HICOMB 2012, May 21, 2012


8:25-8:30am      Introductory Remarks
                        Mark Clement

 (Session I: Next-generation Data Analysis)

8:30-9am           Investigating Memory Optimization of Hash-index for Next Generation Sequencing on Multi-core Architecture
                        Wendi Wang, Wen Tang, Linchuan Li, Guangming Tan, Peiheng Zhang, and Ninghui Sun

9-9:30am           Parallel Pair-HMM SNP Detection
                        Nathan L. Clement, Brent A. Shepherd, Paul Bodily, Sukhbat Tumur-Ochir, Younghoon Gim, Quinn Snell, Mark J. Clement, and W. Evan Johnson

9:30-10am         Evaluation of GPU-based Seed Generation for Computational Genomics Using Burrows-Wheeler Transform
                        Yongchao Liu and Bertil Schmidt

10-10:30am       COFFEE BREAK 1

 (Session II: Analysis of Evolution)

10:30-11am       The Multi-Processor Scheduling Problem in Phylogenetics
                        Jiajie Zhang and Alexandros Stamatakis

11-11:30am       Optimizing the Execution of Statistical Simulations for Human Evolution in Hyper-threaded Multicore Architectures
                        Raquel Dias, César A.F. De Rose, Antônio Tadeu Azevedo Gomes, and Nelson J.R. Fagundes

11:30-12pm       SlimCodeML: An Optimized Version of CodeML for the Branch-Site Model
Hannes Schabauer, Mario Valle, Christoph Pacher, Heinz Stockinger, Alexandros Stamatakis, Marc Robinson-Rechavi, Ziheng Yang, and Nicolas Salamin

12-1:30pm        LUNCH BREAK

1:30-2:00pm      Keynote Talk: Dr Lin Fang, Director of the Bioinformatics Center at Beijing Genomics Institute

(Session III: Sequence and Structure)

2:30-3pm          Finding Common RNA Secondary Structures: A Case Study on the Dynamic Parallelization of a Data-driven Recurrence
                        Steven T. Stewart, Eric Aubanel, and Patricia A. Evans

3-3:30pm          The Development of Parallel Adaptive Sampling Algorithms for Analyzing Biological Networks CUDA Enabled Devices
                        Kathryn Dempsey, Kanimathi Duraisamy, Sanjukta Bhowmick, and Hesham Ali

3:00-3:30pm          COFFEE BREAK 2

(Session IV: GPU Approaches)

3:30-4pm          A Speculative HMMER Search Implementation on GPU
Xiaoqiang Li, Wenting Han, Gu Liu, Hong An, Mu Xu, Wei Zhou, and Qi Li

4-4:30pm          Probabilistic Brain Fiber Tractography on GPUs
Mo Xu, Xiaorui Zhang, Yu Wang, Ling Ren, Ziyu Wen, Yi Xu, Gaolang Gong, Ningyi Xu, and Huazhong Yang

4:30-5pm          Quantitative Trait Locus Analysis Using a Partitioned Linear Model on a GPU Cluster
Peter E. Bailey, Tapasya Patki, Gregory M. Striemer, Ali Akoglu, David K. Lowenthal, Peter Bradbury, Matt Vaughn, Liya Wang, and Stephen Goff