{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,9]],"date-time":"2026-03-09T00:41:24Z","timestamp":1773016884487,"version":"3.50.1"},"reference-count":31,"publisher":"Springer Science and Business Media LLC","issue":"1","funder":[{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","award":["MR\/M01326X\/1"],"award-info":[{"award-number":["MR\/M01326X\/1"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000266","name":"Engineering and Physical Sciences Research Council","doi-asserted-by":"publisher","award":["EP\/K008250\/1"],"award-info":[{"award-number":["EP\/K008250\/1"]}],"id":[{"id":"10.13039\/501100000266","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000265","name":"Medical Research Council","doi-asserted-by":"publisher","award":["MCUU12013\/8"],"award-info":[{"award-number":["MCUU12013\/8"]}],"id":[{"id":"10.13039\/501100000265","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2017,12]]},"DOI":"10.1186\/s12859-017-1862-y","type":"journal-article","created":{"date-parts":[[2017,10,6]],"date-time":"2017-10-06T12:23:19Z","timestamp":1507292599000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":50,"title":["An integrative approach to predicting the functional effects of small indels in non-coding regions of the human genome"],"prefix":"10.1186","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-1812-9286","authenticated-orcid":false,"given":"Michael","family":"Ferlaino","sequence":"first","affiliation":[]},{"given":"Mark F.","family":"Rogers","sequence":"additional","affiliation":[]},{"given":"Hashem A.","family":"Shihab","sequence":"additional","affiliation":[]},{"given":"Matthew","family":"Mort","sequence":"additional","affiliation":[]},{"given":"David N.","family":"Cooper","sequence":"additional","affiliation":[]},{"given":"Tom R.","family":"Gaunt","sequence":"additional","affiliation":[]},{"given":"Colin","family":"Campbell","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2017,10,6]]},"reference":[{"key":"1862_CR1","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1002\/humu.22225","volume":"34","author":"HA Shihab","year":"2013","unstructured":"Shihab HA, Gough J, Cooper DN, Stenson PD, Barker GL, Edwards KJ, Day IN, Gaunt TR. Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden markov models. Hum Mutat. 2013; 34:57\u201365.","journal-title":"Hum Mutat"},{"key":"1862_CR2","doi-asserted-by":"crossref","first-page":"310","DOI":"10.1038\/ng.2892","volume":"46","author":"M Kircher","year":"2014","unstructured":"Kircher M, Witten DM, Jain P, O\u2019Roak BJ, Cooper GM, Shendure J. A general framework for estimating the relative pathogenicity of human genetic variants. Nat Genet. 2014; 46:310\u20135.","journal-title":"Nat Genet"},{"key":"1862_CR3","doi-asserted-by":"crossref","first-page":"294","DOI":"10.1038\/nmeth.2832","volume":"11","author":"GR Ritchie","year":"2014","unstructured":"Ritchie GR, Dunham I, Zeggini E, Flicek P. Functional annotation of noncoding sequence variants. Nat Methods. 2014; 11:294\u20136.","journal-title":"Nat Methods"},{"key":"1862_CR4","doi-asserted-by":"crossref","first-page":"761","DOI":"10.1093\/bioinformatics\/btu703","volume":"31","author":"D Quang","year":"2015","unstructured":"Quang D, Chen Y, Xie X. Dann: a deep learning approach for annotating the pathogenicity of genetic variants. Bioinformatics. 2015; 31:761\u2013763.","journal-title":"Bioinformatics"},{"key":"1862_CR5","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1002\/humu.22911","volume":"37","author":"C Douville","year":"2016","unstructured":"Douville C, Masica DL, Stenson PD, Cooper DN, Gygax DM, Kim R, Ryan M, Karchin R. Assessing the pathogenicity of insertion and deletion variants with the variant effect scoring tool (vest-indel). Hum Mutat. 