{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,19]],"date-time":"2025-11-19T06:57:28Z","timestamp":1763535448481,"version":"3.37.3"},"reference-count":36,"publisher":"Springer Science and Business Media LLC","issue":"1","funder":[{"name":"FP7- People-2012-ITN","award":["316978"],"award-info":[{"award-number":["316978"]}]},{"name":"FP7 project EMTICS","award":["278367"],"award-info":[{"award-number":["278367"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2017,12]]},"DOI":"10.1186\/s12859-017-1752-3","type":"journal-article","created":{"date-parts":[[2017,7,17]],"date-time":"2017-07-17T11:54:43Z","timestamp":1500292483000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":18,"title":["Variant Ranker: a web-tool to rank genomic data according to functional significance"],"prefix":"10.1186","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0697-5541","authenticated-orcid":false,"given":"John","family":"Alexander","sequence":"first","affiliation":[]},{"given":"Dimitris","family":"Mantzaris","sequence":"additional","affiliation":[]},{"given":"Marianthi","family":"Georgitsi","sequence":"additional","affiliation":[]},{"given":"Petros","family":"Drineas","sequence":"additional","affiliation":[]},{"given":"Peristera","family":"Paschou","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2017,7,17]]},"reference":[{"doi-asserted-by":"crossref","unstructured":"Adzhubei IA, Schmidt S, Peshkin L, Ramensky VE, Gerasimova A, Bork P. A method and server for predicting damaging missense mutations. Nat Methods. 2010;7. Available from: https:\/\/www.nature.com\/nmeth\/journal\/v7\/n4\/full\/nmeth0410-248.html .","key":"1752_CR1","DOI":"10.1038\/nmeth0410-248"},{"issue":"7","key":"1752_CR2","doi-asserted-by":"crossref","first-page":"1073","DOI":"10.1038\/nprot.2009.86","volume":"4","author":"P Kumar","year":"2009","unstructured":"Kumar P, Henikoff S, Ng PC. Predicting the effects of coding non-synonymous variants on protein function using the SIFT algorithm. Nat Protoc. 2009; 4(7):1073\u201381.","journal-title":"Nat Protoc"},{"doi-asserted-by":"crossref","unstructured":"Schwarz JM, Rodelsperger C, Schuelke M, Seelow D. MutationTaster evaluates disease-causing potential of sequence alterations. 2010. Available from: http:\/\/www.nature.com\/nmeth\/journal\/v7\/n8\/full\/nmeth0810-575.html .","key":"1752_CR3","DOI":"10.1038\/nmeth0810-575"},{"doi-asserted-by":"crossref","unstructured":"Siepel A, Pollard K, Haussler D. New Methods for Detecting Lineage-Specific Selection In: Apostolico A, Guerra C, Istrail S, Pevzner P, Waterman M, editors. Research in Computational Molecular Biology SE - 17. vol. 3909 of Lecture Notes in Computer Science. Springer Berlin Heidelberg: 2006. p. 190\u2013205. Available from: http:\/\/dx.doi.org\/10.1007\/11732990_17 .","key":"1752_CR4","DOI":"10.1007\/11732990_17"},{"issue":"12","key":"1752_CR5","doi-asserted-by":"crossref","first-page":"i54","DOI":"10.1093\/bioinformatics\/btp190","volume":"25","author":"M Garber","year":"2009","unstructured":"Garber M, Guttman M, Clamp M, Zody MC, Friedman N, Xie X. Identifying novel constrained elements by exploiting biased substitution patterns. Bioinformatics. 2009; 25(12):i54\u2013i62. Available from: http:\/\/bioinformatics.oxfordjournals.org\/content\/25\/12\/i54.abstract . ( https:\/\/academic.oup.com\/bioinformatics\/article\/25\/12\/i54\/187307\/Identifying-novel-constrained-elements-by ).","journal-title":"Bioinformatics"},{"issue":"12","key":"1752_CR6","doi-asserted-by":"crossref","first-page":"e1001025","DOI":"10.1371\/journal.pcbi.1001025","volume":"6","author":"EV Davydov","year":"2010","unstructured":"Davydov EV, Goode DL, Sirota M, Cooper GM, Sidow A, Batzoglou S. Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++. PLoS Comput Biol. 2010; 6(12):e1001025. Available from: http:\/\/journals.plos.org\/ploscompbiol\/article?id=10.1371\/journal.pcbi.1001025 .","journal-title":"PLoS Comput Biol"},{"issue":"2","key":"1752_CR7","doi-asserted-by":"crossref","first-page":"80","DOI":"10.4161\/fly.19695","volume":"6","author":"P Cingolani","year":"2012","unstructured":"Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly. 2012; 6(2):80\u201392.","journal-title":"Fly"},{"issue":"1","key":"1752_CR8","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1038\/ng.499","volume":"42","author":"SB Ng","year":"2010","unstructured":"Ng SB, Buckingham KJ, Lee C, Bigham AW, Tabor HK, Dent KM, et al.Exome sequencing identifies the cause of a mendelian disorder. Nat Genet. 2010; 42(1):30\u20135. Available from: http:\/\/www.pubmedcentral.nih.gov\/articlerender.fcgi?artid=2847889&tool=pmcentrez&rendertype=abstract .","journal-title":"Nat Genet"},{"issue":"16","key":"1752_CR9","doi-asserted-by":"crossref","first-page":"e164","DOI":"10.1093\/nar\/gkq603","volume":"38","author":"K Wang","year":"2010","unstructured":"Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010; 38(16):e164. Available from: http:\/\/www.pubmedcentral.nih.gov\/articlerender.fcgi?artid=2938201&tool=pmcentrez&rendertype=abstract .","journal-title":"Nucleic Acids Res"},{"issue":"11","key":"1752_CR10","doi-asserted-by":"crossref","first-page":"1083","DOI":"10.1038\/nmeth.2656","volume":"10","author":"A Sifrim","year":"2013","unstructured":"Sifrim A, Popovic D, Tranchevent LC, Ardeshirdavani A, Sakai R, Konings P, et al.eXtasy: variant prioritization by genomic data fusion. Nat Meth. 2013; 10(11):1083\u20131084. Available from: https:\/\/www.nature.com\/nmeth\/journal\/v10\/n11\/full\/nmeth.2656.html .","journal-title":"Nat Meth."},{"issue":"3","key":"1752_CR11","doi-asserted-by":"crossref","first-page":"e1004237","DOI":"10.1371\/journal.pgen.1004237","volume":"10","author":"J Wu","year":"2014","unstructured":"Wu J, Li Y, Jiang R. Integrating Multiple Genomic Data to Predict Disease-Causing Nonsynonymous Single Nucleotide Variants in Exome Sequencing Studies. PLoS Genet. 2014; 10(3):e1004237. Available from: http:\/\/journals.plos.org\/plosgenetics\/article?id=10.1371\/journal.pgen.1004237 .","journal-title":"PLoS Genet"},{"issue":"9","key":"1752_CR12","doi-asserted-by":"crossref","first-page":"1529","DOI":"10.1101\/gr.123158.111","volume":"21","author":"M Yandell","year":"2011","unstructured":"Yandell M, Huff C, Hu H, Singleton M, Moore B, Xing J, et al. A probabilistic disease-gene finder for personal genomes A probabilistic disease-gene finder for personal genomes. Genome research. 2011; 21(9):1529\u201342. Available from: https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/21700766 .","journal-title":"Genome research"},{"issue":"7","key":"1752_CR13","doi-asserted-by":"crossref","first-page":"e53","DOI":"10.1093\/nar\/gkr1257","volume":"40","author":"MX Li","year":"2012","unstructured":"Li MX, Gui HS, Kwan JSH, Bao SY, Sham PC. A comprehensive framework for prioritizing variants in exome sequencing studies of Mendelian diseases. Nucleic Acids Res. 2012; 40(7):e53\u2013e53.","journal-title":"Nucleic Acids Res"},{"unstructured":"Danecek P, Auton A, Abecasis G, Albers CA, Banks E, Depristo MA, et al. The Variant Call Format and VCFtools. 2011.: p. 3\u20135. Available from: https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/21653522 .","key":"1752_CR14"},{"issue":"1","key":"1752_CR15","doi-asserted-by":"crossref","first-page":"44","DOI":"10.1038\/nprot.2008.211","volume":"4","author":"DW Huang","year":"2009","unstructured":"Huang DW, Lempicki RA, Sherman BT. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc. 2009; 4(1):44\u201357. Available from: http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/19131956 .","journal-title":"Nat Protoc"},{"issue":"1","key":"1752_CR16","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/nar\/gkn923","volume":"37","author":"DW Huang","year":"2009","unstructured":"Huang DW, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: Paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 2009; 37(1):1\u201313.","journal-title":"Nucleic Acids Res"},{"issue":"7422","key":"1752_CR17","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1038\/nature11632","volume":"491","author":"GR Abecasis","year":"2012","unstructured":"Abecasis GR, Auton A, Brooks LD, DePristo MA, Durbin RM, Handsaker RE, et al.An integrated map of genetic variation from 1,092 human genomes. Nature. 