2) 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.

3) 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

4) 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.

5) 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.

6) 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.

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

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

9) 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.

10) 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. (Technical paper presented at the conference.)