The Theory of Parsing, Translation and Compiling, 1973. ,
Initial Experiences Porting a Bioinformatics Application to a Graphics Processor, Adv. in Informatics, pp.415-425, 2005. ,
DOI : 10.1007/11573036_39
Biological Sequence Analysis, 1998. ,
DOI : 10.1017/CBO9780511790492
A discipline of dynamic programming over sequence data, Science of Computer Programming, vol.51, issue.3, pp.215-263, 2004. ,
DOI : 10.1016/j.scico.2003.12.005
Challenges in the compilation of a domain specific language for dynamic programming, Proceedings of the 2006 ACM symposium on Applied computing , SAC '06, 2006. ,
DOI : 10.1145/1141277.1141653
Parallel position weight matrices algorithms, International Symposium on Parallel and Distributed Computing, 2009. ,
URL : https://hal.archives-ouvertes.fr/inria-00438215
An efficient implementation of Smith Waterman algorithm on GPU using CUDA, for massively parallel scanning of sequence databases, 2009 IEEE International Symposium on Parallel & Distributed Processing, 2009. ,
DOI : 10.1109/IPDPS.2009.5160931
GPU-ClustalW: Using Graphics Hardware to Accelerate Multiple Sequence Alignment, High Performance Computing, pp.363-374, 2006. ,
DOI : 10.1007/11945918_37
CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units, BMC Research Notes, vol.2, issue.1, p.73, 2009. ,
DOI : 10.1186/1756-0500-2-73
Parallel reconstruction of neighbor-joining trees for large multiple sequence alignments using CUDA, IEEE International Workshop on High Performance Computational Biology, 2009. ,
CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment, BMC Bioinformatics, vol.9, issue.2, p.10, 2008. ,
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure, Journal of Molecular Biology, vol.288, issue.5, pp.911-940, 1999. ,
DOI : 10.1006/jmbi.1999.2700
Algorithms for Loop Matchings, SIAM Journal on Applied Mathematics, vol.35, issue.1, pp.68-82, 1978. ,
DOI : 10.1137/0135006
Design, implementation and evaluation of a practical pseudoknot folding algorithm based on thermodynamics, BMC Bioinformatics, vol.5, issue.104, 2004. ,
Locomotif: from graphical motif description to RNA motif search, Bioinformatics, vol.23, issue.13, pp.391-400, 2007. ,
DOI : 10.1093/bioinformatics/btm179
GPU accelerated RNA folding algorithm, Using Emerging Parallel Architectures for Computational Science / International Conference on Computational Science, 2009. ,
URL : https://hal.archives-ouvertes.fr/hal-00637827
Highthroughput sequence alignment using graphics processing units, BMC Bioinformatics, vol.8, p.474, 2007. ,
Linguistic approaches to biological sequences, Bioinformatics, vol.13, issue.4, pp.333-344, 1997. ,
DOI : 10.1093/bioinformatics/13.4.333
Accelerating error correction in high-throughput short-read DNA sequencing data with CUDA, IEEE International Workshop on High Performance Computational Biology, 2009. ,
Compiling a Domain Specific Language for Dynamic Programming, 2006. ,
Versatile and declarative dynamic programming using pair algebras, BMC Bioinformatics, vol.6, issue.224, 2005. ,