{"id":"https://openalex.org/W2164982811","doi":"https://doi.org/10.1109/gensips.2012.6507722","title":"A Bayesian model for SNP discovery based on next-generation sequencing data","display_name":"A Bayesian model for SNP discovery based on next-generation sequencing data","publication_year":2012,"publication_date":"2012-12-01","ids":{"openalex":"https://openalex.org/W2164982811","doi":"https://doi.org/10.1109/gensips.2012.6507722","mag":"2164982811","pmid":"https://pubmed.ncbi.nlm.nih.gov/26726304"},"language":"en","primary_location":{"id":"doi:10.1109/gensips.2012.6507722","is_oa":false,"landing_page_url":"https://doi.org/10.1109/gensips.2012.6507722","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings 2012 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref","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/A5056825063","display_name":"Yanxun Xu","orcid":"https://orcid.org/0000-0001-5554-8637"},"institutions":[{"id":"https://openalex.org/I74775410","display_name":"Rice University","ror":"https://ror.org/008zs3103","country_code":"US","type":"education","lineage":["https://openalex.org/I74775410"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yanxun Xu","raw_affiliation_strings":["Department of Statistics Rice University Houston, TX","Department of Statistics, Rice University, Houston, TX, USA"],"affiliations":[{"raw_affiliation_string":"Department of Statistics Rice University Houston, TX","institution_ids":["https://openalex.org/I74775410"]},{"raw_affiliation_string":"Department of Statistics, Rice University, Houston, TX, USA","institution_ids":["https://openalex.org/I74775410"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103139999","display_name":"Xiaofeng Zheng","orcid":"https://orcid.org/0000-0002-3771-3632"},"institutions":[{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"funder","lineage":["https://openalex.org/I1343551460"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xiaofeng Zheng","raw_affiliation_strings":["Department of Bioinformatics and Computational Biology The University of Texas MD Anderson Cancer Center Houston, TX","Department of Bioinformatics and Computational Biology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics and Computational Biology The University of Texas MD Anderson Cancer Center Houston, TX","institution_ids":["https://openalex.org/I1343551460"]},{"raw_affiliation_string":"Department of Bioinformatics and Computational Biology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA","institution_ids":["https://openalex.org/I1343551460"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100334810","display_name":"Yuan Yuan","orcid":"https://orcid.org/0000-0003-4706-7897"},"institutions":[{"id":"https://openalex.org/I181547552","display_name":"Baylor College of Medicine","ror":"https://ror.org/02pttbw34","country_code":"US","type":"education","lineage":["https://openalex.org/I181547552","https://openalex.org/I2801539370"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yuan Yuan","raw_affiliation_strings":["Graduate Program in Structural and Computational Biology and Molecular Biophysics Baylor College of Medicine Houston, TX","Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX, USA"],"affiliations":[{"raw_affiliation_string":"Graduate Program in Structural and Computational Biology and Molecular Biophysics Baylor College of Medicine Houston, TX","institution_ids":["https://openalex.org/I181547552"]},{"raw_affiliation_string":"Graduate Program in Structural and Computational Biology and Molecular Biophysics, Baylor College of Medicine, Houston, TX, USA","institution_ids":["https://openalex.org/I181547552"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036633061","display_name":"Marcos R. Estecio","orcid":"https://orcid.org/0000-0002-6874-7413"},"institutions":[{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"funder","lineage":["https://openalex.org/I1343551460"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Marcos R Estecio","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology The University of Texas MD Anderson Cancer Center Houston, TX","Department of Biochemistry and Molecular Biology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA"],"affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology The University of Texas MD Anderson Cancer Center Houston, TX","institution_ids":["https://openalex.org/I1343551460"]},{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA","institution_ids":["https://openalex.org/I1343551460"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062330946","display_name":"Jean\u2010Pierre