{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,21]],"date-time":"2025-02-21T15:39:16Z","timestamp":1740152356768,"version":"3.37.3"},"reference-count":36,"publisher":"Springer Science and Business Media LLC","issue":"1","funder":[{"DOI":"10.13039\/501100000266","name":"Engineering and Physical Sciences Research Council","doi-asserted-by":"publisher","award":["EP\/M025853\/1"],"award-info":[{"award-number":["EP\/M025853\/1"]}],"id":[{"id":"10.13039\/501100000266","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BioData Mining"],"published-print":{"date-parts":[[2017,12]]},"DOI":"10.1186\/s13040-017-0149-1","type":"journal-article","created":{"date-parts":[[2017,8,2]],"date-time":"2017-08-02T11:12:46Z","timestamp":1501672366000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Genetically improved BarraCUDA"],"prefix":"10.1186","volume":"10","author":[{"given":"W. B.","family":"Langdon","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Brian Yee Hong","family":"Lam","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2017,8,2]]},"reference":[{"issue":"5","key":"149_CR1","doi-asserted-by":"crossref","first-page":"879","DOI":"10.1109\/JPROC.2008.917757","volume":"96","author":"JD Owens","year":"2008","unstructured":"Owens JD, Houston M, Luebke D, Green S, Stone JE, Phillips JC. GPU Computing. Proc IEEE. 2008; 96(5):879\u201399. \n                        http:\/\/dx.doi.org\/doi:10.1109\/JPROC.2008.917757\n                        \n                    . Invited paper.","journal-title":"Proc IEEE"},{"key":"149_CR2","doi-asserted-by":"crossref","unstructured":"Klus P, Lam S, Lyberg D, Cheung MS, Pullan G, McFarlane I, Yeo GSH, Lam BYH. BarraCUDA - a fast short read sequence aligner using graphics processing units. BMC Res Notes. 2012; 5(27). \n                        http:\/\/dx.doi.org\/doi:10.1186\/1756-0500-5-27\n                        \n                    .","DOI":"10.1186\/1756-0500-5-27"},{"key":"149_CR3","volume-title":"GECCO \u201915: Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation","author":"WB Langdon","year":"2015","unstructured":"Langdon WB, Lam BYH, Petke J, Harman M. Improving CUDA DNA Analysis Software with Genetic Programming In: Silva S, Esparcia-Alcazar AI, Lopez-Ibanez M, Mostaghim S, Timmis J, Zarges C, Correia L, Soule T, Giacobini M, Urbanowicz R, Akimoto Y, Glasmachers T, Fernandez de Vega F, Hoover A, Larranaga P, Soto M, Cotta C, Pereira FB, Handl J, Koutnik J, Gaspar-Cunha A, Trautmann H, Mouret JB, Risi S, Costa E, Schuetze O, Krawiec K, Moraglio A, Miller JF, Widera P, Cagnoni S, Merelo J, Hart E, Trujillo L, Kessentini M, Ochoa G, Chicano F, Doerr C, editors. GECCO \u201915: Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation. Madrid: ACM: 2015. p. 1063\u201370. \n                        http:\/\/dx.doi.org\/doi:10.1145\/2739480.2754652\n                        \n                    ."},{"key":"149_CR4","unstructured":"Koza JR. Genetic Programming: On the Programming of Computers by Natural Selection: MIT press; 1992."},{"key":"149_CR5","unstructured":"Poli R, Langdon WB, McPhee NF. A field guide to genetic programming; 2008. Published via \n                        http:\/\/lulu.com\n                        \n                     and freely available at \n                        http:\/\/www.gp-field-guide.org.uk\n                        \n                    . (With contributions by J. R. Koza)."},{"key":"149_CR6","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1109\/TEVC.2013.2281544","volume":"19","author":"WB Langdon","year":"2015","unstructured":"Langdon WB, Harman M. Optimising Existing Software with Genetic Programming. IEEE Trans Evol Comput. 