{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,9]],"date-time":"2026-07-09T15:50:42Z","timestamp":1783612242593,"version":"3.55.0"},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"W1","license":[{"start":{"date-parts":[[2018,5,11]],"date-time":"2018-05-11T00:00:00Z","timestamp":1525996800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"London Charity Strategic Research Large Project","award":["MGU0344"],"award-info":[{"award-number":["MGU0344"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018,7,2]]},"DOI":"10.1093\/nar\/gky399","type":"journal-article","created":{"date-parts":[[2018,4,30]],"date-time":"2018-04-30T23:14:26Z","timestamp":1525130066000},"page":"W109-W113","source":"Crossref","is-referenced-by-count":160,"title":["SNPnexus: assessing the functional relevance of genetic variation to facilitate the promise of precision medicine"],"prefix":"10.1093","volume":"46","author":[{"given":"Abu Z","family":"Dayem\u00a0Ullah","sequence":"first","affiliation":[{"name":"Bioinformatics Unit, Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jorge","family":"Oscanoa","sequence":"additional","affiliation":[{"name":"Bioinformatics Unit, Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2509-9599","authenticated-orcid":false,"given":"Jun","family":"Wang","sequence":"additional","affiliation":[{"name":"Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ai","family":"Nagano","sequence":"additional","affiliation":[{"name":"Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicholas R","family":"Lemoine","sequence":"additional","affiliation":[{"name":"Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claude","family":"Chelala","sequence":"additional","affiliation":[{"name":"Bioinformatics Unit, Centre for Molecular Oncology, Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK"},{"name":"Centre for Computational Biology, Life Sciences Initiative, Queen Mary University of London, London EC1M 6BQ, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2018,5,11]]},"reference":[{"key":"key\n\t\t\t\t20180630061751_B1","first-page":"W65","article-title":"SNPnexus: a web server for functional annotation of novel and publicly known genetic variants (2012 update)","volume":"40","author":"Dayem\u00a0Ullah","year":"2012","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180630061751_B2","first-page":"655","article-title":"SNPnexus: a web database for functional annotation of newly discovered and public domain Single Nucleotide Polymorphisms","volume":"25","author":"Chelala","year":"2009","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180630061751_B3","first-page":"437","article-title":"A practical guide for the functional annotation of genetic variations using SNPnexus","volume":"14","author":"Dayem\u00a0Ullah","year":"2013","journal-title":"Brief Bioinform."},{"key":"key\n\t\t\t\t20180630061751_B4","first-page":"718","article-title":"Tabix: fast retrieval of sequence features from generic TAB-delimited files","volume":"27","author":"Li","year":"2011","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180630061751_B5","first-page":"308","article-title":"dbSNP: the NCBI database of genetic variation","volume":"29","author":"Sherry","year":"2001","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180630061751_B6","first-page":"57","article-title":"An integrated encyclopedia of DNA elements in the human genome","volume":"489","author":"The ENCODE project consortium","year":"2012","journal-title":"Nature"},{"key":"key\n\t\t\t\t20180630061751_B7","first-page":"462","article-title":"A promoter-level mammalian expression atlas","volume":"507","author":"The FANTOM Consortium and the RIKEN PMI and CLST (DGT)","year":"2014","journal-title":"Nature"},{"key":"key\n\t\t\t\t20180630061751_B8","first-page":"56","article-title":"The Ensembl Regulatory Build","volume":"16","author":"Zerbino","year":"2015","journal-title":"Genome Biol."},{"key":"key\n\t\t\t\t20180630061751_B9","first-page":"310","article-title":"A general framework for estimating the relative pathogenicity of human genetic variants","volume":"46","author":"Kircher","year":"2014","journal-title":"Nat. genet."},{"key":"key\n\t\t\t\t20180630061751_B10","first-page":"931","article-title":"Predicting effects of noncoding variants with deep learning-based sequence model","volume":"12","author":"Zhou","year":"2015","journal-title":"Nat. Methods"},{"key":"key\n\t\t\t\t20180630061751_B11","first-page":"214","article-title":"A spectral approach integrating functional genomic annotations for coding and noncoding variants","volume":"48","author":"Ionita-Laza","year":"2016","journal-title":"Nat. Genet."