Bioinformatics & High-Performance Computing Papers

Pairwise Sequence Alignment

• Parallel Computation in Biological Sequence Analysis
  Yap, Frieder, Martino
  
• 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
  
• Massively Parallel Solutions for Molecular Sequence Analysis
  B. Schmidt, H. Schröder, and M. Schimmler
  
• Whole Genome Alignment Using a Multithreaded Parallel Implementation
  W Martins, J del Civillo, W Cui, and G Gao
  

  Multiple Sequence Alignment

• Performance Optimization of Clustal W
  D Mikhailov, H Cofer, R Gomperts
  
• Improving Performance of Multiple Sequence Alignment Analysis in Multi-client Environments
  U. Catalyurek, R. Ferreira, T. Kurc, and J. Saltz
  

  Gene Finding & Prediction

• A Study of GeneWise with the Drosophila Adh Region
  Y Mo, M Regelson, and M Sievers
  
• Parallel EST Clustering
  A. Kalyanaraman, S. Aluru, and S. Kothari, Iowa State University
  

  Phylogenetic Analysis

• High-Performance Algorithm Engineering for Computational Phylogenetics
  B Moret, D Bader, and T Warnow
  

  Protein Folding

• Solving the Protein Threading Problem in Parallel
  Nicola Yanev and Rumen Andonov
  
• Using Metacomputing Tools to Facilitate Large-Scale Analyses of Biological Databases
  A Waugh, G Williams, L Wei, and R Altman
  
• Atomistic Protein Folding Simulations on the Submillisecond Timescale Using Worldwide Distributed Computing
  V Pande et al.
  

  Genetic Networks

• Gene Clustering using Self-Organizing Maps and Particle Swarm Optimization
  X. Xiao, E. Dow, R. Eberhart, Z. Ben Miled, and R. J. Oppelt
  
• Parallel Detection of Regulatory Elements with gMP
  Bertil Schmidt, Lin Feng, Amey Laud, and Yusdi Santoso
  

  Gene Linkage Analysis

• Parallel Genehunter:Implementation of a linkage analysis package for distributed memory architectures
  G. Conant, A. Wagner, S. Plimpton, W. Old, and P. Fain
  
• Parallelisation of IBD computation for determining genetic disease map
  Nouhad J. Rizk
  

  Microarray Design

• 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