J. Issa","orcid":"https://orcid.org/0000-0003-2258-5030"},"institutions":[{"id":"https://openalex.org/I84392919","display_name":"Temple University","ror":"https://ror.org/00kx1jb78","country_code":"US","type":"education","lineage":["https://openalex.org/I84392919"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jean-Pierre Issa","raw_affiliation_strings":["Fels Institute for Cancer Research and Molecular Biology Temple University Philadelphia, PA","Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA, USA"],"affiliations":[{"raw_affiliation_string":"Fels Institute for Cancer Research and Molecular Biology Temple University Philadelphia, PA","institution_ids":["https://openalex.org/I84392919"]},{"raw_affiliation_string":"Fels Institute for Cancer Research and Molecular Biology, Temple University, Philadelphia, PA, USA","institution_ids":["https://openalex.org/I84392919"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080090747","display_name":"Yuan Ji","orcid":"https://orcid.org/0000-0003-4712-5567"},"institutions":[{"id":"https://openalex.org/I1339509835","display_name":"NorthShore University HealthSystem","ror":"https://ror.org/04tpp9d61","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1339509835"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yuan Ji","raw_affiliation_strings":["CCRI NorthShore University HealthSystem Chicago, IL","CCRI, NorthShore University HealthSystem, Chicago, IL, USA"],"affiliations":[{"raw_affiliation_string":"CCRI NorthShore University HealthSystem Chicago, IL","institution_ids":["https://openalex.org/I1339509835"]},{"raw_affiliation_string":"CCRI, NorthShore University HealthSystem, Chicago, IL, USA","institution_ids":["https://openalex.org/I1339509835"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5110445048","display_name":"Shoudan Liang","orcid":null},"institutions":[{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"funder","lineage":["https://openalex.org/I1343551460"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shoudan Liang","raw_affiliation_strings":["Department of Bioinformatics and Computational Biology The University of Texas MD Anderson Cancer Center Houston, TX","Department of Bioinformatics and Computational Biology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics and Computational Biology The University of Texas MD Anderson Cancer Center Houston, TX","institution_ids":["https://openalex.org/I1343551460"]},{"raw_affiliation_string":"Department of Bioinformatics and Computational Biology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA","institution_ids":["https://openalex.org/I1343551460"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5056825063"],"corresponding_institution_ids":["https://openalex.org/I74775410"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.12575507,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"2012","issue":null,"first_page":"42","last_page":"45"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9991999864578247,"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":0.9991999864578247,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9975000023841858,"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":0.9959999918937683,"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/dbsnp","display_name":"dbSNP","score":0.9918510913848877},{"id":"https://openalex.org/keywords/single-nucleotide-polymorphism","display_name":"Single-nucleotide polymorphism","score":0.7753154039382935},{"id":"https://openalex.org/keywords/snp","display_name":"SNP","score":0.7011042833328247},{"id":"https://openalex.org/keywords/tag-snp","display_name":"Tag SNP","score":0.577093243598938},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5083851218223572},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4657828211784363},{"id":"https://openalex.org/keywords/dna-sequencing","display_name":"DNA sequencing","score":0.44845953583717346},{"id":"https://openalex.org/keywords/snp-genotyping","display_name":"SNP genotyping","score":0.4170646667480469},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3886547386646271},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3649154603481293},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.23305729031562805},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1705910563468933}],"concepts":[{"id":"https://openalex.org/C35794970","wikidata":"https://www.wikidata.org/wiki/Q5243761","display_name":"dbSNP","level":5,"score":0.9918510913848877},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.7753154039382935},{"id":"https://openalex.org/C139275648","wikidata":"https://www.wikidata.org/wiki/Q17134011","display_name":"SNP","level":5,"score":0.7011042833328247},{"id":"https://openalex.org/C55060382","wikidata":"https://www.wikidata.org/wiki/Q7675093","display_name":"Tag