Ninth IEEE International Workshop on High Performance Computational Biology
Atlanta, GA, April 19, 2010
- Introductory Remarks
George Karypis, Srinivas Aluru, and David A. Bader
- GPU-Accelerated Multi-scoring Functions Protein Loop Structure Sampling
Yaohang Li and Weihang Zhu
- Acceleration of Spiking Neural Networks in Emerging Multi-core and GPU Architectures
Mohammad A. Bhuiyan, Vivek K. Pallipuram and Melissa C. Smith
- A Tile-based Parallel Viterbi Algorithm for Biological Sequence Alignment on GPU with CUDA
Zhihui Du, Zhaoming Yin, and David A. Bader
- Fast Binding Site Mapping using GPU and CUDA
Bharat Sukhwani and Martin Herbordt
- Hybrid MPI/Pthreads Parallelization of the RAxML Phylogenetics Code
Wayne Pfeiffer and Alexandros Stamatakis
- Measuring Properties of Molecular Surfaces Using Ray Casting
Mike Phillips, Iliyan Georgiev, Anna Dehof, Lukas Marsalek, Hans-Peter Lenhof, Andreas Hildebrandt, and Philipp Slusallek
- On the Parallelisation of MCMC-based Image Processing
Jonathan M.R. Byrd, Stephen A. Jarvis, and Abhir H. Bhalerao
- Exploring Parallelism in Short Sequence Mapping Using Burrows-Wheeler Transform
Doruk Bozdag, Ayat Hatem, Umit V. Catalyurek
- pFANGS: Parallel High Speed Sequence Mapping for Next Generation 454-Roche Sequencing Reads
Sanchit Misra, Ramanathan Narayanan, Wei-keng Liao, Alok Choudhary, and Simon Lin
- Efficient and scalable parallel reconstruction of sibling relationships from genetic data in wild- populations
Saad Sheikh, Ashfaq Khokhar, and Tanya Berger-Wolf
Eighth IEEE International Workshop on High Performance Computational Biology
Rome, Italy, May 25, 2009
- Introductory Remarks
Michela Taufer, Srinivas Aluru, and David A. Bader
- De Novo Modeling of GPCR Class A Structures
Charles L. Brooks III
- Parallel Reconstruction of Neighbor-Joining Trees for Large Multiple Sequence Alignments using CUDA
Yongchao Liu, Bertil Schmidt, and Douglas Maskell
- Accelerating Error Correction in High-Throughput Short-Read DNA Sequencing Data with CUDA
Haixiang Shi, Bertil Schmidt, Weiguo Liu, and Wolfgang Mueller-Wittig
- Parallel Monte Carlo Study on Caffeine-DNA Interaction in Aqueous Solution
Michael Kalugin and Alexandr Teplukhin
- Dynamic Parallelization for RNA Structure Comparison
Eric Aubanel, Patricia Evans, and Eric Snow
- HMMer Acceleration Using Systolic Array Based Reconfigurable Architecture
Yanteng Sun, Peng Li, Guochang Gu, Yuan Wen, Yuan Liu, and Dong Liu
- A Resource-Efficient Computing Paradigm for Computational Protein Modeling Applications
Yaohang Li, Dougalas Wardell, and Vincent Freeh
- Exploring FPGAs for Accelerating the Phylogenetic Likelihood Function
Nikolaos Alachiotis, Euripides Sotiriades, Apostolos Dollas, and Alexandros Stamatakis
- Long Time-scale Simulations of in vivo Diffusion using GPU Hardware
Elijah Roberts, John Stone, Leonardo Sepulveda, Wen-Mei Hwu, and Zaida Luthey-Schulten
- An Efficient Implementation Smith Waterman Algorithm on GPU using CUDA, for Massively Parallel Scanning of Sequence Databases
Lukasz Ligowski and Witold Rudnicki
- A Novel Framework for Modeling Ion Channels
May Siksik and Vikram Krishnamurthy
- High-throughput Protein Structure Determination using Grid Computing
Jason W. Schmidberger, Blair Bethwaite, Colin Enticott, Mark A. Bate, Steve G. Androulakis, Noel Faux, Cyril F. Reboul, Jennifer M. N. Phan, James C. Whisstock, Wojtek J. Goscinski, Slavisa Garic, David Abramson, and Ashley M. Buckle
- Folding@home: Lessons From Eight Years of Volunteer Distributed Computing
Adam L. Beberg, Guha Jayachandran, Siraj Khaliq, Vijay S. Pande
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
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
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
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
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
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
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
This material is presented to ensure timely dissemination of scholarly
and technical work. Copyright and all rights therein are retained by
authors or by other copyright holders. All persons copying this
information are expected to adhere to the terms and constraints
invoked by each author's copyright. In most cases, these works may not
be reposted without the explicit permission of the copyright holder.