@ARTICLE{Walters09:hmmer,
author = {John Paul Walters and Vidyananth Balu and Suryaprakash Kompalli and Vipin Chaudhary},
journal = {IEEE International Symposium on Parallel & Distributed Processing (IPDPS'09)},
pages = {1-12},
title = {Evaluating the use of GPUs in liver image segmentation and HMMER database searches},
volume = {0},
year = {2009}
}
@INPROCEEDINGS{Elijah-Roberts09:invivo,
author = {Elijah Roberts and John Stone and Leonardo Sepulveda and Wen-Mei Hwu and Zaida Luthey-Schulten},
booktitle = {IEEE International Workshop on High Performance Computational Biology (HiCOMB 2009)},
title = {Long Time-scale Simulations of in vivo Diffusion using GPU Hardware},
year = {2009}
}
@INPROCEEDINGS{Ligowski09:sw,
author = {Lukasz Ligowski and Witold Rudnicki },
booktitle = {IEEE International Workshop on High Performance Computational Biology (HiCOMB 2009)},
title = {An Efficient Implementation Smith Waterman Algorithm on GPU using CUDA, for Massively Parallel Scanning of Sequence Databases},
year = {2009}
}
@INPROCEEDINGS{Shi09:error,
author = {Haixiang Shi and Bertil Schmidt and Weiguo Liu and Wolfgang Mueller-Wittig },
booktitle = {IEEE International Workshop on High Performance Computational Biology (HiCOMB 2009)},
title = {Accelerating Error Correction in High-Throughput Short-Read DNA Sequencing Data with CUDA},
year = {2009}
}
@INPROCEEDINGS{Liu09:nj,
author = {Yongchao Liu and Bertil Schmidt and Douglas Maskell},
booktitle = {IEEE International Workshop on High Performance Computational Biology (HiCOMB 2009)},
title = {Parallel Reconstruction of Neighbor-Joining Trees for Large Multiple Sequence Alignments using CUDA},
year = {2009}
}
@INPROCEEDINGS{Rizk09:rnafold,
author = {Guillaume Rizk and Dominique Lavenier},
booktitle = {Using Emerging Parallel Architectures for Computational Science / International Conference on Computational Science (ICCS 2009)},
title = {GPU accelerated RNA folding algorithm},
year = {2009}
}
@INPROCEEDINGS{Giraud09:cudapwm,
author = {Mathieu Giraud and Jean-St{\'e}phane Varr{\'e}},
booktitle = {International Symposium on Parallel and Distributed Computing (ISPDC 2009)},
title = {Parallel Position Weight Matrices Algorithms},
year = {2009}
}
@INPROCEEDINGS{Manavski08:geagpu,
author = {Svetlin A. Manavski and Alessandro Albiero and Claudio Forcato and Nicola Vitulo and Giorgio Valle},
booktitle = {ECCB 2008},
pages = {poster},
title = {GEAgpu: Improved alignment of spliced DNA sequences to genomic data using Graphics Processing Units},
year = {2008}
}
@ARTICLE{Ogoubi08:rna,
author = {Ogoubi, {\'E}tienne and Pouliot, David and Turcotte, Marcel and Hafid, Abdelhakim},
journal = {Parallel Processing and Applied Mathematics},
pages = {1230--1239},
title = {Parallel Multiprocessor Approaches to the RNA Folding Problem},
year = {2008}
}
@ARTICLE{Manavski08:sw,
author = {Manavski, Svetlin A and Valle, Giorgio},
journal = {BMC Bioinformatics},
pages = {S10},
title = {CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment.},
volume = {9 Suppl 2},
year = {2008}
}
@ARTICLE{Schatz07:mummer,
author = {Schatz, Michael C and Trapnell, Cole and Delcher, Arthur L and Varshney, Amitabh},
journal = {BMC Bioinformatics},
pages = {474},
title = {High-throughput sequence alignment using Graphics Processing Units.},
volume = {8},
year = {2007}
}
@INPROCEEDINGS{Liu06:gpuclustalw,
author = {Weiguo Liu and Bertil Schmidt and Gerrit Voss and Wolfgang M{\"u}ller-Wittig},
booktitle = {IEEE International Conference on High Performance Computing (HiPC 2006)},
pages = {363-374},
series = {Lecture Notes in Computer Science (LNCS)},
title = {GPU-ClustalW: Using Graphics Hardware to Accelerate Multiple Sequence Alignment},
volume = {4297},
year = {2006}
}
@ARTICLE{Charalambous05:phylo,
author = {Charalambous, Maria and Trancoso, Pedro and Stamatakis, Alexandros},
journal = {Advances in Informatics},
pages = {415--425},
title = {Initial Experiences Porting a Bioinformatics Application to a Graphics Processor},
year = {2005}
}
@ARTICLE{Schatz09:mummer2,
author = {Schatz, Michael C and Trapnell, Cole },
journal = {Parallel Computing },
pages = {429:440},
title = {Optimizing data intensive GPGPU computations for DNA sequence alignment },
volume = {35},
year = {2009}
}
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