2015; 19:118\u201335. \n                        http:\/\/dx.doi.org\/doi:10.1109\/TEVC.2013.2281544\n                        \n                    .","journal-title":"IEEE Trans Evol Comput"},{"key":"149_CR7","doi-asserted-by":"crossref","unstructured":"Petke J, Harman M, Langdon WB, Weimer W. Specialising Software for Different Downstream Applications Using Genetic Improvement and Code Transplantation. IEEE Trans Softw Eng. \n                        http:\/\/dx.doi.org\/doi:10.1109\/TEVC.2017.2693219\n                        \n                    .","DOI":"10.1109\/TEVC.2017.2693219"},{"key":"149_CR8","volume-title":"18th International Conference on Soft Computing, MENDEL 2012","author":"WB Langdon","year":"2012","unstructured":"Langdon WB. Genetic Improvement of Programs In: Matousek R, editor. 18th International Conference on Soft Computing, MENDEL 2012. 2nd edition. Brno, Czech Republic: Brno University of Technology: 2012. \n                        http:\/\/www.cs.ucl.ac.uk\/staff\/W.Langdon\/ftp\/papers\/Langdon_2012_mendel.pdf\n                        \n                    . Invited keynote."},{"key":"149_CR9","doi-asserted-by":"crossref","unstructured":"Jia Y, Harman M, Langdon WB, Marginean A. Grow and Serve: Growing Django Citation Services Using SBSE In: Yoo S, Minku L, editors. SSBSE 2015 Challenge Track, Volume 9275 of LNCS. Bergamo: 2015. p. 269\u201375. \n                        http:\/\/dx.doi.org\/doi:10.1007\/978-3-319-22183-0_22\n                        \n                    .","DOI":"10.1007\/978-3-319-22183-0_22"},{"key":"149_CR10","doi-asserted-by":"crossref","unstructured":"Langdon WB. Genetically Improved Software In: Gandomi AH, Alavi AH, Ryan C, editors. Handbook of Genetic Programming Applications. Springer: 2015. p. 181\u2013220. \n                        http:\/\/dx.doi.org\/doi:10.1007\/978-3-319-20883-1_8\n                        \n                    .","DOI":"10.1007\/978-3-319-20883-1_8"},{"key":"149_CR11","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1007\/s10710-016-9273-9","volume":"18","author":"WB Langdon","year":"2017","unstructured":"Langdon WB, Lam BYH, Modat M, Petke J, Harman M. Genetic Improvement of GPU Software. Genet Program Evolvable Mach. 2017; 18:5\u201344. \n                        http:\/\/dx.doi.org\/doi:10.1007\/s10710-016-9273-9\n                        \n                    .","journal-title":"Genet Program Evolvable Mach"},{"key":"149_CR12","doi-asserted-by":"crossref","unstructured":"Petke J, Haraldsson SO, Harman M, Langdon WB, White DR, Woodward JR. Genetic Improvement of Software: a Comprehensive Survey. EEE Trans Evol Comput. \n                        http:\/\/dx.doi.org\/doi:10.1109\/TEVC.2017.2693219\n                        \n                    .","DOI":"10.1109\/TEVC.2017.2693219"},{"key":"149_CR13","volume-title":"Genetic Improvement 2016 Workshop","author":"WB Langdon","year":"2016","unstructured":"Langdon WB, Vilella A, Lam BYH, Petke J, Harman M. Benchmarking Genetically Improved BarraCUDA on Epigenetic Methylation NGS datasets and nVidia GPUs In: Petke J, Weimer W, White DR, editors. Genetic Improvement 2016 Workshop. Denver: ACM: 2016. p. 1131\u201332. \n                        http:\/\/dx.doi.org\/doi:10.1145\/2908961.2931687\n                        \n                    ."},{"key":"149_CR14","doi-asserted-by":"crossref","unstructured":"Langdon WB. Mycoplasma Contamination in The 1000 Genomes Project. BioData Min. 2014;7(3). \n                        http:\/\/dx.doi.org\/doi:10.1186\/1756-0381-7-3\n                        \n                    .","DOI":"10.1186\/1756-0381-7-3"},{"key":"149_CR15","doi-asserted-by":"crossref","unstructured":"Highnam G, Wang JJ, Kusler D, Zook J, Vijayan V, Leibovich N, Mittelman D. An analytical framework for optimizing variant discovery from personal genomes. Nat Commun. 