2016; 37:28\u201335.","journal-title":"Hum Mutat"},{"key":"1862_CR6","doi-asserted-by":"crossref","first-page":"1599","DOI":"10.1093\/bioinformatics\/btu862","volume":"31","author":"L Folkman","year":"2015","unstructured":"Folkman L, Yang Y, Li Z, Stantic B, Sattar A, Mort M, Cooper DN, Liu Y, Zhou Y. Ddig-in: detecting disease-causing genetic variations due to frameshifting indels and nonsense mutations employing sequence and structural properties at nucleotide and protein levels. Bioinformatics. 2015; 31:1599\u20131606.","journal-title":"Bioinformatics"},{"key":"1862_CR7","doi-asserted-by":"crossref","first-page":"R9","DOI":"10.1186\/gb-2012-13-2-r9","volume":"13","author":"J Hu","year":"2012","unstructured":"Hu J, Ng PC. Predicting the effects of frameshifting indels. Genome Biol. 2012; 13:R9. doi: 10.1186\/gb-2012-13-2-r9 .","journal-title":"Genome Biol."},{"key":"1862_CR8","doi-asserted-by":"crossref","first-page":"861","DOI":"10.1038\/nrg3074","volume":"12","author":"M Esteller","year":"2011","unstructured":"Esteller M. Non-coding rnas in human disease. Nat Rev Genet. 2011; 12:861\u201374.","journal-title":"Nat Rev Genet"},{"key":"1862_CR9","doi-asserted-by":"crossref","first-page":"1026","DOI":"10.1038\/ng.915","volume":"43","author":"L de Pontual","year":"2011","unstructured":"de Pontual L, Yao E, Callier P, Faivre L, Drouin V, Cariou S, Van Haeringen A, Genevi\u00e8ve D, Goldenberg A, Oufadem M, Manouvrier S, Munnich A, Vidigal JA, Vekemans M, Lyonnet S, Henrion-Caude A, Ventura A, Amiel J. Germline deletion of the mir-17-92 cluster causes skeletal and growth defects in humans. Nat Genet. 2011; 43:1026\u201330.","journal-title":"Nat Genet"},{"issue":"6","key":"1862_CR10","doi-asserted-by":"crossref","first-page":"e1002128","DOI":"10.1371\/journal.pgen.1002128","volume":"7","author":"X Luo","year":"2011","unstructured":"Luo X, Yang W, Ye DQ, Cui H, Zhang Y, Hirankarn N, Qian X, Tang Y, Lau YL, de Vries N, Tak PP, Tsao BP, Shen N. A functional variant in microrna-146a promoter modulates its expression and confers disease risk for systemic lupus erythematosus. PLoS Genet. 2011; 7(6):e1002128. doi: 10.1371\/journal.pgen.1002128 .","journal-title":"PLoS Genet."},{"key":"1862_CR11","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1093\/hmg\/ddv259","volume":"24","author":"F Zhang","year":"2015","unstructured":"Zhang F, Lupski JR. Non-coding genetic variants in human disease. Hum Mol Genet. 2015; 24:102\u201310.","journal-title":"Hum Mol Genet"},{"key":"1862_CR12","doi-asserted-by":"crossref","first-page":"980","DOI":"10.1093\/nar\/gkt1113","volume":"42","author":"MJ Landrum","year":"2014","unstructured":"Landrum MJ, Lee JM, Riley GR, Jang W, Rubinstein WS, Church DM, Maglott DR. Clinvar: public archive of relationships among sequence variation and human phenotype. Nucleic Acids Res. 2014; 42:980\u20135.","journal-title":"Nucleic Acids Res"},{"key":"1862_CR13","doi-asserted-by":"crossref","first-page":"216","DOI":"10.1038\/nature11690","volume":"493","author":"W Fu","year":"2013","unstructured":"Fu W, O\u2019Connor TD, Jun G, Kang HM, Abecasis G, Leal SM, Gabriel S, Rieder MJ, Altshuler D, Shendure J, Nickerson DA, Bamshad MJ, NHLBI Exome Sequencing Project, Akey JM. Analysis of 6,515 exomes reveals the recent origin of most human protein-coding variants. Nature. 