{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,8]],"date-time":"2026-05-08T07:48:26Z","timestamp":1778226506215,"version":"3.51.4"},"reference-count":30,"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":[[2017,12]]},"DOI":"10.1186\/s12859-017-1896-1","type":"journal-article","created":{"date-parts":[[2017,12,28]],"date-time":"2017-12-28T08:30:09Z","timestamp":1514449809000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["Effective computational detection of piRNAs using n-gram models and support vector machine"],"prefix":"10.1186","volume":"18","author":[{"given":"Chun-Chi","family":"Chen","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaoning","family":"Qian","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Byung-Jun","family":"Yoon","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2017,12,28]]},"reference":[{"issue":"5785","key":"1896_CR1","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1126\/science.1130164","volume":"313","author":"NC Lau","year":"2006","unstructured":"Lau NC, Seto AG, Kim J, Kuramochi-Miyagawa S, Nakano T, Bartel DP, Kingston RE. Characterization of the piRNA complex from rat testes. Science. 2006; 313(5785):363\u20137.","journal-title":"Science"},{"issue":"5851","key":"1896_CR2","doi-asserted-by":"crossref","first-page":"761","DOI":"10.1126\/science.1146484","volume":"318","author":"AA Aravin","year":"2007","unstructured":"Aravin AA, Hannon GJ, Brennecke J. The Piwi-piRNA pathway provides an adaptive defense in the transposon arms race. Science. 2007; 318(5851):761\u20134.","journal-title":"Science"},{"issue":"18","key":"1896_CR3","doi-asserted-by":"crossref","first-page":"3458","DOI":"10.1242\/dev.094037","volume":"141","author":"E-M Weick","year":"2014","unstructured":"Weick E-M, Miska EA. piRNAs: from biogenesis to function. Development. 2014; 141(18):3458\u201371.","journal-title":"Development"},{"issue":"1","key":"1896_CR4","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1016\/j.canlet.2013.04.008","volume":"336","author":"Y Mei","year":"2013","unstructured":"Mei Y, Clark D, Mao L. Novel dimensions of piRNAs in cancer. Cancer Lett. 2013; 336(1):46\u201352.","journal-title":"Cancer Lett"},{"issue":"1","key":"1896_CR5","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1186\/s12943-016-0491-9","volume":"15","author":"KW Ng","year":"2016","unstructured":"Ng KW, Anderson C, Marshall EA, Minatel BC, Enfield KS, Saprunoff HL, Lam WL, Martinez VD. Piwi-interacting RNAs in cancer: emerging functions and clinical utility. Mol Cancer. 2016; 15(1):5.","journal-title":"Mol Cancer"},{"issue":"5","key":"1896_CR6","doi-asserted-by":"crossref","first-page":"603","DOI":"10.1016\/j.molcel.2007.05.021","volume":"26","author":"AG Seto","year":"2007","unstructured":"Seto AG, Kingston RE, Lau NC. The coming of age for Piwi proteins. Mol Cell. 2007; 26(5):603\u20139.","journal-title":"Mol Cell"},{"issue":"suppl 1","key":"1896_CR7","first-page":"D173\u20147","volume":"36","author":"SS Lakshmi","year":"2008","unstructured":"Lakshmi SS, Agrawal S. piRNABank: a web resource on classified and clustered Piwi-interacting RNAs. Nucleic Acids Res. 2008; 36(suppl 1):D173\u20147.","journal-title":"Nucleic Acids Res"},{"issue":"7099","key":"1896_CR8","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1038\/nature04916","volume":"442","author":"A Aravin","year":"2006","unstructured":"Aravin A, Gaidatzis D, Pfeffer S, Lagos-Quintana M, Landgraf P, Iovino N, Morris P, Brownstein MJ, Kuramochi-Miyagawa S, Nakano T, et al.A novel class of small RNAs bind to MILI protein in mouse testes. Nature. 