Our Science – Shapiro Website

Bruce A. Shapiro, Ph.D.

Selected Publications

1) Wang J, Zuo X, Yu P, Xu H, Starich MR, Tiede DM, Shapiro BA, Schwieters CD, Wang Y.
A method for helical RNA global structure determination in solution using small-angle x-ray scattering and NMR measurements.
J. Mol. Biol. 393(3): 717-34, 2009. [Journal]

2) Shiao YH, Lupascu ST, Gu YD, Kasprzak W, Hwang CJ, Fields JR, Leighty RM, Quiñones O, Shapiro BA, Alvord WG, Anderson LM.
An Intergenic Non-Coding rRNA Correlated with Expression of the rRNA and Frequency of an rRNA Single Nucleotide Polymorphism in Lung Cancer Cells.
PLoS ONE. 4: e7505, 2009. [Journal]

3) Paliy M, Melnik R, Shapiro BA.
Molecular dynamics study of the RNA ring nanostructure: a phenomenon of self-stabilization.
Physical biology. 6(4): 46003, 2009. [Journal]

4) Paliy M, Melnik R, Shapiro BA.
A mesoscopic model for molecular dynamics studies of RNA nanostructures (8th International Conference on Computational Systems Bioinformatics).
Volume . In Press. [Meeting Proceeding]

5) Spirollari J, Wang J, Zhang K, Bellofatto V, Park Y, Shapiro BA.
Predicting consensus structures for RNA alignments via pseudo-energy minimization.
Bioinformatics and Biology Insights. 3: 51-69, 2009. [Journal]

6) Severcan I, Geary C, Jaeger L, Bindewald E, Kasprzak W, Shapiro B. Alterovitz G, Ramoni M, Benson R, eds.
Computational and Experimental RNA Nanoparticle Design. In: Automation in Genomics and Proteomics: An Engineering Case-Based Approach. Volume .
Hoboken: Wiley Publishing; 2009. p. 193-220 [Book Chapter]

7) de Sousa Abreu R, Sanchez-Diaz PC, Vogel C, Burns SC, Ko D, Burton TL, Vo DT, Chennasamudaram S, Le SY, Shapiro BA, Penalva LO.
Genomic analyses of musashi1 downstream targets show a strong association with cancer-related processes.
J. Biol. Chem. 284: 12125-35, 2009. [Journal]

8) Santhanam AN, Bindewald E, Rajasekhar VK, Larsson O, Sonenberg N, Colburn NH, Shapiro BA.
Role of 3'UTRs in the translation of mRNAs regulated by oncogenic eIF4E--a computational inference.
PLoS ONE. 4(3): e4868, 2009. [Journal]

9) Linnstaedt SD, Kasprzak WK, Shapiro BA, Casey JL.
The fraction of RNA that folds into the correct branched secondary structure determines hepatitis delta virus type 3 RNA editing levels.
RNA. 15: 1177-87, 2009. [Journal]

10) Shapiro B, Bindewald E, Kasprzak W, Yingling Y. Gazit E, Nussinov R, eds.
Protocols for the In silico Design of RNA Nanostructures. In: Nanostructure Design Methods and Protocols. Volume .
Totowa, NJ: Humana Press; 2008. p. 93-115 [Book Chapter]

Click Here to View Expanded Bibliography.

This page was last updated on 11/3/2009.