HiCOMB 2003 Online Proceedings

Second IEEE International Workshop on High Performance Computational Biology

Nice, France, April 22, 2003

• Introductory Remarks
  S. Aluru and D.A. Bader
• Sequence Alignment on the Cray MTA-2
  Shahid H. Bokhari and Jon R. Sauer
• Using Hybrid Alignment for Iterative Sequence Database Searches
  Yuheng Li, Mario Lauria, and Ralf Bundschuh
• A Fast Algorithm for the Exhaustive Analysis of 12-Nucleotide-Long DNA Sequences: Applications to Human Genomics
  Vicente Arnau and Ignacio Marín
• Realtime Primer Design for DNA chips
  Harald Simmler, H. Singpiel, and R. Männer
• Accurate method for fast design of diagnostic oligonucleotide probe sets for DNA microarrays
  Andreas Krause, Markus Kräutner, and Harald Meier
• Gene Clustering using Self-Organizing Maps and Particle Swarm Optimization
  X. Xiao, E. Dow, R. Eberhart, Z. Ben Miled, and R. J. Oppelt
• Protein Structure Prediction by Applying an Evolutionary Algorithm
  Richard O. Day, Gary B. Lamont, and Ruth Pachter
• PROSIDIS: a Special Purpose Processor for PROtein SImilarity DIScovery
  A. Marongiu, P. Palazzari, and V. Rosato
• Parallelisation of IBD computation for determining genetic disease map
  Nouhad J. Rizk
• Parallel Detection of Regulatory Elements with gMP
  Bertil Schmidt, Lin Feng, Amey Laud, and Yusdi Santoso
• Solving the Protein Threading Problem in Parallel
  Nicola Yanev and Rumen Andonov
• Phylogenetic Tree Inference on PC Architectures with AxML/PAxML
  Alexandros P. Stamatakis and Thomas Ludwig

HiCOMB 2002 Online Proceedings

First IEEE International Workshop on High Performance Computational Biology

Fort Lauderdale, FL, April 15, 2002

• Introductory Remarks
  S. Aluru and D.A. Bader
• 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.
• Improving Performance of Multiple Sequence Alignment Analysis in Multi-client Environments
  U. Catalyurek, R. Ferreira, T. Kurc, J. Saltz, Ohio State University
• TCS: Estimating Gene Genealogies
  M. Clement, Q. Snell, P. Walker, D. Posada and K.A. Crandall, Brigham Young University
• 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
• Parallel EST Clustering
  A. Kalyanaraman, S. Aluru, and S. Kothari, Iowa State University
• 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
  
• Massively Parallel Solutions for Molecular Sequence Analysis
  B. Schmidt and H. Schorder, Nanyang Technological University
  M. Schimmler, Institut fur Datenverarbeitungsanlagen
• 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
• Aligning Two Fragmented Sequences
  V. Veeramachaneni, P. Berman, W. Miller, Pennsylvania State University
• Quasiperiodic Biosequences and Modulo Incidence Matrices
  H. Wan, National Center for Biotechnology Information
  E. Song, University of California at San Francisco