{"id":"https://openalex.org/W2153508883","doi":"https://doi.org/10.1093/bioinformatics/btp103","title":"An integrative scoring system for ranking SNPs by their potential deleterious effects","display_name":"An integrative scoring system for ranking SNPs by their potential deleterious effects","publication_year":2009,"publication_date":"2009-02-19","ids":{"openalex":"https://openalex.org/W2153508883","doi":"https://doi.org/10.1093/bioinformatics/btp103","mag":"2153508883","pmid":"https://pubmed.ncbi.nlm.nih.gov/19228803"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp103","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp103","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"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/A5110242139","display_name":"Phil Hyoun Lee","orcid":null},"institutions":[{"id":"https://openalex.org/I204722609","display_name":"Queen's University","ror":"https://ror.org/02y72wh86","country_code":"CA","type":"education","lineage":["https://openalex.org/I204722609"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"Phil Hyoun Lee","raw_affiliation_strings":["Computational Biology and Machine Learning Lab, School of Computing, Queen's University, Kingston, ON, K7L 3N6, Canada"],"affiliations":[{"raw_affiliation_string":"Computational Biology and Machine Learning Lab, School of Computing, Queen's University, Kingston, ON, K7L 3N6, Canada","institution_ids":["https://openalex.org/I204722609"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5043310715","display_name":"Hagit Shatkay","orcid":"https://orcid.org/0000-0001-6953-3970"},"institutions":[{"id":"https://openalex.org/I204722609","display_name":"Queen's University","ror":"https://ror.org/02y72wh86","country_code":"CA","type":"education","lineage":["https://openalex.org/I204722609"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Hagit Shatkay","raw_affiliation_strings":["Computational Biology and Machine Learning Lab, School of Computing, Queen's University, Kingston, ON, K7L 3N6, Canada"],"affiliations":[{"raw_affiliation_string":"Computational Biology and Machine Learning Lab, School of Computing, Queen's University, Kingston, ON, K7L 3N6, Canada","institution_ids":["https://openalex.org/I204722609"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5110242139"],"corresponding_institution_ids":["https://openalex.org/I204722609"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":4.1786,"has_fulltext":false,"cited_by_count":96,"citation_normalized_percentile":{"value":0.94906857,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"25","issue":"8","first_page":"1048","last_page":"1055"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","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/T10521","display_name":"RNA and protein synthesis mechanisms","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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9983999729156494,"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":0.9976000189781189,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/single-nucleotide-polymorphism","display_name":"Single-nucleotide polymorphism","score":0.8741225004196167},{"id":"https://openalex.org/keywords/snp-genotyping","display_name":"SNP genotyping","score":0.637227475643158},{"id":"https://openalex.org/keywords/snp","display_name":"SNP","score":0.6022630929946899},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5121957659721375},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5110279321670532},{"id":"https://openalex.org/keywords/human-genome","display_name":"Human genome","score":0.4975304901599884},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.49298664927482605},{"id":"https://openalex.org/keywords/genome-wide-association-study","display_name":"Genome-wide association study","score":0.4614914655685425},{"id":"https://openalex.org/keywords/genotyping","display_name":"Genotyping","score":0.45955953001976013},{"id":"https://openalex.org/keywords/genetic-association","display_name":"Genetic association","score":0.43144500255584717},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.37375372648239136},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.28668150305747986},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.2648235857486725},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.2623007893562317}],"concepts":[{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.8741225004196167},{"id":"https://openalex.org/C163691529","wikidata":"https://www.wikidata.org/wiki/Q7391886","display_name":"SNP genotyping","level":5,"score":0.637227475643158},{"id":"https://openalex.org/C139275648","wikidata":"https://www.wikidata.org/wiki/Q17134011","display_name":"SNP","level":5,"score":0.6022630929946899},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5121957659721375},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5110279321670532},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.4975304901599884},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.49298664927482605},{"id":"https://openalex.org/C106208931","wikidata":"https://www.wikidata.org/wiki/Q1098876","display_name":"Genome-wide