2015;6(6275). \n                        http:\/\/dx.doi.org\/doi:10.1038\/ncomms7275\n                        \n                    .","DOI":"10.1038\/ncomms7275"},{"issue":"4","key":"149_CR16","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","volume":"9","author":"B Langmead","year":"2012","unstructured":"Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012; 9(4):357\u20139. \n                        http:\/\/dx.doi.org\/doi:10.1038\/nmeth.1923\n                        \n                    .","journal-title":"Nat Methods"},{"issue":"5","key":"149_CR17","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1093\/bioinformatics\/btp698","volume":"26","author":"H Li","year":"2010","unstructured":"Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010; 26(5):589\u201395. \n                        http:\/\/dx.doi.org\/doi:10.1093\/bioinformatics\/btp698\n                        \n                    .","journal-title":"Bioinformatics"},{"key":"149_CR18","doi-asserted-by":"crossref","unstructured":"Lenis J, Senar MA. Euro-Par 2016: Parallel Processing Workshops, Volume 10104 of Lecture Notes in Computer Science In: Desprez F, Dutot PF, Kaklamanis C, Marchal L, Molitorisz K, Ricci L, Scarano V, Vega-Rodr\u00edguez MA, Varbanescu AL, Hunold S, Scott SL, Lankes S, Weidendorfer J, editors. Grenoble: Springer: 2016. p. 492\u2013503. \n                        http:\/\/dx.doi.org\/doi:10.1007\/978-3-319-58943-5_40\n                        \n                    . Revised Selected Papers, published 2017.","DOI":"10.1007\/978-3-319-58943-5_40"},{"issue":"12","key":"149_CR19","doi-asserted-by":"crossref","first-page":"1185","DOI":"10.1038\/nmeth.2221","volume":"9","author":"S Marco-Sola","year":"2012","unstructured":"Marco-Sola S, Sammeth M, Guigo R, Ribeca P. The GEM mapper: fast, accurate and versatile alignment by filtration. Nat Methods. 2012; 9(12):1185\u20138. \n                        http:\/\/dx.doi.org\/doi:10.1038\/nmeth.2221\n                        \n                    .","journal-title":"Nat Methods"},{"key":"149_CR20","unstructured":"Zaharia M, Bolosky WJ, Curtis K, Fox A, Patterson DA, Shenker S, Stoica I, Karp RM, Sittler T. Faster and More Accurate Sequence Alignment with SNAP. 2011. \n                        https:\/\/arxiv.org\/abs\/1111.5572v1\n                        \n                    ."},{"issue":"Supplement 7","key":"149_CR21","doi-asserted-by":"crossref","first-page":"S10","DOI":"10.1186\/1471-2105-16-S7-S10","volume":"16","author":"R Luo","year":"2015","unstructured":"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. MICA: A fast short-read aligner that takes full advantage of Many Integrated Core Architecture (MIC). BMC Bioinforma. 2015; 16(Supplement 7):S10. \n                        http:\/\/dx.doi.org\/doi:10.1186\/1471-2105-16-S7-S10\n                        \n                    . Selected articles from The 11th Annual Biotechnology and Bioinformatics Symposium (BIOT-2014): Bioinformatics.","journal-title":"BMC Bioinforma"},{"issue":"5","key":"149_CR22","doi-asserted-by":"crossref","first-page":"e65632","DOI":"10.1371\/journal.pone.0065632","volume":"8","author":"R Luo","year":"2013","unstructured":"Luo R, Wong T, Zhu J, Liu CM, Zhu X, Wu E, Lee LK, Lin H, Zhu W, Cheung DW, Ting HF, Yiu SM, Peng S, Yu C, Li Y, Li R, Lam TW. SOAP3-dp: Fast, Accurate and Sensitive GPU-Based Short Read Aligner. PLoS ONE. 2013; 8(5):e65632. \n                        http:\/\/dx.doi.org\/doi:10.1371\/journal.pone.0065632\n                        \n                    .","journal-title":"PLoS ONE"},{"issue":"6","key":"149_CR23","doi-asserted-by":"crossref","first-page":"878","DOI":"10.1093\/bioinformatics\/bts061","volume":"28","author":"CM Liu","year":"2012","unstructured":"Liu CM, Wong T, Wu E, Luo R, Yiu SM, Li Y, Wang B, Yu C, Chu X, Zhao K, Li R, Lam TW. SOAP3: ultra-fast GPU-based parallel alignment tool for short reads. Bioinformatics. 