{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,30]],"date-time":"2026-03-30T12:19:05Z","timestamp":1774873145298,"version":"3.50.1"},"reference-count":25,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2010,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec><jats:title>Background<\/jats:title><jats:p>Many analyses of microarray association studies involve permutation, bootstrap resampling and cross-validation, that are ideally formulated as embarrassingly parallel computing problems. Given that these analyses are computationally intensive, scalable approaches that can take advantage of multi-core processor systems need to be developed.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We have developed a CUDA based implementation, , that employs graphics processing units in microarray association studies. We illustrate the performance and applicability of within the context of permutation resampling for a number of test statistics. An extensive simulation study demonstrates a dramatic increase in performance when using on an NVIDIA GTX 280 card compared to an optimized C\/C++ solution running on a conventional Linux server.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>is available as an open-source stand-alone application and as an extension package for the statistical environment. It provides a dramatic increase in performance for permutation resampling analysis in the context of microarray association studies. The current version offers six test statistics for carrying out permutation resampling analyses for binary, quantitative and censored time-to-event traits.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2105-11-329","type":"journal-article","created":{"date-parts":[[2010,6,17]],"date-time":"2010-06-17T06:13:48Z","timestamp":1276755228000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":16,"title":["permGPU: Using graphics processing units in RNA microarray association studies"],"prefix":"10.1186","volume":"11","author":[{"given":"Ivo D","family":"Shterev","sequence":"first","affiliation":[]},{"given":"Sin-Ho","family":"Jung","sequence":"additional","affiliation":[]},{"given":"Stephen L","family":"George","sequence":"additional","affiliation":[]},{"given":"Kouros","family":"Owzar","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2010,6,16]]},"reference":[{"key":"3786_CR1","volume-title":"Designing and Building Parallel Programs: Concepts and Tools for Parallel Software Engineering","author":"I Foster","year":"1995","unstructured":"Foster I: Designing and Building Parallel Programs: Concepts and Tools for Parallel Software Engineering. Addison-Wesley; 1995."},{"key":"3786_CR2","unstructured":"The Message Passing Interface (MPI) standard[http:\/\/www.mcs.anl.gov\/research\/projects\/mpi\/]"},{"key":"3786_CR3","unstructured":"The OpenMP API specification for parallel programming[http:\/\/openmp.org\/wp\/]"},{"key":"3786_CR4","doi-asserted-by":"publisher","first-page":"1937","DOI":"10.1093\/bioinformatics\/btp294","volume":"25","author":"R Hussong","year":"2009","unstructured":"Hussong R, Gregorius B, Tholey A, Hildebrandt A: Highly accelerated feature detection in proteomics data sets using modern graphics processing units. Bioinformatics 2009, 25: 1937\u20131943. 10.1093\/bioinformatics\/btp294","journal-title":"Bioinformatics"},{"key":"3786_CR5","volume-title":"BMC Bioinformatics","author":"NA Sinnott-Armstrong","year":"2009","unstructured":"Sinnott-Armstrong NA, Greene CS, Cancare F, Moore JH: Accelerating epistasis analysis in human genetics with consumer graphics hardware. BMC Bioinformatics 2009., 2:"},{"key":"3786_CR6","doi-asserted-by":"publisher","first-page":"1370","DOI":"10.1093\/bioinformatics\/btp244","volume":"25","author":"MA Suchard","year":"2009","unstructured":"Suchard MA, Rambaut A: Many-core algorithms for statistical phylogenetics. Bioinformatics 2009, 25: 1370\u20131376. 