{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,2]],"date-time":"2026-05-02T09:26:01Z","timestamp":1777713961791,"version":"3.51.4"},"reference-count":24,"publisher":"Springer Science and Business Media LLC","issue":"S14","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2012,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Multifactorial diseases arise from complex patterns of interaction between a set of genetic traits and the environment. To fully capture the genetic biomarkers that jointly explain the heritability component of a disease, thus, all SNPs from a genome-wide association study should be analyzed simultaneously.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>In this paper, we present Bag of Na\u00efve Bayes (BoNB), an algorithm for genetic biomarker selection and subjects classification from the simultaneous analysis of genome-wide SNP data. BoNB is based on the Na\u00efve Bayes classification framework, enriched by three main features: bootstrap aggregating of an ensemble of Na\u00efve Bayes classifiers, a novel strategy for ranking and selecting the attributes used by each classifier in the ensemble and a permutation-based procedure for selecting significant biomarkers, based on their marginal utility in the classification process. BoNB is tested on the Wellcome Trust Case-Control study on Type 1 Diabetes and its performance is compared with the ones of both a standard Na\u00efve Bayes algorithm and HyperLASSO, a penalized logistic regression algorithm from the state-of-the-art in simultaneous genome-wide data analysis.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>The significantly higher classification accuracy obtained by BoNB, together with the significance of the biomarkers identified from the Type 1 Diabetes dataset, prove the effectiveness of BoNB as an algorithm for both classification and biomarker selection from genome-wide SNP data.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Availability<\/jats:title>\n            <jats:p>Source code of the BoNB algorithm is released under the GNU General Public Licence and is available at <jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" xlink:href=\"http:\/\/www.dei.unipd.it\/~sambofra\/bonb.html\" ext-link-type=\"uri\">http:\/\/www.dei.unipd.it\/~sambofra\/bonb.html<\/jats:ext-link>.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1471-2105-13-s14-s2","type":"journal-article","created":{"date-parts":[[2012,10,17]],"date-time":"2012-10-17T22:31:28Z","timestamp":1350513088000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":25,"title":["Bag of Na\u00efve Bayes: biomarker selection and classification from genome-wide SNP data"],"prefix":"10.1186","volume":"13","author":[{"given":"Francesco","family":"Sambo","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Emanuele","family":"Trifoglio","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Barbara","family":"Di Camillo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gianna M","family":"Toffolo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Claudio","family":"Cobelli","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2012,9,7]]},"reference":[{"issue":"4","key":"5329_CR1","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1038\/jhg.2010.19","volume":"55","author":"CS Ku","year":"2010","unstructured":"Ku CS, Loy EY, Pawitan Y, Chia KS: The pursuit of genome-wide association studies: where are we now?. Journal of Human Genetics. 2010, 55 (4): 195-206. 10.1038\/jhg.2010.19.","journal-title":"Journal of Human Genetics"},{"issue":"7317","key":"5329_CR2","doi-asserted-by":"publisher","first-page":"832","DOI":"10.1038\/nature09410","volume":"467","author":"The GIANT Consortium","year":"2010","unstructured":"The GIANT Consortium: Hundreds of variants clustered in genomic loci and biological pathways affect human height. Nature. 2010, 467 (7317): 832-838. 10.1038\/nature09410.","journal-title":"Nature"},{"key":"5329_CR3","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1038\/ng.287","volume":"41","author":"The GIANT Consortium","year":"2009","unstructured":"The GIANT Consortium: Six new loci associated with body mass index highlight a neuronal influence on body weight regulation. Nature Genetics. 2009, 41: 25-34. 