2013; 493:216\u201320.","journal-title":"Nature"},{"key":"1862_CR14","doi-asserted-by":"crossref","first-page":"8","DOI":"10.3389\/fbioe.2015.00008","volume":"3","author":"G Narzisi","year":"2015","unstructured":"Narzisi G, Schatz MC. The challenge of small-scale repeats for indel discovery. Front Bioeng Biotechnol. 2015; 3:8. doi:doi:103389\/fbioe.2015.00008.","journal-title":"Front Bioeng Biotechnol"},{"key":"1862_CR15","doi-asserted-by":"crossref","first-page":"1536","DOI":"10.1093\/bioinformatics\/btv009","volume":"31","author":"HA Shihab","year":"2015","unstructured":"Shihab HA, Rogers MF, Gough J, Mort M, Cooper DN, Day IN, Gaunt TR, Campbell C. An integrative approach to predicting the functional effects of non-coding and coding sequence variation. Bioinformatics. 2015; 31:1536\u201343.","journal-title":"Bioinformatics"},{"key":"1862_CR16","doi-asserted-by":"crossref","first-page":"1034","DOI":"10.1101\/gr.3715005","volume":"15","author":"A Siepel","year":"2005","unstructured":"Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, Weinstock GM, Wilson RK, Gibbs RA, Kent WJ, Miller W, Haussler D. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genom Res. 2005; 15:1034\u201350.","journal-title":"Genom Res"},{"key":"1862_CR17","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1101\/gr.097857.109","volume":"20","author":"KS Pollard","year":"2010","unstructured":"Pollard KS, Hubisz MJ, Rosenbloom KR, Siepel A. Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res. 2010; 20:110\u201321.","journal-title":"Genome Res"},{"key":"1862_CR18","doi-asserted-by":"crossref","DOI":"10.1017\/CBO9780511809682","volume-title":"Kernel Methods for Pattern Analysis","author":"J Shawe-Taylor","year":"2004","unstructured":"Shawe-Taylor J, Cristianini N. Kernel Methods for Pattern Analysis. Cambridge: Cambridge University Press; 2004."},{"key":"1862_CR19","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-031-01552-6","volume-title":"Learning with Support Vector Machines","author":"C Campbell","year":"2011","unstructured":"Campbell C, Ying Y. Learning with Support Vector Machines. USA: Morgan and Claypool; 2011."},{"issue":"10","key":"1862_CR20","doi-asserted-by":"crossref","first-page":"e1000173","DOI":"10.1371\/journal.pcbi.1000173","volume":"4","author":"A Ben-Hur","year":"2008","unstructured":"Ben-Hur A, Ong CS, Sonnenburg S, Sch\u00f6lkopf B, R\u00e4tsch G. Support vector machines and kernels for computational biology. PLoS Comput Biol. 2008; 4(10):e1000173. doi: 10.1371\/journal.pcbi.1000173 .","journal-title":"PLoS Comput Biol."},{"issue":"4","key":"1862_CR21","doi-asserted-by":"crossref","first-page":"e1005465","DOI":"10.1371\/journal.pcbi.1005465","volume":"13","author":"F Afsar Minhas","year":"2017","unstructured":"Afsar Minhas F, Ross ED, Ben-Hur A. Amino acid composition predicts prion activity. PLoS Comput Biol. 2017; 13(4):e1005465. https:\/\/doi.org\/10.1371\/journal.pcbi.1005465 .","journal-title":"PLoS Comput Biol."},{"key":"1862_CR22","volume-title":"Advances in Large Margin Classifiers","author":"J Platt","year":"1999","unstructured":"Platt J. Probabilities for sv machines In: Smola J, Bartlett PL, Sch\u00f6lkopf B, Schuurmans D, editors. Advances in Large Margin Classifiers. Massachusetts: MIT Press: 1999. p. 61\u201374."