HiCOMB 2008 Online Proceedings

Seventh IEEE International Workshop on High Performance Computational Biology

Miami, FL, April 14, 2008

• Introductory Remarks
  Bertil Schmidt, Srinivas Aluru, and David A. Bader
• Ordered Index Seed Algorithm for Intensive DNA Sequence Comparison
  D. Lavenier
• Parallel, Scalable, Memory-Efficient Backtracking for Combinatorial Modeling of Large-Scale Biological Systems
  B.-H. Park, M. Schmidt, K. Thomas, T. Karpinets, N.F. Samatova
• Parallelized preprocessing algorithms for high-density oligonucleotide array data
  M. Schmidberger, U. Mansmann
• On the Effectiveness of Rebuilding RNA Secondary Structures from Sequence Chunks
  M. Taufer, T. Solorio, A. Licon, D. Mireles, M.-Y. Leung
• A Parallel Architecture for Regulatory Motif Algorithm Assessment
  D. Quest, K. Dempsey, D. Bastola, H. Ali
• Design and Development of a FPGA-based Cascade Markov Model for Recognition of Steroid Hormone Response Elements
  M. Stepanova, F. Lin, V. Lin
• Supporting High Performance Bioinformatics Flat-File Data Processing
  X. Zhang, G. Agrawal
• Sample-Align-D: A High Performance Multiple Sequence Alignment System using Phylogenetic Sampling and Domain Decomposition
  F. Saeed, A. Khokhar
• Adaptive Locality-Effective Kernel Methods for Phosphorylation Site Prediction
  P. Yoo, Y.S. Ho, B.B. Zhou, A. Zomaya
• Impacts of Multicores on Large-scale Molecular Dynamics Simulations
  S. Alam, J. Vetter, P. Agarwal, H. Ong, S. Hampton

HiCOMB 2007 Online Proceedings

Sixth IEEE International Workshop on High Performance Computational Biology

Long Beach, CA, March 26, 2007

• Introductory Remarks
  Ananth Grama, Shankar Subramaniam, Srinivas Aluru, and David A. Bader
• On the path to enable multi-scale biomolecular simulations on Petaflop supercomputer with multi-core processors
  Sadaf Alam, Pratul Agarwal
• Analysis of a Computational Biology Simulation Technique on Emerging Processing Architectures
  Jeremy Meredith, Sadaf Alam, Jeffrey S. Vetter
• A Graph-Theoretic Analysis of the Human Protein-Interaction Network Using Multicore Parallel Algorithms
  David A. Bader, Kamesh Madduri
• Biomolecular Path Sampling Enabled by Processing in Network Storage
  Paul Brenner, Justin Wozniak, Jesus Izaguirre, Aaron Striegel, Douglas Thain, Jeff Peng
• Preliminary results in accelerating profile HMM search on FPGAs
  Arpith Jacob, Joseph Lancaster, Jeremy Buhler, Roger Chamberlain
• High Performance Database Searching with HMMer on FPGAs
  Tim Oliver, Leow Yuan Yeow, Bertil Schmidt
• Exploring the viability of the Cell Broadband Engine for bioinformatics applications
  Vipin Sachdeva, Mike Kistler, Evan Speight, Tzy-Hwa Kathy Tzeng
• Data-Driven Time-Parallelization in the AFM Simulation of Proteins
  Lei Ji, Hugh Nymeyer, Ashok Srinivasan, Yanan Yu
• RNAVLab: A unified environment for computational RNA structure analysis based on grid computing technology
  Michela Taufer, Ming-Ying Leung, Kyle L. Johnson, Abel Licon
• An Automated Data Processing Pipeline for Virus Structure Determination at High Resolution
  Chen Yu, Dan C. Marinescu, John P. Morrison, Brian C. Clayton, David A. Power

HiCOMB 2006 Online Proceedings

Fifth IEEE International Workshop on High Performance Computational Biology

Rhodes Island, Greece, April 25, 2006

• Introductory Remarks
  Chau-Wen Tseng, David A. Bader, and Srinivas Aluru
• Bio-Sequence Database Scanning on a GPU
  Weiguo Liu, Bertil Schmidt, Gerrit Voss, Andre Schroder, Wolfgang Muller-wittig
• Some Initial Results on Hardware BLAST Acceleration with a Reconfigurable Architecture
  Euripides Sotiriades, Christos Kozanitis, Apostolos Dollas
• Phylospaces: Reconstructing Evolutionary Trees in Tuple Space
  Marc L. Smith, Tiffani L. Williams
• Parallel Implementation of a Quartet-Based Algorithm for Phylogenetic Analysis
  B. B. Zhou, D. Chu, M. Tarawneh, P. Wang, C. Wang, A. Y. Zomaya, R. P. Brent
• Phylogenetic Models of Rate Heterogeneity: A High Performance Computing Perspective
  Alexandros Stamatakis
• Parallel Multiple Sequence Alignment with Local Phylogeny Search by Simulated Annealing
  Jaroslaw Zola, Denis Trystram, Andrei Tchernykh, Carlos Brizuela
• MT-ClustalW: Multithreading Multiple Sequence Alignment
  Kridsadakorn Chaichoompu, Surin Kittitornkun, Sissades Tongsima
• Parallel Implementation of the Replica Exchange Molecular Dynamics Algorithm on Blue Gene/L
  M. Eleftheriou, A. Rayshubski, J. W. Pitera, B. G. Fitch, R. Zhou, R. S. Germain
• Application Re-Structuring and Data Management on a GRID Environment: a Case Study for Bioinformatics
  Giovanni Ciriello, Matteo Comin, Concettina Guerra
• A Method to Improve Structural Modeling Based on Conserved Domain Clusters
  Fa Zhang, Lin Xu, Bo Yuan
• An Experimental Study of Optimizing Bioinformatics Applications
  Guangming Tan, Lin Xu, Shengzhong Feng, Ninghui Sun

