HICOMB 2011, May 16, 2011


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