},{"key":"key\n\t\t\t\t20180630061751_B12","first-page":"1536","article-title":"An integrative approach to predicting the functional effects of non-coding and coding sequence variation","volume":"31","author":"Shihab","year":"2015","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180630061751_B13","first-page":"276","article-title":"A method for calculating probabilities of fitness consequences for point mutations across the human genome","volume":"47","author":"Gulko","year":"2015","journal-title":"Nat. Genet."},{"key":"key\n\t\t\t\t20180630061751_B14","first-page":"480","article-title":"FunSeq2: a framework for prioritizing noncoding regulatory variants in cancer","volume":"15","author":"Fu","year":"2014","journal-title":"Genome Biol."},{"key":"key\n\t\t\t\t20180630061751_B15","first-page":"294","article-title":"Functional annotation of noncoding sequence variants","volume":"11","author":"Ritchie","year":"2014","journal-title":"Nat. Methods"},{"key":"key\n\t\t\t\t20180630061751_B16","first-page":"595","article-title":"A Whole-Genome analysis framework for effective identification of pathogenic regulatory variants in mendelian disease","volume":"99","author":"Smedley","year":"2016","journal-title":"Am. J. Hum. Genet."},{"key":"key\n\t\t\t\t20180630061751_B17","first-page":"285","article-title":"Analysis of protein-coding genetic variation in 60, 706 humans","volume":"536","author":"Lek","year":"2016","journal-title":"Nature"},{"key":"key\n\t\t\t\t20180630061751_B18","first-page":"D862","article-title":"ClinVar: public archive of interpretations of clinically relevant variants","volume":"44","author":"Landrum","year":"2016","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180630061751_B19","first-page":"431","article-title":"The genetic association database","volume":"36","author":"Becker","year":"2004","journal-title":"Nat. Genet."},{"key":"key\n\t\t\t\t20180630061751_B20","first-page":"D896","article-title":"The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog)","volume":"45","author":"MacArthur","year":"2017","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180630061751_B21","first-page":"D945","article-title":"COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer","volume":"39","author":"Forbe","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"key\n\t\t\t\t20180630061751_B22","first-page":"361","article-title":"Neoepitopes as cancer immunotherapy targets: key challenges and opportunities","volume":"9","author":"Brennick","year":"2017","journal-title":"Immunotherapy"},{"key":"key\n\t\t\t\t20180630061751_B23","first-page":"1123","article-title":"MuPeXI: Prediction of neo-epitopes from tumor sequencing data","volume":"66","author":"Bjerregaard","year":"2017","journal-title":"Cancer Immunol. Immunother."},{"key":"key\n\t\t\t\t20180630061751_B24","first-page":"1","article-title":"NetMHCpan, a method for MHC class I binding prediction beyond humans","volume":"61","author":"Hoof","year":"2009","journal-title":"Immunogenetics"},{"key":"key\n\t\t\t\t20180630061751_B25","first-page":"2174","article-title":"Automated benchmarking of peptide-MHC class I binding predictions","volume":"31","author":"Trolle","year":"2015","journal-title":"Bioinformatics"},{"key":"key\n\t\t\t\t20180630061751_B26","first-page":"1556","article-title":"Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR","volume":"10","author":"Yang","year":"2015","journal-title":"Nat. Protoc."},{"key":"key\n\t\t\t\t20180630061751_B27","first-page":"122","article-title":"The ensembl variant effect predictor","volume":"17","author":"McLaren","year":"2016","journal-title":"Genome Biol."},{"key":"key\n\t\t\t\t20180630061751_B28","first-page":"80","article-title":"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","volume":"6","author":"Cingolani","year":"2012","journal-title":"Fly"},{"key":"key\n\t\t\t\t20180630061751_B29","first-page":"622","article-title":"VAAST 2.0: Improved variant classification and Disease-Gene identification using a Conservation-Controlled amino acid substitution matrix","volume":"37","author":"Hu","year":"2013","journal-title":"Genet Epidemiol."},{"key":"key\n\t\t\t\t20180630061751_B30","first-page":"433","article-title":"wANNOVAR: annotating genetic variants for personal genomes via the web","volume":"49","author":"Chang","year":"2012","journal-title":"J. Med. Genet."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/academic.oup.com\/nar\/article-pdf\/46\/W1\/W109\/25110473\/gky399.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2018,6,30]],"date-time":"2018-06-30T06:18:28Z","timestamp":1530339508000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/46\/W1\/W109\/4994954"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,5,11]]},"references-count":30,"journal-issue":{"issue":"W1","published-online":{"date-parts":[[2018,5,11]]},"published-print":{"date-parts":[[2018,7,2]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gky399","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2018,7,2]]},"published":{"date-parts":[[2018,5,11]]}}}