhang, M.; Miller, J. T.; Le Grice, S.; Clubb, R. T.; Chow, S. A.
  3. Journal of Biological Chemistry. 2009 284(12): 7931-7936.
  1. 16.   Computational strategies for the automated design of RNA nanoscale structures from building blocks using NanoTiler
  2. Bindewald, E.; Grunewald, C.; Boyle, B.; O'Connor, M.; Shapiro, B. A.
  3. Journal of Molecular Graphics & Modelling. 2008 27(3): 299-308.
  1. 17.   RNAJunction: a database of RNA junctions and kissing loops for three-dimensional structural analysis and nanodesign
  2. Bindewald, E.; Hayes, R.; Yingling, Y. G.; Kasprzak, W.; Shapiro, B. A.
  3. Nucleic Acids Research. 2008 36: D392-D397.
  1. 18.   Human T-Cell Lymphotropic Virus Type 1 Nucleocapsid Protein-Induced Structural Changes in Transactivation Response DNA Hairpin Measured by Single-Molecule Fluorescence Resonance Energy Transfer
  2. Darugar, Q.; Kim, H.; Gorelick, R. J.; Landes, C.
  3. Journal of Virology. 2008 82(24): 12164-12171.
  1. 19.   Ty3 nucleocapsid controls localization of particle assembly
  2. Larsen, L.; Beliakova-Bethell, N.; Bilanchone, V.; Zhang, M.; Lamsa, A.; DaSilva, R.; Hatfield, G. W.; Nagashima, K.; S, meyer
  3. Journal of Virology. 2008 82(5): 2501-2514.
  1. 20.   Periodicity, planarity, and pixel (3P): A program using the intrinsic residual dipolar coupling periodicity-to-peptide plane correlation and phi/psi angles to derive protein backbone structures
  2. Wang, J.; Walsh, J. D.; Kuszewski, J.; Wang, Y. X.
  3. Journal of Magnetic Resonance. 2007, Nov; 189(1): 90-103.
  1. 21.   Biophysical studies of DNA modified with conformationally constrained nucleotides: comparison of 2 '-exo (north) and 3 '-exo (south) 'locked' templates
  2. Maderia, M.; Shenoy, S.; Van, Q. N.; Marquez, V. E.; Barchi, J. J.
  3. Nucleic Acids Research. 2007, Mar; 35(6): 1978-1991.
  1. 22.   The impact of dyskeratosis congenita mutations on the structure and dynamics of the human telomerase RNA pseudoknot domain
  2. Yingling, Y. G.; Shapiro, B. A.
  3. Journal of Biomolecular Structure & Dynamics. 2007, Feb; 24(4): 303-319.
  1. 23.   Graphical exploratory data analysis of RNA secondary structure dynamics predicted by the massively parallel genetic algorithm
  2. Shapiro, B. A.; Kasprzak, W.; Grunewald, C.; Aman, J.
  3. Journal of Molecular Graphics & Modelling. 2006, Dec; 25(4): 514-531.
  1. 24.   The prediction of the wild-type telomerase RNA pseudoknot structure and the pivotal role of the bulge in its formation
  2. Yingling, Y. G.; Shapiro, B. A.
  3. Journal of Molecular Graphics & Modelling. 2006, Oct; 25(2): 261-274.
  1. 25.   Antisense treatments for biothreat agents
  2. Warfield, K. L.; Panchal, R. G.; Aman, M. J.; Bavari, S.
  3. Current Opinion in Molecular Therapeutics. 2006, Apr; 8(2): 93-103.
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