HICOMB 2012, May 21, 2012
ADVANCE PROGRAM
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