HiCOMB 2005 Online Proceedings

Fourth IEEE International Workshop on High Performance Computational Biology

Denver, CO, April 4, 2005

• Introductory Remarks
  Nancy Amato, David A. Bader, and Srinivas Aluru
• BioFilter: An architecture for parallel deployment and dynamic chaining of standalone bioinformatics tools
  Thomas Brettin and Avinash Kewalramani
• Comparison of Different Versions of Current BLAST Software on Nucleotide Sequences
  I. Elizabeth Cha and Eric Rouchka
• Statistical Methods for the Discovery of Co-operative Transcription Factors: the Co-bind code revised
  Giovanni Lavorgna, Alessandro Marongiu, Simone Melchionna, Paolo Palazzari, Vittorio Rosato, and Paolo Verrecchia
• A Case Study on Pattern-based Systems for High Performance
  Weiguo Liu and Bertil Schmidt
• High-Performance Direct Pairwise Comparison of Large Genomic Sequences
  Chris Mueller, Mehmet Dalkilic and Andrew Lumsdaine
• RC-BLAST: Towards an Open Source Hardware Implementation
  Krishna Muriki, Keith Underwood and Ron Sass
• FROST: Revisited and Distributed
  Vincent Poirriez, Antoine Marin, Rumen Andonov and Jean-Francois Gibrat
• An Efficient Program for Phylogenetic Inference Using Simulated Annealing
  Alexandros Stamatakis
• Predictor@Home: A "Protein Structure Prediction Supercomputer" Based on Public-Resource Computing
  Michela Taufer and C. An and A. Kerstens and C.L. Brooks III
• ESTmapper: Efficiently Aligning DNA Sequences to Genomes
  Xue Wu, Woei-Jyh (Adam) Lee and Chau-Wen Tseng
• Folding@Home: Advances in biophysics and biomedicine from world-wide grid computing (invited keynote)
  Vijay Pande

HiCOMB 2004 Online Proceedings

Third IEEE International Workshop on High Performance Computational Biology

Santa Fe, NM, April 26, 2004

• Introductory Remarks
  Dan C. Marinescu, David A. Bader, and Srinivas Aluru
• Three-dimensional reconstruction of viruses: challenges and strategies
  Timothy S. Baker
• Study of a Highly Accurate and Fast-Protein Ligand Docking Algorithm Based Upon Molecular Dynamics
  M. Taufer, M. Crowley, D. Price, A.A. Chien, and C. L. Brooks III
• Parallel Protein Folding with STAPL
  S. Thomas and N. Amato
• A Hypergraph Model for the Yeast Protein Complex Network
  E. Ramadan, A. Tarafdar, and A. Pothen
• Dynamic Programming for LR-PCR Segmentation of Bacterium Genomes
  R. Andonov, D. Lavenier, N. Yanev, and P. Veber
• Parallel RNA Sequence-Structure Alignment
  T. Liu and B. Schmidt
• Constrained De Novo Peptide Identification via Multiobjective Optimization
  J. M. Mallard, A. Heredia-Langner, D.J. Baxter, K. H. Jarman, and W. R. Cannon
• Identification of Mycobacteriun Species Using Curated Custom Databases
  D. Kuyper, H. Ali, A. M. Mohamed, and S. H. Hinrichs
• High Performance Computational Tools for Motif Discovery
  N. E. Baldwin, R. L. Collins, M. A. Langston, M. R. Leuze, C. T. Symons, and B. H. Voy
• High Performance Biosequence Database Scanning on Reconfigurable Platforms
  T. Oliver and B. Schmidt
• New Fast and Acurate Heuristics for Inference of Large Phylogenic Trees
  A.P. Stamatakis, T. Ludwig, and H. Meier
• Large-Scale Simulation of Eukaryotic Cell Signaling Processes
  J. H. Miller and F. Zheng
• Particle Swarm Optimization and Neural Network Application for QSAR
  Z. Wang, G. L. Durst, R.C. Eberhart, D.B. Boyd, and Z. B. Miled

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
• Improving Performance of Multiple Sequence Alignment Analysis in Multi-client Environments
  U. Catalyurek, R. Ferreira, T. Kurc, and J. Saltz
• TCS: Estimating Gene Genealogies
  M. Clement, Q. Snell, P. Walker, D. Posada, and K.A. Crandall
• Parallel Genehunter:Implementation of a linkage analysis package for distributed memory architectures
  G. Conant, A. Wagner, S. Plimpton, W. Old, and P. Fain
• 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, G. Ostrouchov, and A.V. Melechko
• Massively Parallel Solutions for Molecular Sequence Analysis
  B. Schmidt, H. Schröder, and M. Schimmler
• Monte Carlo Simulation of HIV-1 Evolution in Response to Selection by Antibodies
  J. Silva and A. Hughes
• Aligning Two Fragmented Sequences
  V. Veeramachaneni, P. Berman, and W. Miller
• Quasiperiodic Biosequences and Modulo Incidence Matrices
  H. Wan and E. Song