Papers related to GPU/Manycores Bioinformatics
Sequence comparison, sequence alignment
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Lukasz Ligowski and Witold Rudnicki.
An efficient implementation of Smith-Waterman algorithm on GPU
using CUDA, for massively parallel scanning of sequence databases.
In IEEE International Workshop on High Performance Computational
Biology (HiCOMB 2009), 2009.
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Weiguo Liu, Bertil Schmidt, Gerrit Voss, and Wolfgang Müller-Wittig.
GPU-ClustalW: Using graphics hardware to accelerate multiple
sequence alignment.
In IEEE International Conference on High Performance Computing
(HiPC 2006), volume 4297 of Lecture Notes in Computer Science (LNCS),
pages 363-374, 2006.
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Yongchao Liu, Bertil Schmidt, and Douglas Maskell.
Parallel reconstruction of neighbor-joining trees for large multiple
sequence alignments using CUDA.
In IEEE International Workshop on High Performance Computational
Biology (HiCOMB 2009), 2009.
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Yongchao Liu, Douglas Maskell, and Bertil Schmidt.
CUDASW++: optimizing Smith-Waterman sequence database searches for
CUDA-enabled graphics processing units.
BMC Research Notes, 2(1):73, 2009.
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Svetlin A. Manavski and Giorgio Valle.
CUDA compatible GPU cards as efficient hardware accelerators for
Smith-Waterman sequence alignment.
BMC Bioinformatics, 9 Suppl 2:S10, 2008.
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Svetlin A. Manavski, Alessandro Albiero, Claudio Forcato, Nicola Vitulo, and
Giorgio Valle.
GEAgpu: Improved alignment of spliced DNA sequences to genomic
data using graphics processing units.
In ECCB 2008, page poster, 2008.
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Michael C Schatz, Cole Trapnell, Arthur L Delcher, and Amitabh Varshney.
High-throughput sequence alignment using graphics processing units.
BMC Bioinformatics, 8:474, 2007.
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Michael C Schatz, Cole Trapnell.
Optimizing data intensive GPGPU computations for DNA sequence alignment
Parallel Computing, vol 35,pages 429:440, 2009.
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Other applications
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Maria Charalambous, Pedro Trancoso, and Alexandros Stamatakis.
Initial experiences porting a bioinformatics application to a
graphics processor.
Advances in Informatics, pages 415-425, 2005.
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Mathieu Giraud and Jean-Stéphane Varré.
Parallel position weight matrices algorithms.
In International Symposium on Parallel and Distributed Computing
(ISPDC 2009), 2009.
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Guillaume Rizk and Dominique Lavenier.
GPU accelerated RNA folding algorithm.
In Using Emerging Parallel Architectures for Computational
Science / International Conference on Computational Science (ICCS 2009),
2009.
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Elijah Roberts, John Stone, Leonardo Sepulveda, Wen-Mei Hwu, and Zaida
Luthey-Schulten.
Long time-scale simulations of in vivo diffusion using GPU
hardware.
In IEEE International Workshop on High Performance Computational
Biology (HiCOMB 2009), 2009.
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Haixiang Shi, Bertil Schmidt, Weiguo Liu, and Wolfgang Mueller-Wittig.
Accelerating error correction in high-throughput short-read DNA
sequencing data with CUDA.
In IEEE International Workshop on High Performance Computational
Biology (HiCOMB 2009), 2009.
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John Paul Walters, Vidyananth Balu, Suryaprakash Kompalli, and Vipin Chaudhary.
Evaluating the use of gpus in liver image segmentation and hmmer
IEEE International Symposium on Parallel & Distributed Processing (IPDPS'09),
pages:1-12, 2009.
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