association study","level":5,"score":0.4614914655685425},{"id":"https://openalex.org/C31467283","wikidata":"https://www.wikidata.org/wiki/Q912147","display_name":"Genotyping","level":4,"score":0.45955953001976013},{"id":"https://openalex.org/C186413461","wikidata":"https://www.wikidata.org/wiki/Q744727","display_name":"Genetic association","level":5,"score":0.43144500255584717},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.37375372648239136},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.28668150305747986},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.2648235857486725},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.2623007893562317}],"mesh":[{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","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":true},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btp103","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp103","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:19228803","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19228803","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.566.6454","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.566.6454","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://research.cs.queensu.ca/~shatkay/papers/Bioinformatics2009.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.800000011920929}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":28,"referenced_works":["https://openalex.org/W1991525204","https://openalex.org/W2010473234","https://openalex.org/W2023648355","https://openalex.org/W2039157797","https://openalex.org/W2046508931","https://openalex.org/W2060228768","https://openalex.org/W2109372707","https://openalex.org/W2111854851","https://openalex.org/W2112582434","https://openalex.org/W2117526725","https://openalex.org/W2122732537","https://openalex.org/W2123340910","https://openalex.org/W2127640118","https://openalex.org/W2129682060","https://openalex.org/W2134129243","https://openalex.org/W2134968568","https://openalex.org/W2142598435","https://openalex.org/W2148830266","https://openalex.org/W2149385661","https://openalex.org/W2155684118","https://openalex.org/W2157567137","https://openalex.org/W2158356009","https://openalex.org/W2162797435","https://openalex.org/W2164004777","https://openalex.org/W2916427899","https://openalex.org/W3215573568","https://openalex.org/W4210241463","https://openalex.org/W6684393416"],"related_works":["https://openalex.org/W2329658823","https://openalex.org/W3139651602","https://openalex.org/W4383816439","https://openalex.org/W2403925359","https://openalex.org/W2609704764","https://openalex.org/W2413478641","https://openalex.org/W2583457094","https://openalex.org/W2884795428","https://openalex.org/W2791888721","https://openalex.org/W3165207581"],"abstract_inverted_index":{"We":[0,20,110],"propose":[1],"a":[2,17,114],"new":[3],"integrative":[4],"scoring":[5,54],"system":[6,23,119],"for":[7,67,125],"prioritizing":[8],"SNPs":[9,71,89,137],"based":[10,90],"on":[11,91],"their":[12,92],"possible":[13],"deleterious":[14,88],"effects":[15],"within":[16],"probabilistic":[18],"framework.":[19],"applied":[21],"our":[22,118],"to":[24,133,139],"580":[25],"disease-susceptibility":[26],"genes":[27,49],"obtained":[28],"from":[29,75],"the":[30,42,59,62],"OMIM":[31],"(Online":[32],"Mendelian":[33],"Inheritance":[34],"in":[35],"Man)":[36],"database,":[37],"which":[38],"is":[39,72],"one":[40],"of":[41,47,61,77,86],"most":[43],"widely":[44],"used":[45],"databases":[46],"human":[48],"and":[50],"genetic":[51],"disorders.":[52],"The":[53],"results":[55],"clearly":[56],"show":[57],"that":[58,76,106,117],"distribution":[60],"functional":[63,97],"significance":[64],"(FS)":[65],"scores":[66,132],"already":[68,134],"known":[69,135],"disease-related":[70,136],"significantly":[73,129],"different":[74],"neutral":[78,140],"SNPs.":[79,141],"In":[80],"addition,":[81],"we":[82],"summarize":[83],"distinct":[84],"features":[85],"potentially":[87],"FS":[93,131],"score,":[94],"such":[95],"as":[96],"genomic":[98],"regions":[99],"where":[100],"they":[101,107],"occur":[102],"or":[103],"bio-molecular":[104],"functions":[105],"mainly":[108],"affect.":[109],"also":[111],"demonstrate,":[112],"through":[113],"comparative":[115],"study,":[116],"improves":[120],"upon":[121],"other":[122],"function-assessment":[123],"systems":[124],"SNPs,":[126],"by":[127],"assigning":[128],"higher":[130],"than":[138]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":7},{"year":2015,"cited_by_count":6},{"year":2014,"cited_by_count":16},{"year":2013,"cited_by_count":20},{"year":2012,"cited_by_count":15}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}
