Advance Program

Introductory Remarks, S. Aluru and D.A. Bader
8:45 a.m

Session I: Sequence Alignments
9:00 - 10:00

• Aligning Two Fragmented Sequences
  V. Veeramachaneni, P. Berman, W. Miller, Pennsylvania State University
• Improving Performance of Multiple Sequence Alignment Analysis in Multi-client Environments
  U. Catalyurek, R. Ferreira, T. Kurc, J. Saltz, Ohio State University

Break
10:00 - 10:30 

Session II: Gene Identification
10:30 - 12:00

• Parallel Genehunter:Implementation of a linkage analysis package for distributed memory architectures
  G. Conant and A. Wagner, University of New Mexico
  S. Plimpton, Sandia National Laboratories
  W. Old and P. Fain, University of Colorado
• TCS: Estimating Gene Genealogies
  M. Clement, Q. Snell, P. Walker, D. Posada and K.A. Crandall, Brigham Young University
• Parallel EST Clustering
  A. Kalyanaraman, S. Aluru, and S. Kothari, Iowa State University

Lunch Break
12:00 - 1:30 

Session III: Sequence Analysis and Molecular Simulation
1:30 - 3:00 

• Massively Parallel Solutions for Molecular Sequence Analysis
  B. Schmidt and H. Schorder, Nanyang Technological University
  M. Schimmler, Institut fur Datenverarbeitungsanlagen
• Quasiperiodic Biosequences and Modulo Incidence Matrices
  H. Wan, National Center for Biotechnology Information
  E. Song, University of California at San Francisco
• Monte Carlo Simulation of HIV-1 Evolution in Response to Selection by Antibodies
  J. Silva, North Carolina Supercomputing Center
  A. Hughes, University of South Carolina

Break
3:00 - 3:30 

Session IV: Databases and Out-of-Core Algorithms
3:30 - 4:30 

• TurboBLAST: A Parallel Implementation of BLAST Based on the TurboHub Architecture for High Performance Bioinformatics
  R.D. Bjornson, A.H. Sherman, S.B. Weston, N.Willard, and J. Wing, TurboGenomics, Inc.
• Parallel Out-of-core Algorithm for Genome-Scale Enumeration of Metabolic Systematic Pathways
  N.F. Samatova, A. Geist, and G. Ostrouchov, Oak Ridge National Laboratory
  A.V. Melechko, University of Tennessee