10.1038\/ng.287.","journal-title":"Nature Genetics"},{"issue":"2","key":"5329_CR4","doi-asserted-by":"publisher","first-page":"539","DOI":"10.2337\/db09-0653","volume":"59","author":"AD Paterson","year":"2010","unstructured":"Paterson AD, Waggott D, Boright AP, Hosseini SM, Shen E, Sylvestre MPP, Wong I, Bharaj B, Cleary PA, Lachin JM, MAGIC (Meta-Analyses of Glucose and Insulin-related traits Consortium), Below JE, Nicolae D, Cox NJ, Canty AJ, Sun L, Bull SB, Diabetes Control and Complications Trial\/Epidemiology of Diabetes Interventions and Complications Research Group: A genome-wide association study identifies a novel major locus for glycemic control in type 1 diabetes, as measured by both A1C and glucose. Diabetes. 2010, 59 (2): 539-549. 10.2337\/db09-0653.","journal-title":"Diabetes"},{"issue":"1-2","key":"5329_CR5","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1007\/s00335-011-9386-7","volume":"23","author":"R Wayne","year":"2012","unstructured":"Wayne R, Vonholdt B: Evolutionary genomics of dog domestication. Mammalian Genome. 2012, 23 (1-2): 3-18. 10.1007\/s00335-011-9386-7.","journal-title":"Mammalian Genome"},{"issue":"10","key":"5329_CR6","doi-asserted-by":"publisher","first-page":"232","DOI":"10.1186\/gb-2011-12-10-232","volume":"12","author":"B Brachi","year":"2011","unstructured":"Brachi B, Morris G, Borevitz J: Genome-wide association studies in plants: the missing heritability is in the field. Genome Biology. 2011, 12 (10): 232-10.1186\/gb-2011-12-10-232.","journal-title":"Genome Biology"},{"issue":"7145","key":"5329_CR7","doi-asserted-by":"publisher","first-page":"661","DOI":"10.1038\/nature05911","volume":"447","author":"The Wellcome Trust Case Control Consortium","year":"2007","unstructured":"The Wellcome Trust Case Control Consortium: Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature. 2007, 447 (7145): 661-678. 10.1038\/nature05911.","journal-title":"Nature"},{"issue":"5","key":"5329_CR8","doi-asserted-by":"publisher","first-page":"638","DOI":"10.1038\/ng.120","volume":"40","author":"E Zeggini","year":"2008","unstructured":"Zeggini E, Scott LJ, Saxena R, Voight BF, Marchini JL, Hu T, de Bakker PIW, Abecasis GR, Almgren P, Andersen G, Ardlie K, Bostrom KB, Bergman RN, Bonnycastle LL, Borch-Johnsen K, Burtt NP, Chen H, Chines PS, Daly MJ, Deodhar P, Ding CJ, Doney ASF, Duren WL, Elliott KS, Erdos MR, Frayling TM, Freathy RM, Gianniny L, Grallert H, Grarup N: Meta-analysis of genome-wide association data and large-scale replication identifies additional susceptibility loci for type 2 diabetes. Nature Genetics. 2008, 40 (5): 638-645. 10.1038\/ng.120.","journal-title":"Nature Genetics"},{"issue":"6","key":"5329_CR9","doi-asserted-by":"publisher","first-page":"703","DOI":"10.1038\/ng.381","volume":"41","author":"JC Barrett","year":"2009","unstructured":"Barrett JC, Clayton DG, Concannon P, Akolkar B, Cooper JD, Erlich HA, Julier C, Morahan G, Nerup J, Nierras C, Plagnol V, Pociot F, Schuilenburg H, Smyth DJ, Stevens H, Todd JA, Walker NM, Rich SS: Genome-wide association study and meta-analysis find that over 40 loci affect risk of type 1 diabetes. Nature Genetics. 2009, 41 (6): 703-707. 10.1038\/ng.381.","journal-title":"Nature Genetics"},{"issue":"7","key":"5329_CR10","doi-asserted-by":"publisher","first-page":"e1000130","DOI":"10.1371\/journal.pgen.1000130","volume":"4","author":"CJ Hoggart","year":"2008","unstructured":"Hoggart CJ, Whittaker JC, De Iorio M, Balding DJ: Simultaneous Analysis of All SNPs in Genome-Wide and Re-Sequencing Association Studies. PLoS Genet. 2008, 4 (7): e1000130-10.1371\/journal.pgen.1000130.","journal-title":"PLoS Genet"},{"key":"5329_CR11","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1093\/bioinformatics\/btq600","volume":"27","author":"Q He","year":"2011","unstructured":"He Q, Lin DY: A variable selection method for genome-wide association studies. Bioinformatics. 2011, 27: 1-8. 10.1093\/bioinformatics\/btq600.","journal-title":"Bioinformatics"},{"issue":"6","key":"5329_CR12","doi-asserted-by":"publisher","first-page":"714","DOI":"10.1093\/bioinformatics\/btp041","volume":"25","author":"TT Wu","year":"2009","unstructured":"Wu TT, Chen YF, Hastie T, Sobel E, Lange K: Genome-wide association analysis by lasso penalized logistic regression. Bioinformatics. 2009, 25 (6): 714-721. 