{"id":"https://openalex.org/W2010124885","doi":"https://doi.org/10.1093/bib/bbt004","title":"A practical guide for the functional annotation of genetic variations using SNPnexus","display_name":"A practical guide for the functional annotation of genetic variations using SNPnexus","publication_year":2013,"publication_date":"2013-02-08","ids":{"openalex":"https://openalex.org/W2010124885","doi":"https://doi.org/10.1093/bib/bbt004","mag":"2010124885","pmid":"https://pubmed.ncbi.nlm.nih.gov/23395730"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbt004","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbt004","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5064899320","display_name":"Abu Z M Dayem Ullah","orcid":"https://orcid.org/0000-0002-2567-4648"},"institutions":[{"id":"https://openalex.org/I166337079","display_name":"Queen Mary University of London","ror":"https://ror.org/026zzn846","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I166337079"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"A. Z. Dayem Ullah","raw_affiliation_strings":["Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK","Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Barts Cancer Institute, Queen Mary University of London, London EC1M 6BQ, UK","institution_ids":["https://openalex.org/I166337079"]},{"raw_affiliation_string":"Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK","institution_ids":["https://openalex.org/I166337079"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025477800","display_name":"Nicholas R. Lemoine","orcid":"https://orcid.org/0000-0001-8675-058X"},"institutions":[{"id":"https://openalex.org/I166337079","display_name":"Queen Mary University of London","ror":"https://ror.org/026zzn846","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I166337079"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"N. R. Lemoine","raw_affiliation_strings":["Nicholas R. Lemoine is the director of Barts Cancer Institute at Queen Mary University of London. He is also the lead for the Centre for Experimental Cancer Medicine"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Nicholas R. Lemoine is the director of Barts Cancer Institute at Queen Mary University of London. He is also the lead for the Centre for Experimental Cancer Medicine","institution_ids":["https://openalex.org/I166337079"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5072249752","display_name":"Claude Chelala","orcid":"https://orcid.org/0000-0002-2488-0669"},"institutions":[{"id":"https://openalex.org/I166337079","display_name":"Queen Mary University of London","ror":"https://ror.org/026zzn846","country_code":"GB","type":"education","lineage":["https://openalex.org/I124357947","https://openalex.org/I166337079"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"C. Chelala","raw_affiliation_strings":["Claude Chelala is a senior lecturer in bioinformatics in the Centre for Molecular Oncology of Barts Cancer Institute at Queen Mary University of London"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Claude Chelala is a senior lecturer in bioinformatics in the Centre for Molecular Oncology of Barts Cancer Institute at Queen Mary University of London","institution_ids":["https://openalex.org/I166337079"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I166337079"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":2.9498,"has_fulltext":false,"cited_by_count":115,"citation_normalized_percentile":{"value":0.91272036,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"14","issue":"4","first_page":"437","last_page":"447"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9986000061035156,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9986000061035156,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.996999979019165,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9959999918937683,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.8079257607460022},{"id":"https://openalex.org/keywords/international-hapmap-project","display_name":"International HapMap Project","score":0.7425891160964966},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5814813375473022},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4810788333415985},{"id":"https://openalex.org/keywords/proteome","display_name":"Proteome","score":0.4715295732021332},{"id":"https://openalex.org/keywords/human-genetic-variation","display_name":"Human genetic variation","score":0.46237489581108093},{"id":"https://openalex.org/keywords/genotyping","display_name":"Genotyping","score":0.42996761202812195},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3821259140968323},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2878137528896332},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.231612890958786},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.22490033507347107},{"id":"https://openalex.org/keywords/human-genome","display_name":"Human genome","score":0.21909365057945251},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.14751306176185608},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10478931665420532}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.8079257607460022},{"id":"https://openalex.org/C177580304","wikidata":"https://www.wikidata.org/wiki/Q1147298","display_name":"International HapMap Project","level":5,"score":0.7425891160964966},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5814813375473022},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4810788333415985},{"id":"https://openalex.org/C104397665","wikidata":"https://www.wikidata.org/wiki/Q860947","display_name":"Proteome","level":2,"score":0.4715295732021332},{"id":"https://openalex.org/C40583040","wikidata":"https://www.wikidata.org/wiki/Q1502105","display_name":"Human