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  1. 1.   Structural basis for cell type specific DNA binding of C/EBPß: the case of cell cycle inhibitor p15INK4b promoter
  2. Lountos, George T; Cherry, Scott; Tropea, Joseph E; Wlodawer, Alexander; Miller, Maria
  3. Journal of Structural Biology. 2022, Nov 04; 214(4): 107918.
  1. 2.   Predicting RNA SHAPE scores with deep learning
  2. Bliss, Noah; Bindewald,Eckart; Shapiro,Bruce
  3. RNA biology. 2020, JUN 1; 1-7.
  1. 3.   Targeting the Oncogenic Long Non-coding RNA SLNCR1 by Blocking Its Sequence-Specific Binding to the Androgen Receptor
  2. Schmidt, Karyn; Weidmann, Chase A; Hilimire, Thomas A; Yee, Elaine; Hatfield, Breanne M; Schneekloth,Jay; Weeks, Kevin M; Novina, Carl D
  3. Cell reports. 2020, Jan 14; 30(2): 541-554.e5.
  1. 4.   Structural Fluidity of the Human Immunodeficiency Virus Rev Response Element
  2. Sherpa,Chringma; Le Grice,Stuart
  3. Viruses. 2020, Jan; 12(1):
  1. 5.   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. 6.   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. 7.   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. 8.   Femtomole SHAPE Reveals Regulatory Structures in the Authentic XMRV RNA Genome
  2. Grohman, J. K.; Kottegoda, S.; Gorelick, R. J.; Allbritton, N. L.; Weeks, K. M.
  3. Journal of the American Chemical Society. 2011, Dec; 133(50): 20326-20334.
  1. 9.   Correlating SHAPE signatures with three-dimensional RNA structures
  2. Bindewald, E.; Wendeler, M.; Legiewicz, M.; Bona, M. K.; Wang, Y.; Pritt, M. J.; Le Grice, S. F. J.; Shapiro, B. A.
  3. Rna-a Publication of the Rna Society. 2011, Sep; 17(9): 1688-1696.
  1. 10.   The RNA Transport Element of the Murine musD Retrotransposon Requires Long-range Intramolecular Interactions for Function
  2. Legiewicz, M.; Zolotukhin, A. S.; Pilkington, G. R.; Purzycka, K. J.; Mitchell, M.; Uranishi, H.; Bear, J.; Pavlakis, G. N.; Le Grice, S. F. J.; Felber, B. K.
  3. Journal of Biological Chemistry. 2010, Dec; 285(53): 42097-42104.
  1. 11.   beta-Barrel Topology of Alzheimer's beta-Amyloid Ion Channels
  2. Jang, H.; Arce, F. T.; Ramachandran, S.; Capone, R.; Lal, R.; Nussinov, R.
  3. Journal of Molecular Biology. 2010, Dec; 404(5): 917-934.
  1. 12.   Definition of a high-affinity Gag recognition structure mediating packaging of a retroviral RNA genome
  2. Gherghe, C.; Lombo, T.; Leonard, C. W.; Datta, S. A. K.; Bess, J. W.; Gorelick, R. J.; Rein, A.; Weeks, K. M.
  3. Proceedings of the National Academy of Sciences of the United States of America. 2010, Nov; 107(45): 19248-19253.
  1. 13.   In vitro assembly of cubic RNA-based scaffolds designed in silico
  2. Afonin, K. A.; Bindewald, E.; Yaghoubian, A. J.; Voss, N.; Jacovetty, E.; Shapiro, B. A.; Jaeger, L.
  3. Nature Nanotechnology. 2010, Sep; 5(9): 676-682.
  1. 14.   Secondary Structure of the Mature Ex Virio Moloney Murine Leukemia Virus Genomic RNA Dimerization Domain
  2. Gherghe, C.; Leonard, C. W.; Gorelick, R. J.; Weeks, K. M.
  3. Journal of Virology. 2010, Jan; 84(2): 898-906.
  1. 15.   Architecture and secondary structure of an entire HIV-1 RNA genome
  2. Watts, J. M.; Dang, K. K.; Gorelick, R. J.; Leonard, C. W.; Bess, J. W.; Swanstrom, R.; Burch, C. L.; Weeks, K. M.
  3. Nature. 2009 460(7256): 711-U87.
  1. 16.   Structural Basis of Focal Adhesion Localization of LIM-only Adaptor PINCH by Integrin-linked Kinase
  2. Yang, Y. W.; Wang, X. X.; Hawkins, C. A.; Chen, K.; Vaynberg, J.; Mao, X.; Tu, Y. Z.; Zuo, X. B.; Wang, J. B.; Wang, Y. X.; Wu, C. Y.; Tjandra, N.; Qin, J.
  3. Journal of Biological Chemistry. 2009 284(9): 5836-5844.
  1. 17.   Preparation and preliminary evaluation of a biotin-targeted, lectin-targeted dendrimer-based probe for dual-modality magnetic resonance and fluorescence Imaging
  2. Xu, H.; Regino, C. A. S.; Koyama, Y.; Hama, Y.; Gunn, A. J.; Bernardo, M.; Kobayashi, H.; Choyke, P. L.; Brechbiel, M. W.
  3. Bioconjugate Chemistry. 2007, Sep-Oct; 18(5): 1474-1482.
  1. 18.   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. 19.   Prelamin A and lamin A appear to be dispensable in the nuclear lamina
  2. Fong, L. G.; Ng, J. K.; Lammerding, J.; Vickers, T. A.; Meta, M.; Cote, N.; Gavino, B.; Qiao, X.; Chang, S. Y.; Young, S. R.; Yang, S. H.; Stewart, C. L.; Lee, R. T.; Bennett, C. F.; Bergo, M. O.; Young, S. G.
  3. Journal of Clinical Investigation. 2006, MAR; 116(3): 743-752.
  1. 20.   Structural and dynamical classification of RNA single-base bulges for nanostructure design
  2. Hastings, W. A.; Yingling, Y. G.; Chirikjian, G. S.; Shapiro, B. A.
  3. Journal of Computational and Theoretical Nanoscience. 2006, FEB; 3(1): 63-77.
  1. 21.   Combinatorial docking approach for structure prediction of large proteins and multi-molecular assemblies
  2. Inbar, Y.; Benyamini, H.; Nussinov, R.; Wolfson, H. J.
  3. Physical Biology. 2005, DEC; 2(4, Sp. Iss.): S156-S165.
  1. 22.   Prediction of multimolecular assemblies by multiple docking
  2. Inbar, Y.; Benyamini, H.; Nussinov, R.; Wolfson, H. J.
  3. Journal of Molecular Biology. 2005, JUN 3; 349(2): 435-447.
  1. 23.   Structural basis for the function of stringent starvation protein A as a transcription factor
  2. Hansen, A. M.; Gu, Y. J.; Li, M.; Andrykovitch, M.; Waugh, D. S.; Jin, D. J.; Ji, X. H.
  3. Journal of Biological Chemistry. 2005, APR 29; 280(17): 17380-17391.
  1. 24.   From structure to function: Methods and applications
  2. Wolfson, H. J.; Shatsky, M.; Schneidman-Duhovny, D.; Dror, O.; Shulman-Peleg, A.; Ma, B. Y.; Nussinov, R.
  3. Current Protein & Peptide Science. 2005, APR; 6(2): 171-183.
  1. 25.   Multiple docking for protein structure prediction
  2. Inbar, Y.; Wolfson, H. J.; Nussinov, R.
  3. International Journal of Robotics Research. 2005, FEB-MAR; 24(2-3): 131-150.
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