10.1093\/bioinformatics\/btp041.","journal-title":"Bioinformatics"},{"key":"5329_CR13","volume-title":"Science","author":"P Sebastiani","year":"2010","unstructured":"Sebastiani P, Solovieff N, Puca A, Hartley SW, Melista E, Andersen S, Dworkis DA, Wilk JB, Myers RH, Steinberg MH, Montano M, Baldwin CT, Perls TT: Genetic Signatures of Exceptional Longevity in Humans. Science. 2010, science.1190532+"},{"issue":"4","key":"5329_CR14","doi-asserted-by":"publisher","first-page":"445","DOI":"10.1093\/bioinformatics\/btp713","volume":"26","author":"JH Moore","year":"2010","unstructured":"Moore JH, Asselbergs FW, Williams SM: Bioinformatics challenges for genome-wide association studies. Bioinformatics. 2010, 26 (4): 445-455. 10.1093\/bioinformatics\/btp713.","journal-title":"Bioinformatics"},{"key":"5329_CR15","volume-title":"Machine Learning","author":"TM Mitchell","year":"1997","unstructured":"Mitchell TM: Machine Learning. 1997, New York: McGraw-Hill"},{"issue":"5","key":"5329_CR16","doi-asserted-by":"publisher","first-page":"412","DOI":"10.1093\/bioinformatics\/16.5.412","volume":"16","author":"P Baldi","year":"2000","unstructured":"Baldi P, Brunak S, Chauvin Y, Andersen CAF, Nielsen H: Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics. 2000, 16 (5): 412-424. 10.1093\/bioinformatics\/16.5.412.","journal-title":"Bioinformatics"},{"issue":"2","key":"5329_CR17","first-page":"123","volume":"24","author":"L Breiman","year":"1996","unstructured":"Breiman L: Bagging Predictors. Machine Learning. 1996, 24 (2): 123-140.","journal-title":"Machine Learning"},{"key":"5329_CR18","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4899-4541-9","volume-title":"An Introduction to the Bootstrap","author":"B Efron","year":"1993","unstructured":"Efron B, Tibshirani RJ: An Introduction to the Bootstrap. 1993, New York: Chapman & Hall"},{"key":"5329_CR19","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1023\/A:1010933404324","volume":"45","author":"L Breiman","year":"2001","unstructured":"Breiman L: Random Forests. Machine Learning. 2001, 45: 5-32. 10.1023\/A:1010933404324.","journal-title":"Machine Learning"},{"issue":"8","key":"5329_CR20","doi-asserted-by":"publisher","first-page":"879","DOI":"10.1002\/gepi.20543","volume":"34","author":"KL Ayers","year":"2010","unstructured":"Ayers KL, Cordell HJ: SNP selection in genome-wide and candidate gene studies via penalized logistic regression. Genet Epidemiol. 2010, 34 (8): 879-91. 10.1002\/gepi.20543.","journal-title":"Genet Epidemiol"},{"key":"5329_CR21","unstructured":"T1DBase. [http:\/\/www.t1dbase.org]"},{"key":"5329_CR22","first-page":"349","volume-title":"Database and Expert Systems Applications, Volume 4653 of Lecture Notes in Computer Science","author":"A Prinzie","year":"2007","unstructured":"Prinzie A, Van den Poel D: Random Multiclass Classification: Generalizing Random Forests to Random MNL and Random NB. Database and Expert Systems Applications, Volume 4653 of Lecture Notes in Computer Science. 2007, Springer, Heidelberg, 349-358."},{"issue":"6","key":"5329_CR23","doi-asserted-by":"publisher","first-page":"415","DOI":"10.1038\/nrg2779","volume":"11","author":"ET Cirulli","year":"2010","unstructured":"Cirulli ET, Goldstein DB: Uncovering the roles of rare variants in common disease through whole-genome sequencing. Nature Reviews Genetics. 2010, 11 (6): 415-425. 10.1038\/nrg2779.","journal-title":"Nature Reviews Genetics"},{"issue":"6","key":"5329_CR24","doi-asserted-by":"publisher","first-page":"446","DOI":"10.1038\/nrg2809","volume":"11","author":"EE Eichler","year":"2010","unstructured":"Eichler EE, Flint J, Gibson G, Kong A, Leal SM, Moore JH, Nadeau JH: Missing heritability and strategies for finding the underlying causes of complex disease. Nature reviews Genetics. 2010, 11 (6): 446-450. 10.1038\/nrg2809.","journal-title":"Nature reviews Genetics"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-13-S14-S2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T19:46:32Z","timestamp":1630525592000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-13-S14-S2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,9]]},"references-count":24,"journal-issue":{"issue":"S14","published-print":{"date-parts":[[2012,9]]}},"alternative-id":["5329"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-13-s14-s2","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2012,9]]},"assertion":[{"value":"7 September 2012","order":1,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"S2"}}