GENIE: A software package for gene-gene interaction analysis in genetic association studies using multiple GPU or CPU cores

BMC Research Notes

Volumn 4, Issue , 2011, Pages

  Chikkagoudar, Satish ^a   Wang, Kai ^b   Li, Mingyao ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

^b UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 79957461750     PISSN: None     EISSN: 17560500     Source Type: Journal    
DOI: 10.1186/1756-0500-4-158     Document Type: Article

References (15)

1. Detecting gene-gene interactions that underlie human diseases. HJ Cordell, Nat Rev Genet 2009 10 6 392 404 19434077
2. Gene-based interaction analysis by incorporating external linkage disequilibrium information. J He K Wang AC Edmondson DJ Rader C Li M Li, Eur J Hum Genet 2011 19 2 164 172 10.1038/ejhg.2010.164 20924406
3. Genome-wide strategies for detecting multiple loci that influence complex diseases. J Marchini P Donnelly LR Cardon, Nat Genet 2005 37 4 413 417 10.1038/ng1537 15793588
4. GPU computing for systems biology. L Dematte D Prandi, Brief Bioinform 2010 11 3 323 333 10.1093/bib/bbq006 20211843
5. High-throughput sequence alignment using Graphics Processing Units. MC Schatz C Trapnell AL Delcher A Varshney, BMC Bioinformatics 2007 8 474 10.1186/1471-2105-8-474 18070356
6. Graphics Processing Units and High-Dimensional Optimization. H Zhou K Lange MA Suchard, Statistical Science 2010 25 311 324 10.1214/10-STS336
7. Real-world comparison of CPU and GPU implementations of SNPrank: a network analysis tool for GWAS. NA Davis A Pandey BA McKinney, Bioinformatics 2011 27 2 284 285 10.1093/bioinformatics/btq638 21115438
8. FastEpistasis: a high performance computing solution for quantitative trait epistasis. T Schupbach I Xenarios S Bergmann K Kapur, Bioinformatics 2010 26 11 1468 1469 10.1093/bioinformatics/btq147 20375113
9. PLINK: a tool set for whole-genome association and population-based linkage analyses. S Purcell B Neale K Todd-Brown L Thomas MA Ferreira D Bender J Maller P Sklar PI de Bakker MJ Daly PC Sham, Am J Hum Genet 2007 81 3 559 575 10.1086/519795 17701901 (Pubitemid 47330214)
10. NVIDIA CUDA C Best Practices Guide. http://developer.download.nvidia.com/ compute/cuda/3-1/toolkit/docs/NVIDIA-CUDA-C-BestPracticesGuide-3.1.pdf
11. NVIDIA CUDA Programming Guide. http://developer.download.nvidia.com/ compute/cuda/3-1/toolkit/docs/NVIDIA-CUDA-C-ProgrammingGuide-3.1.pdf
12. Concept, design and implementation of a cardiovascular gene-centric 50 k SNP array for large-scale genomic association studies. BJ Keating S Tischfield SS Murray T Bhangale TS Price JT Glessner L Galver JC Barrett SF Grant DN Farlow HR Chandrupatla M Hansen S Ajmal GJ Papanicolaou Y Guo M Li S Derohannessian PI de Bakker SD Bailey A Montpetit AC Edmondson K Taylor X Gai SS Wang M Fornage T Shaikh L Groop M Boehnke AS Hall AT Hattersley,, et al. PLoS One 2008 3 10 3583 10.1371/journal.pone.0003583 18974833
13. Debunking the 100X GPU vs. CPU myth: an evaluation of throughput computing on CPU and GPU. VW Lee C Kim J Chhugani M Deisher D Kim AD Nguyen N Satish M Smelyanskiy S Chennupaty P Hammarlund R Singhal P Dubey, Proceedings of the 37th annual international symposium on Computer architecture Saint-Malo, France: ACM 2010 451 460
14. Accelerating molecular modeling applications with graphics processors. JE Stone JC Phillips PL Freddolino DJ Hardy LG Trabuco K Schulten, J Comput Chem 2007 28 16 2618 2640 10.1002/jcc.20829 17894371 (Pubitemid 350074136)
15. SWAN A simple tool for porting CUDA to OpenCL. http://www.multiscalelab. org/swan