genetic variation","level":5,"score":0.46237489581108093},{"id":"https://openalex.org/C31467283","wikidata":"https://www.wikidata.org/wiki/Q912147","display_name":"Genotyping","level":4,"score":0.42996761202812195},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3821259140968323},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2878137528896332},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.231612890958786},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.22490033507347107},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.21909365057945251},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.14751306176185608},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10478931665420532}],"mesh":[{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014644","descriptor_name":"Genetic Variation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060148","descriptor_name":"HapMap Project","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060148","descriptor_name":"HapMap Project","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060148","descriptor_name":"HapMap Project","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060148","descriptor_name":"HapMap Project","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbt004","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbt004","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23395730","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23395730","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17","score":0.47999998927116394}],"awards":[{"id":"https://openalex.org/G3492977537","display_name":null,"funder_award_id":"15310","funder_id":"https://openalex.org/F4320319985","funder_display_name":"Cancer Research UK"},{"id":"https://openalex.org/G8155851166","display_name":null,"funder_award_id":"12008","funder_id":"https://openalex.org/F4320319985","funder_display_name":"Cancer Research UK"}],"funders":[{"id":"https://openalex.org/F4320319985","display_name":"Cancer Research UK","ror":"https://ror.org/054225q67"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":33,"referenced_works":["https://openalex.org/W1980740976","https://openalex.org/W1985738984","https://openalex.org/W1989773675","https://openalex.org/W1996760543","https://openalex.org/W2013128868","https://openalex.org/W2014606320","https://openalex.org/W2017426710","https://openalex.org/W2026615227","https://openalex.org/W2038473742","https://openalex.org/W2046234948","https://openalex.org/W2048296798","https://openalex.org/W2059145105","https://openalex.org/W2084748297","https://openalex.org/W2085755265","https://openalex.org/W2095907724","https://openalex.org/W2101735289","https://openalex.org/W2107903949","https://openalex.org/W2111978305","https://openalex.org/W2116753165","https://openalex.org/W2117446594","https://openalex.org/W2119279196","https://openalex.org/W2120303297","https://openalex.org/W2122732537","https://openalex.org/W2125487751","https://openalex.org/W2130919037","https://openalex.org/W2140115103","https://openalex.org/W2145191876","https://openalex.org/W2147505003","https://openalex.org/W2151804955","https://openalex.org/W2152320398","https://openalex.org/W2162276444","https://openalex.org/W2163199119","https://openalex.org/W4210241463"],"related_works":["https://openalex.org/W4297689237","https://openalex.org/W1999913420","https://openalex.org/W2064719795","https://openalex.org/W1984899683","https://openalex.org/W2157224084","https://openalex.org/W2023828027","https://openalex.org/W2156866331","https://openalex.org/W2480643413","https://openalex.org/W2065292076","https://openalex.org/W2115824787"],"abstract_inverted_index":{"Broader":[0],"functional":[1,44],"annotation":[2,102],"of":[3,43,61,108],"known":[4],"as":[5,7,80,82],"well":[6,81],"putative":[8],"genetic":[9,91],"variations":[10],"is":[11],"a":[12,30,35],"valuable":[13],"mean":[14],"for":[15,46],"prioritizing":[16],"targets":[17],"in":[18],"disease":[19,92],"studies":[20],"and":[21,67,85,104],"large-scale":[22],"genotyping":[23],"projects.":[24],"In":[25],"this":[26],"article,":[27],"we":[28],"present":[29],"practical":[31],"guide":[32],"to":[33],"SNPnexus,":[34],"web-based":[36],"tool":[37],"that":[38],"provides":[39],"an":[40],"aggregate":[41],"set":[42],"annotations":[45],"genomic":[47],"variation":[48],"data":[49],"by":[50],"characterizing":[51],"related":[52,71],"consequences":[53],"at":[54],"the":[55,97,105],"transcriptome/proteome":[56],"levels":[57],"with":[58,76,88],"in-depth":[59],"analysis":[60],"potential":[62,77],"deleterious":[63],"effects,":[64],"inferring":[65],"physical":[66],"cytogenetic":[68],"mapping,":[69],"reporting":[70],"HapMap":[72],"data,":[73],"finding":[74],"overlaps":[75],"regulatory,":[78],"structural":[79],"conserved":[83],"elements":[84],"retrieving":[86],"links":[87],"previously":[89],"reported":[90],"studies.":[93],"We":[94],"focus":[95],"on":[96],"SNPnexus":[98],"query":[99],"system,":[100],"its":[101],"categories":[103],"biological":[106],"interpretation":[107],"results.":[109]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":6},{"year":2021,"cited_by_count":15},{"year":2020,"cited_by_count":13},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":21},{"year":2017,"cited_by_count":8},{"year":2016,"cited_by_count":6},{"year":2015,"cited_by_count":8},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":1}],"updated_date":"2026-07-10T07:45:09.275182","created_date":"2025-10-10T00:00:00"}