Alexander John Ropelewski Coordinator, Biomedical Code Development National Resource for Biomedical Supercomputing Pittsburgh Supercomputing Center 4400 Fifth Avenue Pittsburgh PA 15213 412-268-4960

Teaching Projects

• Developing Bioinformatics Programs and Academic Courses: A special technology transfer program aimed at MARC institutions
• Developing Bioinformatics Programs 2008 Summer Institute Lecture Notes

Publications

• Ropelewski, A.J., Nicholas, H.B. Jr, Deerfield, D.W. II, 2004. Mathematically Complete Nucleotide and Protein Sequence Searching Using Ssearch, in Current Protocols in Bioinformatics, Volume I, Baxevanis, A., and Davison, D. ed., pp 3.10.1 - 3.10.13

• Nicholas, H.B. Jr., Deerfield, D.W. II, Ropelewski, A.J. 2003. Strategies for Searching Sequence Databases in "Biocomputing: Computer Tools for Biologists", Eaton Publishing, ed. S.M.Brown., pp 209-231.

• Nicholas, H.B., Ropelewski, A.J., Deerfield II, D.W. (2002) Strategies for Multiple Sequence Alignment. Biotechniques 32, 572-591.

• Ropelewski,A.J., Nicholas, H.B., Deerfield, II, D.W. (2000). Selective and Sensitive Comparison of Genetic Sequence Data. in Industrial Strength Parallel Computing, Konges, A. ed. Morgan Kauffmann, San Francisco CA. 453-479.

• Nicholas, H.B. Jr., Deerfield, D.W. II, Ropelewski, A.J. 2000. Strategies for Searching Sequence Databases Biotechniques 28:2-14.

• Ropelewski, A.J., Nicholas, H.B., Deerfield, D.W., "Implementation of Genetic Sequence Alignment Programs on Supercomputers", Journal of Supercomputing

• Wimberly, F.C., Lambert, M.H., Nystrom, N.A., Ropelewski, A.J., and Young,W.S., "Porting Third-Party Applications Packages to the Cray T3D: Programming Issues and Scalability Results," Parallel Computing, Volume 22, 1073-1089, 1996

• Patrick, T.B., Springer, G.K., Nicholas, H.B., and Ropelewski, A.J. "Information Retrieval Maps for Biomedical Research" MEDINFO 8 Pt 2, R.A. Greens ed., 1443-1446, 1995

• Springer, G.K., Patrick, T.B., Davison, S.E., Nicholas, H.B., and Ropelewski, A.J "Use of a Knowledge Representation to Share Expertise in Molecular Sequence Analysis" Proceedings 2nd International Symposium on Knowledge Aquisition, Representation and Processing, Sponsored by ACM and IEEE, Auburn University, Auburn, Alabama, September 27-30 1995,

• H.B. Nicholas Jr., A.J. Ropelewski, D.W. Deerfield II and J.G. Behrmann A Metric Measure for Comparing Sequence Alignments in Methods in Protein Sequence Analysis, Plenum Press,NY, eds. M.Z. Atassi, E. Appella, 515-525, 1995.

• Nicholas, Jr., H.B., Hempel, J.D., Hinich. A., Deerfield II, D.W., Behrmann, J., and Ropelewski, A.J. Quantitative evaluation of different multiple alignment programs. J. Prot. Chem, vol. 113, pp. 535 (1994).

• Giras, G. , V. Hartonas-Garmhausen, M. Kopko, C. Maher, A. Ropelewski, and Nicholas, H. Distributing the Dynamic Programming Algorithm Across Heterogeneous Supercomputers, Supercomputing 1991 Proceedings 139-146.

• Smith, P.R., Ropelewski, A.J., Balog, D.A., Gottesman, Deerfield II, D.W., A Simple Approach for the Distribution of Computationally Intense Tasks in an Heterogeneous Environment: Distribution of the MDPP Image Processing Package. (1991) CABIOS,7:501-507.