},{"key":"1862_CR23","first-page":"2079","volume":"11","author":"GC Cawley","year":"2010","unstructured":"Cawley GC, Talbot NLC. On over-fitting in model selection and subsequent selection bias in performance evaluation. J Mach Learn Res. 2010; 11:2079\u2013107.","journal-title":"J Mach Learn Res"},{"key":"1862_CR24","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1186\/s13059-016-1141-7","volume":"18","author":"Velde van der","year":"2017","unstructured":"van der Velde KJ, de Boer EN, van Diemen CC, Sikkema-Raddatz B, Abbott KM, Knopperts A, Franke L, Sijmons RH, de Koning TJ, Wijmenga C, Sinke RJ, Swertz MA. Gavin: Gene-aware variant interpretation for medical sequencing. Genome Biol. 2017; 18:6. doi: 10.1186\/s13059-016-1141-7 .","journal-title":"Genome Biol."},{"key":"1862_CR25","doi-asserted-by":"crossref","first-page":"665","DOI":"10.1007\/s00439-017-1779-6","volume":"136","author":"PD Stenson","year":"2017","unstructured":"Stenson PD, Mort M, Ball EV, Evans K, Hayden M, Heywood S, Hussain M, Phillips AD, Cooper DN. The human gene mutation database: towards a comprehensive repository of inherited mutation data for medical research, genetic diagnosis and next-generation sequencing studies. Hum Genet. 2017; 136:665\u201377.","journal-title":"Hum Genet"},{"key":"1862_CR26","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1148\/radiology.143.1.7063747","volume":"143","author":"JA Hanley","year":"1982","unstructured":"Hanley JA, McNeil BJ. The meaning and use of the area under a receiver operating characteristic (roc) curve. Radiology. 1982; 143:29\u201336.","journal-title":"Radiology"},{"key":"1862_CR27","doi-asserted-by":"crossref","first-page":"68","DOI":"10.1038\/nature15393","volume":"526","author":"The 1000 Genomes Project Consortium","year":"2015","unstructured":"The 1000 Genomes Project Consortium. A global reference for human genetic variation. Nature. 2015; 526:68\u201374.","journal-title":"Nature"},{"key":"1862_CR28","doi-asserted-by":"crossref","first-page":"994","DOI":"10.1038\/nature06611","volume":"21","author":"KE Lohmuelle","year":"2008","unstructured":"Lohmuelle KE, Indap AR, Schmidt S, Boyko AR, Hernandez RD, Hubisz MJ, Sninsky JJ, White TJ, Sunyaev SR, Nielsen R, Clark AG, Bustamante CD. Proportionally more deleterious genetic variation in european than in African populations. Nature. 2008; 21:994\u20137.","journal-title":"Nature"},{"key":"1862_CR29","doi-asserted-by":"crossref","first-page":"1245","DOI":"10.1101\/gr.6406307","volume":"17","author":"M Pheasant","year":"2007","unstructured":"Pheasant M, Mattick JS. Raising the estimate of functional human sequences. Genome Res. 2007; 17:1245\u201353.","journal-title":"Genome Res"},{"key":"1862_CR30","first-page":"2211","volume":"12","author":"M G\u00f6nen","year":"2011","unstructured":"G\u00f6nen M, Alpaydin E. Multiple kernel learning algorithms. J Mach Learn Res. 2011; 12:2211\u201368.","journal-title":"J Mach Learn Res"},{"key":"1862_CR31","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nature11247","volume":"489","author":"The ENCODE Project Consortium","year":"2012","unstructured":"The ENCODE Project Consortium. An integrated encyclopedia of dna elements in the human genome. Nature. 2012; 489:57\u201374.","journal-title":"Nature"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-017-1862-y.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,8,4]],"date-time":"2022-08-04T02:01:41Z","timestamp":1659578501000},"score":1,"resource":{"primary":{"URL":"http:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-017-1862-y"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,10,6]]},"references-count":31,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2017,12]]}},"alternative-id":["1862"],"URL":"https:\/\/doi.org\/10.1186\/s12859-017-1862-y","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,10,6]]},"article-number":"442"}}