SNP","level":5,"score":0.577093243598938},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5083851218223572},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4657828211784363},{"id":"https://openalex.org/C51679486","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"DNA sequencing","level":3,"score":0.44845953583717346},{"id":"https://openalex.org/C163691529","wikidata":"https://www.wikidata.org/wiki/Q7391886","display_name":"SNP genotyping","level":5,"score":0.4170646667480469},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3886547386646271},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3649154603481293},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.23305729031562805},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1705910563468933}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1109/gensips.2012.6507722","is_oa":false,"landing_page_url":"https://doi.org/10.1109/gensips.2012.6507722","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings 2012 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS)","raw_type":"proceedings-article"},{"id":"pmid:26726304","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26726304","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":"IEEE International Workshop on Genomic Signal Processing and Statistics : [proceedings]. IEEE International Workshop on Genomic Signal Processing and Statistics","raw_type":null},{"id":"pmh:oai:europepmc.org:3674519","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4697941","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.5899999737739563,"id":"https://metadata.un.org/sdg/3"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":13,"referenced_works":["https://openalex.org/W2044586667","https://openalex.org/W2055335889","https://openalex.org/W2059238813","https://openalex.org/W2074929099","https://openalex.org/W2090705041","https://openalex.org/W2102619694","https://openalex.org/W2112113834","https://openalex.org/W2122732537","https://openalex.org/W2124985265","https://openalex.org/W2127515057","https://openalex.org/W2137503836","https://openalex.org/W2152977846","https://openalex.org/W2170264612"],"related_works":["https://openalex.org/W2145418365","https://openalex.org/W2061407956","https://openalex.org/W45489710","https://openalex.org/W2101398264","https://openalex.org/W2168919926","https://openalex.org/W2331649876","https://openalex.org/W1504890006","https://openalex.org/W2377243617","https://openalex.org/W2019337456","https://openalex.org/W3139651602"],"abstract_inverted_index":{"A":[0,115],"single-nucleotide":[1],"polymorphism":[2],"(SNP)":[3],"is":[4,14],"a":[5,23,55,60,83,88,124],"single":[6],"base":[7],"change":[8],"in":[9,35,98,141],"the":[10,15,43,92,102,109],"DNA":[11],"sequence":[12],"and":[13,48,108],"most":[16],"common":[17],"polymorphism.":[18],"Since":[19],"some":[20],"SNPs":[21,30,97],"have":[22],"major":[24],"influence":[25],"on":[26],"disease":[27],"susceptibility,":[28],"detecting":[29],"plays":[31],"an":[32],"important":[33],"role":[34],"biomedical":[36],"research.":[37],"To":[38],"take":[39],"fully":[40],"advantage":[41],"of":[42,63,78,127],"next-generation":[44],"sequencing":[45],"(NGS)":[46],"technology":[47],"detect":[49,96],"SNP":[50],"more":[51],"effectively,":[52],"we":[53],"propose":[54],"Bayesian":[56],"approach":[57],"that":[58,132],"computes":[59],"posterior":[61,76],"probability":[62,77],"hidden":[64,79],"nucleotide":[65,80],"variations":[66],"at":[67],"each":[68],"covered":[69],"genomic":[70],"position.":[71],"The":[72,130],"position":[73],"with":[74,120],"higher":[75,84],"variation":[81],"has":[82],"chance":[85],"to":[86,95],"be":[87],"SNP.":[89],"We":[90],"apply":[91],"proposed":[93],"method":[94],"two":[99],"cell":[100,105,112],"lines:":[101],"prostate":[103],"cancer":[104],"line":[106,113],"PC3":[107],"embryonic":[110],"stem":[111],"H1.":[114],"comparison":[116],"between":[117],"our":[118,137],"results":[119],"dbSNP":[121,142],"database":[122],"shows":[123],"high":[125],"ratio":[126],"overlap":[128],"(>95%).":[129],"positions":[131],"are":[133],"called":[134],"only":[135],"under":[136],"model":[138],"but":[139],"not":[140],"may":[143],"serve":[144],"as":[145],"candidates":[146],"for":[147],"new":[148],"SNPs.":[149]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2022,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}