HICOMB 2011, May 16, 2011
ADVANCE PROGRAM
8:25-8:30am Introductory Remarks
Ananth Kalyanaraman, Srinivas Aluru, David Bader
(Session I: Genome-scale Analysis; Session Chair: Michela Taufer)
8:30-9am An ultrafast scalable many-core motif discovery algorithm for
multiple GPUs
Yongchao Liu, Bertil Schmidt, Douglas Maskell
9-9:30am Parallel Mapping Approaches for GNUMAP
Nathan Clement, Mark J. Clement, Quinn Snell, W. Evan
Johnson
9:30-10am Computing the Phylogenetic Likelihood Function Out-of-Core
Fernando Izquierdo-Carrasco, Alexandros Stamatakis
10-10:30am COFFEE BREAK 1
(Session II: Modeling and Structure Prediction; Session Chair: Mark Clement)
10:30-11am Algorithms for a parallel implementation of Hidden Markov
Models with a small
state space
Jesper Nielsen, Andreas Sand
11-11:30am Efficient Nonserial Polyadic Dynamic Programming on the Cell
Processor
Li Liu, Mu Wang, Jinlei Jiang, Ruizhe Li, Guangwen Yang
11:30-12pm FENZI: GPU-enabled Molecular Dynamics Simulations of Large
Membrane Regions based on the CHARMM force field and PME
Narayan Ganesan, Brad Bauer, Sandeep Patel, Michela Taufer
12-1:30pm LUNCH BREAK
1:30-2:30pm Keynote Talk: “High-Performance Computing and Biology:
The Quest for Predictive Biological Theory”
Rick Stevens, ANL/U Chicago
(Session III: Sequence Analysis; Session Chair: TBD)
2:30-3pm Parallelizing BLAST and SOM algorithms with MapReduce-MPI
library
Seung-Jin Sul, Andrey Tovchigrechko
3-3:30pm Improving CUDASW++, a Parallelization of Smith-Waterman for
CUDA Enabled Devices
Doug Hains, Zach Cashero, Mark Ottenberg
3:30-4pm COFFEE BREAK 2
(Session IV: Systems Biology and Functional Genomics; Session Chair: Jaroslaw Zola)
4-4:30pm Divide-and-conquer approach to the parallel computation of
elementary flux modes in metabolic networks
Dimitrije Jevremovic, Daniel Boley, Carlos Sosa
4:30-5pm Sensitive and Specific Identification of Protein Complexes in
``Perturbed'' Protein Interaction Networks from Noisy Pull-Down Data
William Hendrix, Tatiana Karpinets, Eric Schendel, Byung-Hoon Park, Nagiza
Samatova
5-5:30pm An Efficient and Scalable Implementation of SNP-pair
Interaction Testing for Genetic Association Studies
Lars Koesterke, Dan Stanzione, Matt Vaughn, Jinliang Wang, Cheng-Ting Yeh, Dan
Nettleton, Patrick S. Schnable