10.1093\/bioinformatics\/btp244","journal-title":"Bioinformatics"},{"key":"3786_CR7","volume-title":"BMC Bioinformatics","author":"MC Schatz","year":"2007","unstructured":"Schatz MC, Trapnell C, Delcher AL, Varshney A: High-throughput sequence alignment using Graphics Processing Units. BMC Bioinformatics 2007., 8: 10.1186\/1471-2105-8-474"},{"key":"3786_CR8","volume-title":"BMC Bioinformatics","author":"S Manavski","year":"2008","unstructured":"Manavski S, Valle G: CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment. BMC Bioinformatics 2008., 9: 10.1186\/1471-2105-9-S2-S10"},{"key":"3786_CR9","volume-title":"BMC Bioinformatics","author":"S Jung","year":"2009","unstructured":"Jung S: Parallelized pairwise sequence alignment using CUDA on multiple GPUs. BMC Bioinformatics 2009., 10: 10.1186\/1471-2105-10-164"},{"key":"3786_CR10","volume-title":"BMC Bioinformatics","author":"Y Liu","year":"2009","unstructured":"Liu Y, Maskell DL, Schmidt B: CUDASW++: Optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units. BMC Bioinformatics 2009., 2:"},{"key":"3786_CR11","volume-title":"R: A Language and Environment for Statistical Computing","author":"R Development Core Team","year":"2009","unstructured":"R Development Core Team:R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria; 2009. [ISBN 3\u2013900051\u201307\u20130] [http:\/\/www.R-project.org] [ISBN 3-900051-07-0]"},{"key":"3786_CR12","doi-asserted-by":"publisher","first-page":"134","DOI":"10.1093\/bioinformatics\/btp608","volume":"26","author":"J Buckner","year":"2010","unstructured":"Buckner J, Wilson J, Seligman M, Athey B, Watson S, Meng F:The gputools package enables GPU computing in R. Bioinformatics 2010, 26: 134\u2013135. 10.1093\/bioinformatics\/btp608","journal-title":"Bioinformatics"},{"issue":"5439","key":"3786_CR13","doi-asserted-by":"publisher","first-page":"531","DOI":"10.1126\/science.286.5439.531","volume":"286","author":"T Golub","year":"1999","unstructured":"Golub T, Slonim D, Tamayo P, Huard C, Gaasenbeek M, Mesirov J, Coller H, Loh M, Downing J, Caligiuri M, Bloomfield C, Lander E: Molecular Classification of Cancer: Class discovery and class prediction by gene expression monitoring. Science 1999, 286(5439):531\u2013537. 10.1126\/science.286.5439.531","journal-title":"Science"},{"issue":"8","key":"3786_CR14","doi-asserted-by":"crossref","first-page":"816","DOI":"10.1038\/nm733","volume":"8","author":"DG Beer","year":"2002","unstructured":"Beer DG, Kardia SLR, Huang CC, Giordano TJ, Levin AM, Misek DE, Lin L, Chen G, Gharib TG, Thomas DG, Lizyness ML, Kuick R, Hayasaka S, Taylor JMG, Iannettoni MD, Orringer MB, Hanash S: Gene-expression profiles predict survival of patients with lung adenocarcinoma. Nat Med 2002, 8(8):816\u2013824.","journal-title":"Nat Med"},{"issue":"8","key":"3786_CR15","doi-asserted-by":"publisher","first-page":"822","DOI":"10.1038\/nm.1790","volume":"14","author":"K Shedden","year":"2008","unstructured":"for the Molecular Classification of Lung Adenocarcinoma DCC, Shedden K, Taylor JMG, Enkemann SA, Tsao MS, Yeatman TJ, Gerald WL, Eschrich S, Jurisica I, Giordano TJ, Misek DE, Chang AC, Zhu CQ, Strumpf D, Hanash S, Shepherd FA, Ding K, Seymour L, Naoki K, Pennell N, Weir B, Verhaak R, Ladd-Acosta C, Golub T, Gruidl M, Sharma A, Szoke J, Zakowski M, Rusch V, Kris M, Viale A, Motoi N, Travis W, Conley B, Seshan VE, Meyerson M, Kuick R, Dobbin KK, Lively T, Jacobson JW, Beer DG: Gene expression-based survival prediction in lung adenocarcinoma: a multi-site, blinded validation study. Nat Med 2008, 14(8):822\u2013827. 10.1038\/nm.1790","journal-title":"Nat Med"},{"issue":"2","key":"3786_CR16","doi-asserted-by":"publisher","first-page":"157","DOI":"10.1158\/1541-7786.MCR-08-0435","volume":"7","author":"S Madhavan","year":"2009","unstructured":"Madhavan S, Zenklusen J, Kotliarov Y, Sahni H, Fine H, Buetow K: Rembrandt: helping personalized medicine become a reality through integrative translational research. Mol Cancer Res 2009, 7(2):157\u2013167. 