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134
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IPPS
2010
IEEE
15 years 1 months ago
pFANGS: Parallel high speed sequence mapping for Next Generation 454-roche Sequencing reads
Millions of DNA sequences (reads) are generated by Next Generation Sequencing machines everyday. There is a need for high performance algorithms to map these sequences to the refer...
Sanchit Misra, Ramanathan Narayanan, Wei-keng Liao...
137
Voted
IPPS
2010
IEEE
15 years 1 months ago
Exploring parallelism in short sequence mapping using Burrows-Wheeler Transform
Next-generation high throughput sequencing instruments are capable of generating hundreds of millions of reads in a single run. Mapping those reads to a reference genome is an ext...
Doruk Bozdag, Ayat Hatem, Ümit V. Çata...
117
Voted
IPPS
2010
IEEE
15 years 1 months ago
Solving the advection PDE on the cell broadband engine
In this paper we present the venture of porting two different algorithms for solving the two-dimensional advection PDE on the CBE platform, an in-place and an outof-place one, and ...
Georgios Rokos, Gerassimos Peteinatos, Georgia Kou...
IPPS
2010
IEEE
15 years 1 months ago
Parallelization of tau-leap coarse-grained Monte Carlo simulations on GPUs
The Coarse-Grained Monte Carlo (CGMC) method is a multi-scale stochastic mathematical and simulation framework for spatially distributed systems. CGMC simulations are important too...
Lifan Xu, Michela Taufer, Stuart Collins, Dionisio...
137
Voted
IPPS
2010
IEEE
15 years 1 months ago
Dynamic analysis of the relay cache-coherence protocol for distributed transactional memory
Transactional memory is an alternative programming model for managing contention in accessing shared in-memory data objects. Distributed transactional memory (TM) promises to alle...
Bo Zhang, Binoy Ravindran
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