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Items: 1 to 20 of 112

1.

MC64-ClustalWP2: a highly-parallel hybrid strategy to align multiple sequences in many-core architectures.

Díaz D, Esteban FJ, Hernández P, Caballero JA, Guevara A, Dorado G, Gálvez S.

PLoS One. 2014 Apr 7;9(4):e94044. doi: 10.1371/journal.pone.0094044. eCollection 2014.

2.

Coupling SIMD and SIMT architectures to boost performance of a phylogeny-aware alignment kernel.

Alachiotis N, Berger SA, Stamatakis A.

BMC Bioinformatics. 2012 Aug 9;13:196. doi: 10.1186/1471-2105-13-196.

3.

Speeding-up Bioinformatics Algorithms with Heterogeneous Architectures: Highly Heterogeneous Smith-Waterman (HHeterSW).

Gálvez S, Ferusic A, Esteban FJ, Hernández P, Caballero JA, Dorado G.

J Comput Biol. 2016 Oct;23(10):801-9. doi: 10.1089/cmb.2015.0237. Epub 2016 Apr 22.

PMID:
27104636
4.

Next-generation bioinformatics: using many-core processor architecture to develop a web service for sequence alignment.

Gálvez S, Díaz D, Hernández P, Esteban FJ, Caballero JA, Dorado G.

Bioinformatics. 2010 Mar 1;26(5):683-6. doi: 10.1093/bioinformatics/btq017. Epub 2010 Jan 16.

PMID:
20081221
5.

MICA: A fast short-read aligner that takes full advantage of Many Integrated Core Architecture (MIC).

Luo R, Cheung J, Wu E, Wang H, Chan SH, Law WC, He G, Yu C, Liu CM, Zhou D, Li Y, Li R, Wang J, Zhu X, Peng S, Lam TW.

BMC Bioinformatics. 2015;16 Suppl 7:S10. doi: 10.1186/1471-2105-16-S7-S10. Epub 2015 Apr 23.

6.

Parallelized computation for computer simulation of electrocardiograms using personal computers with multi-core CPU and general-purpose GPU.

Shen W, Wei D, Xu W, Zhu X, Yuan S.

Comput Methods Programs Biomed. 2010 Oct;100(1):87-96. doi: 10.1016/j.cmpb.2010.06.015. Epub 2010 Jul 31.

PMID:
20674066
7.

Parallel algorithms for large-scale biological sequence alignment on Xeon-Phi based clusters.

Lan H, Chan Y, Xu K, Schmidt B, Peng S, Liu W.

BMC Bioinformatics. 2016 Jul 19;17 Suppl 9:267. doi: 10.1186/s12859-016-1128-0.

8.

CUDA ClustalW: An efficient parallel algorithm for progressive multiple sequence alignment on Multi-GPUs.

Hung CL, Lin YS, Lin CY, Chung YC, Chung YF.

Comput Biol Chem. 2015 Oct;58:62-8. doi: 10.1016/j.compbiolchem.2015.05.004. Epub 2015 May 21.

PMID:
26052076
9.

High performance computing for deformable image registration: towards a new paradigm in adaptive radiotherapy.

Samant SS, Xia J, Muyan-Ozcelik P, Owens JD.

Med Phys. 2008 Aug;35(8):3546-53.

PMID:
18777915
10.

A hybrid short read mapping accelerator.

Chen Y, Schmidt B, Maskell DL.

BMC Bioinformatics. 2013 Feb 26;14:67. doi: 10.1186/1471-2105-14-67.

11.

Using CLUSTAL for multiple sequence alignments.

Higgins DG, Thompson JD, Gibson TJ.

Methods Enzymol. 1996;266:383-402.

PMID:
8743695
13.

Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments.

Daily J.

BMC Bioinformatics. 2016 Feb 10;17:81. doi: 10.1186/s12859-016-0930-z.

14.

Genomic multiple sequence alignments: refinement using a genetic algorithm.

Wang C, Lefkowitz EJ.

BMC Bioinformatics. 2005 Aug 8;6:200.

15.

FPGASW: Accelerating Large-Scale Smith-Waterman Sequence Alignment Application with Backtracking on FPGA Linear Systolic Array.

Fei X, Dan Z, Lina L, Xin M, Chunlei Z.

Interdiscip Sci. 2017 Apr 21. doi: 10.1007/s12539-017-0225-8. [Epub ahead of print]

PMID:
28432608
16.

A data parallel strategy for aligning multiple biological sequences on multi-core computers.

Zhu X, Li K, Salah A.

Comput Biol Med. 2013 May;43(4):350-61. doi: 10.1016/j.compbiomed.2012.12.009. Epub 2013 Feb 14.

PMID:
23414778
17.
18.

SWPS3 - fast multi-threaded vectorized Smith-Waterman for IBM Cell/B.E. and x86/SSE2.

Szalkowski A, Ledergerber C, Krähenbühl P, Dessimoz C.

BMC Res Notes. 2008 Oct 29;1:107. doi: 10.1186/1756-0500-1-107.

19.

Accelerating large-scale protein structure alignments with graphics processing units.

Pang B, Zhao N, Becchi M, Korkin D, Shyu CR.

BMC Res Notes. 2012 Feb 22;5:116. doi: 10.1186/1756-0500-5-116.

20.

Real-world comparison of CPU and GPU implementations of SNPrank: a network analysis tool for GWAS.

Davis NA, Pandey A, McKinney BA.

Bioinformatics. 2011 Jan 15;27(2):284-5. doi: 10.1093/bioinformatics/btq638. Epub 2010 Nov 25.

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