2012; 28(6):878\u20139. \n                        http:\/\/dx.doi.org\/doi:10.1093\/bioinformatics\/bts061\n                        \n                    .","journal-title":"Bioinformatics"},{"key":"149_CR24","unstructured":"NVIDIA GeForce GTX 680, The fastest, most efficient GPU ever built. Tech. Rep. V1.0, nVidia. 2012. \n                        http:\/\/la.nvidia.com\/content\/PDF\/product-specifications\/GeForce_GTX_680_Whitepaper_FINAL.pdf\n                        \n                    . Technology Overview. Accessed 18 June 2017."},{"issue":"18","key":"149_CR25","doi-asserted-by":"crossref","first-page":"2366","DOI":"10.1093\/bioinformatics\/bts450","volume":"28","author":"JC Mu","year":"2012","unstructured":"Mu JC, Jiang H, Kiani A, Mohiyuddin M, Asadi NB, Wong WH. Fast and accurate read alignment for resequencing. Bioinformatics. 2012; 28(18):2366\u201373. \n                        http:\/\/dx.doi.org\/10.1093\/bioinformatics\/bts450\n                        \n                    .","journal-title":"Bioinformatics"},{"issue":"18","key":"149_CR26","doi-asserted-by":"crossref","first-page":"i318","DOI":"10.1093\/bioinformatics\/bts414","volume":"28","author":"Y Liu","year":"2012","unstructured":"Liu Y, Schmidt B. Long read alignment based on maximal exact match seeds. Bioinformatics. 2012; 28(18):i318\u201324. \n                        http:\/\/dx.doi.org\/doi:10.1093\/bioinformatics\/bts414\n                        \n                    . ECCB 2012","journal-title":"Bioinformatics"},{"key":"149_CR27","doi-asserted-by":"crossref","first-page":"e808","DOI":"10.7717\/peerj.808","volume":"3","author":"R Wilton","year":"2015","unstructured":"Wilton R, Budavari T, Langmead B, Wheelan SJ, Salzberg SL, Szalay AS. Arioc: high-throughput read alignment with GPU-accelerated exploration of the seed-and-extend search space. PeerJ. 2015; 3:e808. \n                        http:\/\/dx.doi.org\/doi:10.7717\/peerj.808\n                        \n                    .","journal-title":"PeerJ"},{"key":"149_CR28","volume-title":"Genetic Improvement 2015 Workshop","author":"WB Langdon","year":"2015","unstructured":"Langdon WB, Harman M. Grow and Graft a better CUDA pknotsRG for RNA pseudoknot free energy calculation In: Langdon WB, Petke J, White DR, editors. Genetic Improvement 2015 Workshop. Madrid: ACM: 2015. p. 805\u201310. \n                        http:\/\/dx.doi.org\/doi:10.1145\/2739482.2768418\n                        \n                    ."},{"key":"149_CR29","unstructured":"Williams KP, Williams SA. Genetic compilers: A new technique for automatic parallelisation. L\u2019Alpe d\u2019Hoez: 1996. p. 27\u201330. \n                        http:\/\/citeseerx.ist.psu.edu\/viewdoc\/summary?doi=10.1.1.49.3499\n                        \n                    ."},{"issue":"2","key":"149_CR30","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1145\/2076450.2076469","volume":"55","author":"HH Hoos","year":"2012","unstructured":"Hoos HH. Programming by optimization. Commun ACM. 2012; 55(2):70\u201380. \n                        http:\/\/dx.doi.org\/doi:10.1145\/2739480.2754648\n                        \n                    .","journal-title":"Commun ACM"},{"key":"149_CR31","volume-title":"GECCO \u201915: Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation","author":"F Wu","year":"2015","unstructured":"Wu