2006; 442(7099):203\u20137.","journal-title":"Nature"},{"issue":"9","key":"1896_CR9","doi-asserted-by":"crossref","first-page":"1397","DOI":"10.1261\/rna.659307","volume":"13","author":"Y Kirino","year":"2007","unstructured":"Kirino Y, Mourelatos Z. The mouse homolog of HEN1 is a potential methylase for Piwi-interacting RNAs. Rna. 2007; 13(9):1397\u2013401.","journal-title":"Rna"},{"issue":"11","key":"1896_CR10","doi-asserted-by":"crossref","first-page":"e222","DOI":"10.1371\/journal.pcbi.0030222","volume":"3","author":"D Betel","year":"2007","unstructured":"Betel D, Sheridan R, Marks DS, Sander C. Computational analysis of mouse piRNA sequence and biogenesis. PLoS Comput Biol. 2007; 3(11):e222.","journal-title":"PLoS Comput Biol"},{"issue":"6","key":"1896_CR11","doi-asserted-by":"crossref","first-page":"771","DOI":"10.1093\/bioinformatics\/btr016","volume":"27","author":"Y Zhang","year":"2011","unstructured":"Zhang Y, Wang X, Kang L. A k-mer scheme to predict piRNAs and characterize locust piRNAs. Bioinformatics. 2011; 27(6):771\u20136.","journal-title":"Bioinformatics"},{"issue":"7099","key":"1896_CR12","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1038\/nature04917","volume":"442","author":"A Girard","year":"2006","unstructured":"Girard A, Sachidanandam R, Hannon GJ, Carmell MA. A germline-specific class of small RNAs binds mammalian Piwi proteins. Nature. 2006; 442(7099):199\u2013202.","journal-title":"Nature"},{"issue":"1","key":"1896_CR13","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1186\/1759-8753-5-22","volume":"5","author":"S Yamanaka","year":"2014","unstructured":"Yamanaka S, Siomi MC, Siomi H. piRNA clusters and open chromatin structure. Mob DNA. 2014; 5(1):22.","journal-title":"Mob DNA"},{"issue":"8","key":"1896_CR14","doi-asserted-by":"crossref","first-page":"e1.005332","DOI":"10.1371\/journal.pgen.1005332","volume":"11","author":"AA Erwin","year":"2015","unstructured":"Erwin AA, Galdos MA, Wickersheim ML, Harrison CC, Marr KD, Colicchio JM, Blumenstiel JP. piRNAs are associated with diverse transgenerational effects on gene and transposon expression in a hybrid dysgenic syndrome of D. virilis. PLoS Genet. 2015; 11(8):e1.005332.","journal-title":"PLoS Genet"},{"issue":"1","key":"1896_CR15","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1186\/1471-2105-13-5","volume":"13","author":"D Rosenkranz","year":"2012","unstructured":"Rosenkranz D, Zischler H. proTRAC-a software for probabilistic piRNA cluster detection, visualization and analysis. BMC Bioinformatics. 2012; 13(1):5.","journal-title":"BMC Bioinformatics"},{"key":"1896_CR16","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1016\/j.compbiolchem.2014.01.008","volume":"50","author":"I Jung","year":"2014","unstructured":"Jung I, Park JC, Kim S. piClust: a density based piRNA clustering algorithm. Comput Biol Chem. 2014; 50:60\u20137.","journal-title":"Comput Biol Chem"},{"issue":"17","key":"1896_CR17","doi-asserted-by":"crossref","first-page":"i364\u201470","DOI":"10.1093\/bioinformatics\/btu441","volume":"30","author":"J Brayet","year":"2014","unstructured":"Brayet J, Zehraoui F, Jeanson-Leh L, Israeli D, Tahi F. Towards a piRNA prediction using multiple kernel fusion and support vector machine. Bioinformatics. 2014; 30(17):i364\u201470.","journal-title":"Bioinformatics"},{"key":"1896_CR18","doi-asserted-by":"crossref","first-page":"bau110","DOI":"10.1093\/database\/bau110","volume":"2014","author":"P Zhang","year":"2014","unstructured":"Zhang P, Si X, Skogerb\u00f8 G, Wang J, Cui D, Li Y, Sun X, Liu L, Sun B, Chen R, et al. piRBase: a web resource assisting piRNA functional study. Database. 2014; 2014:bau110.","journal-title":"Database"},{"issue":"4","key":"1896_CR19","doi-asserted-by":"crossref","first-page":"955","DOI":"10.1002\/prot.20373","volume":"58","author":"BYM Cheng","year":"2005","unstructured":"Cheng BYM, Carbonell JG, Klein-Seetharaman J. Protein classification based on text document classification techniques. Proteins Struct Funct Bioinforma. 2005; 58(4):955\u201370.","journal-title":"Proteins Struct Funct Bioinforma"},{"issue":"4","key":"1896_CR20","first-page":"393","volume":"10","author":"Q Dong","year":"2016","unstructured":"Dong Q, Wang K, Liu X. Identifying the missing proteins in human proteome by biological language model. BMC Syst Biol. 2016; 10(4):393.","journal-title":"BMC Syst Biol"},{"issue":"03","key":"1896_CR21","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1142\/S0218001402001691","volume":"16","author":"I Salvador","year":"2002","unstructured":"Salvador I, Benedi J-M. RNA modeling by combining stochastic context-free grammars and n-gram models. Int J Pattern Recognit Artif Intell. 