2012; 491(7422):56\u201365.","journal-title":"Nature"},{"unstructured":"NHLBI-ESP. Available from: https:\/\/esp.gs.washington.edu\/drupal\/ .","key":"1752_CR18"},{"unstructured":"Consortium EA, Lek M, Karczewski K, Minikel E, Samocha K, Banks E, et al. Analysis of protein-coding genetic variation in 60,706 humans. bioRxiv. 2015:030338. Available from: http:\/\/biorxiv.org\/lookup\/doi\/10.1101\/030338 .","key":"1752_CR19"},{"issue":"SUPPL. 1","key":"1752_CR20","doi-asserted-by":"crossref","first-page":"D61","DOI":"10.1093\/nar\/gkl842","volume":"35","author":"KD Pruitt","year":"2007","unstructured":"Pruitt KD, Tatusova T, Maglott DR. NCBI reference sequences (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2007; 35(SUPPL. 1):D61\u20135.","journal-title":"Nucleic Acids Res"},{"issue":"5","key":"1752_CR21","doi-asserted-by":"crossref","first-page":"942","DOI":"10.1101\/gr.1858004","volume":"14","author":"V Curwen","year":"2004","unstructured":"Curwen V, Eyras E, Andrews TD, Clarke L, Mongin E, Searle SMJ, et al.The Ensembl automatic gene annotation system. Genome Res. 2004; 14(5):942\u201350.","journal-title":"Genome Res"},{"issue":"9","key":"1752_CR22","doi-asserted-by":"crossref","first-page":"1553","DOI":"10.1101\/gr.092619.109","volume":"19","author":"S Chun","year":"2009","unstructured":"Chun S, Fay JC. Identification of deleterious mutations within three human genomes. Genome Res. 2009; 19(9):1553\u201361.","journal-title":"Genome Res"},{"issue":"8","key":"1752_CR23","doi-asserted-by":"crossref","first-page":"2125","DOI":"10.1093\/hmg\/ddu733","volume":"24","author":"C Dong","year":"2015","unstructured":"Dong C, Wei P, Jian X, Gibbs R, Boerwinkle E, Wang K, et al. Comparison and integration of deleteriousness prediction methods for nonsynonymous SNVs in whole exome sequencing studies. Hum Mol Genet. 2015; 24(8):2125\u201337. Available from: http:\/\/hmg.oxfordjournals.org\/content\/24\/8\/2125.abstract .","journal-title":"Hum Mol Genet"},{"issue":"17","key":"1752_CR24","doi-asserted-by":"crossref","first-page":"e118","DOI":"10.1093\/nar\/gkr407","volume":"39","author":"B Reva","year":"2011","unstructured":"Reva B, Antipin Y, Sander C. Predicting the functional impact of protein mutations: Application to cancer genomics. Nucleic Acids Res. 2011; 39(17):e118.","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"1752_CR25","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 GLA, Edwards KJ, et al. Predicting the Functional, Molecular, and Phenotypic Consequences of Amino Acid Substitutions using Hidden Markov Models. Hum Mutat. 2013; 34(1):57\u201365.","journal-title":"Hum Mutat"},{"issue":"8","key":"1752_CR26","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, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res. 2005; 15(8):1034\u201350. Available from: http:\/\/www.pubmedcentral.nih.gov\/articlerender.fcgi?artid=1182216&tool=pmcentrez&rendertype=abstract .","journal-title":"Genome Res"},{"issue":"Database issue","key":"1752_CR27","doi-asserted-by":"crossref","first-page":"D871","DOI":"10.1093\/nar\/gkq1017","volume":"39","author":"BJ Raney","year":"2011","unstructured":"Raney BJ, Cline MS, Rosenbloom KR, Dreszer TR, Learned K, Barber GP, et al. ENCODE whole-genome data in the UCSC genome browser (2011 update). Nucleic Acids Res. 2011; 39(Database issue):D871\u20135. Available from: http:\/\/dx.doi.org\/10.1093\/nar\/gkq1017 .","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"1752_CR28","doi-asserted-by":"crossref","first-page":"D1001","DOI":"10.1093\/nar\/gkt1229","volume":"42","author":"D Welter","year":"2014","unstructured":"Welter D, MacArthur J, Morales J, Burdett T, Hall P, Junkins H, et al. The NHGRI GWAS Catalog, a curated resource of SNP-trait associations. Nucleic Acids Res. 2014; 