10.1158\/1541-7786.MCR-08-0435","journal-title":"Mol Cancer Res"},{"key":"3786_CR17","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/jnci\/djp493","volume":"102","author":"J Subramanian","year":"2010","unstructured":"Subramanian J, Simon R: Gene expression-based prognostic signatures in lung cancer ready for clinical use? J Natl Cancer Inst 2010, 102: 1\u201311. 10.1093\/jnci\/djp493","journal-title":"J Natl Cancer Inst"},{"key":"3786_CR18","volume-title":"Compute unified device architecture (CUDA) programing guide","author":"NVIDIA","year":"2008","unstructured":"NVIDIA: Compute unified device architecture (CUDA) programing guide. 2008. [Version 2.2] [Version 2.2]"},{"key":"3786_CR19","volume-title":"Resampling-Based Multiple Testing: Examples and Methods for P-value Adjustment","author":"PH Westfall","year":"1993","unstructured":"Westfall PH, Young SS: Resampling-Based Multiple Testing: Examples and Methods for P-value Adjustment. New York: Wiley-Interscience; 1993."},{"key":"3786_CR20","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/BF02595811","volume":"12","author":"Y Ge","year":"2003","unstructured":"Ge Y, Dudoit S, Speed TP: Resampling-based multiple testing for microarray data analysis. TEST 2003, 12: 1\u201344. 10.1007\/BF02595811","journal-title":"TEST"},{"key":"3786_CR21","doi-asserted-by":"publisher","first-page":"3077","DOI":"10.1002\/sim.2179","volume":"24","author":"SH Jung","year":"2005","unstructured":"Jung SH, Owzar K, George SL: A multiple testing procedure to associate gene expression levels with survival. Statistics in Medicine 2005, 24: 3077\u20133088. 10.1002\/sim.2179","journal-title":"Statistics in Medicine"},{"issue":"2","key":"3786_CR22","doi-asserted-by":"publisher","first-page":"249","DOI":"10.1093\/biostatistics\/4.2.249","volume":"4","author":"R Irizarry","year":"2003","unstructured":"Irizarry R, Hobbs B, Collin F, Beazer-Barclay Y, Antonellis K, Scherf U, Speed T: Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics 2003, 4(2):249\u2013264. 10.1093\/biostatistics\/4.2.249","journal-title":"Biostatistics"},{"key":"3786_CR23","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1111\/j.2517-6161.1995.tb02031.x","volume":"57","author":"Y Benjamini","year":"1995","unstructured":"Benjamini Y, Hochberg Y: Controlling the false discovery rate: A practical and powerful approach to multiple testing. JR Statist Soc B 1995, 57: 289\u2013300.","journal-title":"JR Statist Soc B"},{"issue":"19","key":"3786_CR24","doi-asserted-by":"publisher","first-page":"5959","DOI":"10.1158\/1078-0432.CCR-07-4532","volume":"14","author":"K Owzar","year":"2008","unstructured":"Owzar K, Barry WT, Jung SH, Sohn I, George SL: Statistical challenges in preprocessing in microarray experiments in cancer. Clin Cancer Res 2008, 14(19):5959\u20135966. 10.1158\/1078-0432.CCR-07-4532","journal-title":"Clin Cancer Res"},{"key":"3786_CR25","doi-asserted-by":"publisher","first-page":"157","DOI":"10.1093\/biostatistics\/kxh026","volume":"6","author":"SH Jung","year":"2005","unstructured":"Jung SH, Bang H, Young SS: Sample size calculation for multiple testing in microarray data analysis. Biostatistics 2005, 6: 157\u2013169. 10.1093\/biostatistics\/kxh026","journal-title":"Biostatistics"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-11-329.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,22]],"date-time":"2025-02-22T01:20:38Z","timestamp":1740187238000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-11-329"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,6,16]]},"references-count":25,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2010,12]]}},"alternative-id":["3786"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-11-329","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,6,16]]},"assertion":[{"value":"22 March 2010","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 June 2010","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"16 June 2010","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"329"}}