2002; 16(03):309\u201315.","journal-title":"Int J Pattern Recognit Artif Intell"},{"issue":"2","key":"1896_CR22","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1016\/j.cmpb.2005.11.007","volume":"81","author":"A Tomovi\u0107","year":"2006","unstructured":"Tomovi\u0107 A, Jani\u010bi\u0107 P, Kes\u0307elj V. N-Gram-based classification and unsupervised hierarchical clustering of genome sequences. Comput Methods Prog Biomed. 2006; 81(2):137\u201353.","journal-title":"Comput Methods Prog Biomed"},{"issue":"6","key":"1896_CR23","doi-asserted-by":"crossref","first-page":"1089","DOI":"10.1016\/j.cell.2007.01.043","volume":"128","author":"J Brennecke","year":"2007","unstructured":"Brennecke J, Aravin AA, Stark A, Dus M, Kellis M, Sachidanandam R, Hannon GJ. Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell. 2007; 128(6):1089\u2013103.","journal-title":"Cell"},{"issue":"10","key":"1896_CR24","doi-asserted-by":"crossref","first-page":"1429","DOI":"10.1038\/cr.2012.120","volume":"22","author":"E Beyret","year":"2012","unstructured":"Beyret E, Liu N, Lin H. piRNA biogenesis during adult spermatogenesis in mice is independent of the ping-pong mechanism. Cell Res. 2012; 22(10):1429\u201339.","journal-title":"Cell Res"},{"key":"1896_CR25","volume-title":"Randomization, bootstrap and Monte Carlo methods in biology","author":"BF Manly","year":"2007","unstructured":"Manly BF. Randomization, bootstrap and Monte Carlo methods in biology. 3 edn. Boca Raton: Chapman & Hall\/CRC; 2007."},{"key":"1896_CR26","first-page":"27:1","volume":"2","author":"C-C Chang","year":"2011","unstructured":"Chang C-C, Lin C-J. LIBSVM: A library for support vector machines. ACM Trans Intell Syst Technol. 2011; 2:27:1\u201327:27. software available at http:\/\/www.csie.ntu.edu.tw\/~cjlin\/libsvm .","journal-title":"ACM Trans Intell Syst Technol"},{"issue":"1","key":"1896_CR27","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1093\/nar\/gkg006","volume":"31","author":"S Griffiths-Jones","year":"2003","unstructured":"Griffiths-Jones S, Bateman A, Marshall M, Khanna A, Eddy SR. Rfam: an RNA family database. Nucleic Acids Res. 2003; 31(1):439\u201341.","journal-title":"Nucleic Acids Res"},{"key":"1896_CR28","doi-asserted-by":"crossref","unstructured":"Nawrocki EP, Burge SW, Bateman A, Daub J, Eberhardt RY, Eddy SR, Floden EW, Gardner PP, Jones TA, Tate J, et al. Rfam 12.0: updates to the RNA families database. Nucleic Acids Res. 2014::gku1063.","DOI":"10.1093\/nar\/gku1063"},{"issue":"7","key":"1896_CR29","doi-asserted-by":"crossref","first-page":"1145","DOI":"10.1016\/S0031-3203(96)00142-2","volume":"30","author":"AP Bradley","year":"1997","unstructured":"Bradley AP. The use of the area under the ROC curve in the evaluation of machine learning algorithms. Pattern Recog. 1997; 30(7):1145\u201359.","journal-title":"Pattern Recog"},{"key":"1896_CR30","volume-title":"Conference of the Canadian Society for Computational Studies of Intelligence","author":"CX Ling","year":"2003","unstructured":"Ling CX, Huang J, Zhang H. AUC: a better measure than accuracy in comparing learning algorithms. In: Conference of the Canadian Society for Computational Studies of Intelligence. Berlin: Springer: 2003. p. 329\u201341."}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-017-1896-1.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,10,8]],"date-time":"2019-10-08T19:57:53Z","timestamp":1570564673000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-017-1896-1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,12]]},"references-count":30,"journal-issue":{"issue":"S14","published-print":{"date-parts":[[2017,12]]}},"alternative-id":["1896"],"URL":"https:\/\/doi.org\/10.1186\/s12859-017-1896-1","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,12]]},"article-number":"517"}}