42(D1):D1001\u20136.","journal-title":"Nucleic Acids Res"},{"issue":"D1","key":"1752_CR29","doi-asserted-by":"crossref","first-page":"D862","DOI":"10.1093\/nar\/gkv1222","volume":"44","author":"MJ Landrum","year":"2015","unstructured":"Landrum MJ, Lee JM, Benson M, Brown G, Chao C, Chitipiralla S, et al. ClinVar: public archive of interpretations of clinically relevant variants. Nucleic Acids Res. 2015; 44(D1):D862\u20138. Available from: http:\/\/www.pubmedcentral.nih.gov\/articlerender.fcgi?artid=4702865&tool=pmcentrez&rendertype=abstract .","journal-title":"Nucleic Acids Res"},{"issue":"3","key":"1752_CR30","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(3):310\u2013315. Available from: http:\/\/www.ncbi.nlm.nih.gov\/pubmed\/24487276 .","journal-title":"Nat Genet"},{"issue":"62","key":"1752_CR31","first-page":"41","volume":"12","author":"GJ Lyon","year":"2011","unstructured":"Lyon GJ, Jiang T, Van Wijk R, Wang W, Bodily PM, Xing J, et al. Exome sequencing and unrelated findings in the context of complex disease research: ethical and clinical implications. Discov Med. 2011; 12(62):41\u201355. Available from: http:\/\/www.pubmedcentral.nih.gov\/articlerender.fcgi?artid=3544941&tool=pmcentrez&rendertype=abstract .","journal-title":"Discov Med"},{"doi-asserted-by":"crossref","unstructured":"Chang X, Wang K. wANNOVAR: annotating genetic variants for personal genomes via the web. 2012. Available from: https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/?term=22717648 .","key":"1752_CR32","DOI":"10.1136\/jmedgenet-2012-100918"},{"doi-asserted-by":"crossref","unstructured":"Alexander J, Potamianou H, Xing J, Deng L, Karagiannidis I, Tsetsos F, et al. Targeted re-sequencing approach of candidate genes implicates rare potentially functional variants in Tourette Syndrome etiology. 2016. Available from: http:\/\/journal.frontiersin.org\/article\/10.3389\/fnins.2016.00428 .","key":"1752_CR33","DOI":"10.3389\/fnins.2016.00428"},{"key":"1752_CR34","doi-asserted-by":"crossref","first-page":"199","DOI":"10.1016\/j.neurobiolaging.2016.03.012","volume":"42","author":"J Alexander","year":"2016","unstructured":"Alexander J, Kalev O, Mehrabian S, Traykov L, Raycheva M, Kanakis D, et al. Familial early-onset dementia with complex neuropathologic phenotype and genomic background. Neurobiol Aging. 2016; 42:199\u2013204. Available from: http:\/\/dx.doi.org\/10.1016\/j.neurobiolaging.2016.03.012 .","journal-title":"Neurobiol Aging"},{"issue":"252","key":"1752_CR35","doi-asserted-by":"crossref","first-page":"252ra123","DOI":"10.1126\/scitranslmed.3009262","volume":"6","author":"T Zemojtel","year":"2014","unstructured":"Zemojtel T, Kohler S, Mackenroth L, Jager M, Hecht J, Krawitz P, et al.Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome. Sci Transl Med. 2014; 6(252):252ra123\u2013252ra123. Available from: http:\/\/stm.sciencemag.org\/cgi\/doi\/10.1126\/scitranslmed.3009262 .","journal-title":"Sci Transl Med"},{"issue":"21","key":"1752_CR36","doi-asserted-by":"crossref","first-page":"2810","DOI":"10.1093\/bioinformatics\/btt487","volume":"29","author":"C Fresno","year":"2013","unstructured":"Fresno C, Fernandez EA. RDAVIDWebService: a versatile R interface to DAVID. Bioinformatics (Oxford, England). 2013; 29(21):2810\u20131.","journal-title":"Bioinformatics (Oxford, England)"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12859-017-1752-3.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,9,30]],"date-time":"2019-09-30T11:44:37Z","timestamp":1569843877000},"score":1,"resource":{"primary":{"URL":"http:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/s12859-017-1752-3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2017,7,17]]},"references-count":36,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2017,12]]}},"alternative-id":["1752"],"URL":"https:\/\/doi.org\/10.1186\/s12859-017-1752-3","relation":{},"ISSN":["1471-2105"],"issn-type":[{"type":"electronic","value":"1471-2105"}],"subject":[],"published":{"date-parts":[[2017,7,17]]},"article-number":"341"}}