20) McCormack, J.C., Yuan, X., Yingling, Y.G., Kasprzak, W., Zamora, R.E., Shapiro, B.A., and Simon, A.E.:
Structural Domains Within the 3' UTR of Turnip Crinkle Virus.
Journal of Virology, 2008 (In press).

19} Book chapter:
Severcan, I., Geary, C., Jaeger, L., Bindewald, E., Kasprzak, W., and Shapiro, B.A.:
Computational and Experimantal RNA Nanoparticle Design.
In "Automation in Genomics and Proteomics: An Engineering Case-Based Approach,"
edited by Alterouth, G., Ramoni, M., and Benson, R. Wiley Publishing, 2008 (Submitted).

18) Bindewald, E., Hayes, R., Yingling, Y.G., Kasprzak, W., Shapiro, B.A.:
RNA Junction: A database of RNA Junctions and Kissing Loops for Three-dimensional Structural Analysis and Nanodesign.
Nucleic Acids Research, 36(Database Issue):D392-D397, 2008.

17) Book chapter:
Shapiro, B.A., Bindewald, E., Kasprzak, W., Yingling, Y.G.:
Protocols for the In Silico Design of RNA Nanostructures.
In "Protocols in Nanostructure Design,"
edited by Gazit, E. and Nussinov, R. Totowa, New Jersey, Humana Press Inc., 2007.

16) Shapiro, B.A., Yingling, Y.G., Kasprzak, W., and Bindewald, E.:
Bridging the Gap in RNA Structure Prediction.
Current Opinion in Structural Biology, 17:157-165, 2007.

15) Linstaedt, S.D., Kasprzak, W., Shapiro, B.A., and Casey, J.L.:
The Role of Metastable RNA Secondary Structure in Hepatitis Delta Virus Genotype III RNA Editing.
RNA, 12(8): 1521-1533, 2006.

14) Shapiro, B.A., Kasprzak, W., Grunewald, C., and Aman, J.:
Graphical Exploratory Data Analysis of RNA Secondary Structure Dynamics Predicted by the Massively Parallel Genetic Algorithm.
Journal of Molecular Graphics and Modeling, 25(4): 514-531, 2006.

13) Seko, Y., Cole, S., Kaul, S., Kasprzak, W., Shapiro, B.A., and Ragheb, J.A.:
The Role of Cytokine mRNA Stability in the Pathogenesis of Autoimmune Disease.
Autoimmun. Rev. 5(5): 299-305, 2006.

12) Gee, A.H., Kasprzak, W.,and Shapiro, B.A.:
Structural Differentiation of the HIV-1 Poly(A) Signals.
Journal of Biomolecular Structure and Dynamics, 23:417-428, 2005.

11) Kasprzak, W., Bindewald, E.,and Shapiro, B.A.:
Structural Polymorphism of the HIV-1 Leader Region Explored by Computational Methods.
Nucleic Acids Research, 33:7151-7163, 2005.

10) Book chapter:
Shapiro, B.A., Bengali D., Kasprzak W., and Wu, J-C.:
Exploring RNA Intermediate Conformations with the Massively Parallel Genetic Algorithm.
In "Computational Biology and Genome Informatics,"
edited by Jason T.L. Wang, Cathy H. Wu, and Paul P. Wang,
New Jersey, World Scientific Publishing Co., 2003, pp. 1-33.

9) Kasprzak, W. and Shapiro, B.A.:
Structural Dependencies of the HIV-1 Dimer Initiation Site as Determined by the Massively Parallel Genetic Algorithm.
The Proceedings of the International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences - METMBS '02, June 2002, Vol. 1, pp. 48-54.

8) Atha, D.H., Kasprzak, W., O'Connell, C.D., and Shapiro, B.A.:
Prediction of DNA single strand conformational polymorphism (SSCP): Analysis by capillary electrophoresis and computerized DNA Modeling.
Nucleic Acids Research, 29(22):4643-4653, 2001.

7) Shapiro, B.A., Bengali, D., Kasprzak, W., and Wu, J-C.:
RNA folding pathway functional intermediates: Their prediction and Analysis.
Journal of Molecular Biology, 312:27-44, 2001.

6) Shapiro, B.A., Bengali, D., Kasprzak, W., and Wu, J-C.:
Computational Insights into RNA folding pathways: Getting from here to there.
The Proceedings of the Atlantic Synposium on Computational Biology, Genome Information Systems and Technology, March 15-17, 2001, pp. 10-13.

5) Book chapter:
Shapiro, B.A., Kasprzak, W., Wu, J-C., and Currey, K.:
RNA Structure-analysis: A Multifaceted Approach.
In "Pattern Discovery in Biomolecular Data,"
edited by Wang J.T.L., Shapiro B.A., and Shasha D.,
Oxford University Press, 1999, pp. 183-215.

4) Kasprzak, W. and Shapiro, B.A.:
Stem Trace: an interactive visual tool for comparative RNA structure analysis,
Bioinformatics, 15(1):16-31, 1999.

3) Shapiro, B.A., and Kasprzak, W.:
STRUCTURELAB: A heterogeneous bioinformatics system for RNA structure analysis,
Journal of Molecular Graphics, 14:194-205, 1996.

2) Shapiro, B.A., Chen, J-H., Busse, T., Navetta, J., Kasprzak, W., and Maizel, J.V.: Optimization and performance analysis of a massively parallel dynamic programming algorithm for RNA secondary structure prediction, The International Journal of Supercomputer Applications, 9(1):29-39, 1995.

1) Shapiro, B.A., and Kasprzak, W.:
Structurelab: A heterogeneous computer system for the analysis of RNA structures ,
In Proceedings of the Association of Lisp Users Meeting and Workshop, Boston, MA. August, 1995.
(Software implementation paper presented at the conference.)