F, Weimer W, Harman M, Jia Y, Krinke J. Deep Parameter Optimisation In: Silva S, Esparcia-Alcazar AI, Lopez-Ibanez M, Mostaghim S, Timmis J, Zarges C, Correia L, Soule T, Giacobini M, Urbanowicz R, Akimoto Y, Glasmachers T, Fernandez de Vega F, Hoover A, Larranaga P, Soto M, Cotta C, Pereira FB, Handl J, Koutnik J, Gaspar-Cunha A, Trautmann H, Mouret JB, Risi S, Costa E, Schuetze O, Krawiec K, Moraglio A, Miller JF, Widera P, Cagnoni S, Merelo J, Hart E, Trujillo L, Kessentini M, Ochoa G, Chicano F, Doerr C, editors. GECCO \u201915: Proceedings of the 2015 Annual Conference on Genetic and Evolutionary Computation. Madrid: ACM: 2015. p. 1375\u201382. \n                        http:\/\/dx.doi.org\/doi:10.1145\/2739480.2754648\n                        \n                    ."},{"key":"149_CR32","volume-title":"17th European Conference on Genetic Programming, Volume 8599 of LNCS","author":"WB Langdon","year":"2014","unstructured":"Langdon WB, Harman M. Genetically Improved CUDA C++ Software In: Nicolau M, Krawiec K, Heywood MI, Castelli M, Garcia-Sanchez P, Merelo JJ, Rivas Santos VM, Sim K, editors. 17th European Conference on Genetic Programming, Volume 8599 of LNCS. Granada: Springer: 2014. p. 87\u201399. \n                        http:\/\/dx.doi.org\/doi:10.1007\/978-3-662-44303-3_8\n                        \n                    ."},{"issue":"6822","key":"149_CR33","doi-asserted-by":"crossref","first-page":"860","DOI":"10.1038\/35057062","volume":"409","author":"International Human Genome Sequencing Consortium","year":"2001","unstructured":"International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature. 2001; 409(6822):860\u2013921. \n                        http:\/\/dx.doi.org\/doi:10.1038\/35057062\n                        \n                    .","journal-title":"Nature"},{"issue":"7319","key":"149_CR34","doi-asserted-by":"crossref","first-page":"1061","DOI":"10.1038\/nature09534","volume":"467","author":"RM Durbin","year":"2010","unstructured":"Durbin RM, et al.A map of human genome variation from population-scale sequencing. Nature. 2010; 467(7319):1061\u201373. \n                        http:\/\/dx.doi.org\/doi:10.1038\/nature09534\n                        \n                    .","journal-title":"Nature"},{"key":"149_CR35","doi-asserted-by":"crossref","unstructured":"Langdon WB. Performance of Genetic Programming Optimised Bowtie2 on Genome Comparison and Analytic Testing (GCAT) Benchmarks. BioData Min. 2015;8. \n                        http:\/\/dx.doi.org\/doi:10.1186\/s13040-014-0034-0\n                        \n                    .","DOI":"10.1186\/s13040-014-0034-0"},{"key":"149_CR36","unstructured":"Langdon WB, Lam BYH. Genetically Improved BarraCUDA. Research Note RN\/15\/03, Department of Computer Science, University College London, Gower Street, London WC1E 6BT, UK; 2015. \n                        http:\/\/arxiv.org\/abs\/arXiv:1505.07855\n                        \n                    ."}],"container-title":["BioData Mining"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s13040-017-0149-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2017,8,2]],"date-time":"2017-08-02T11:13:21Z","timestamp":1501672401000},"score":1,"resource":{"primary":{"URL":"http:\/\/biodatamining.biomedcentral.com\/articles\/10.1186\/s13040-017-0149-1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,8,2]]},"references-count":36,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2017,12]]}},"alternative-id":["149"],"URL":"https:\/\/doi.org\/10.1186\/s13040-017-0149-1","relation":{},"ISSN":["1756-0381"],"issn-type":[{"type":"electronic","value":"1756-0381"}],"subject":[],"published":{"date-parts":[[2017,8,2]]},"article-number":"28"}}