{"id":"https://openalex.org/W3197597699","doi":"https://doi.org/10.1186/s12859-021-04326-x","title":"SNPxE: SNP-environment interaction pattern identifier","display_name":"SNPxE: SNP-environment interaction pattern identifier","publication_year":2021,"publication_date":"2021-09-07","ids":{"openalex":"https://openalex.org/W3197597699","doi":"https://doi.org/10.1186/s12859-021-04326-x","mag":"3197597699","pmid":"https://pubmed.ncbi.nlm.nih.gov/34493206"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-021-04326-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04326-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04326-x","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04326-x","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5030129271","display_name":"Hui\u2010Yi Lin","orcid":"https://orcid.org/0000-0002-3307-5549"},"institutions":[{"id":"https://openalex.org/I75420490","display_name":"Louisiana State University Health Sciences Center New Orleans","ror":"https://ror.org/01qv8fp92","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I75420490"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Hui-Yi Lin","raw_affiliation_strings":["Biostatistics Program, School of Public Health, Louisiana State University Health Sciences Center, New Orleans, LA, 70112, USA. hlin1@lsuhsc.edu","Biostatistics Program, School of Public Health, Louisiana State University Health Sciences Center, New Orleans, LA, 70112, USA"],"raw_orcid":"https://orcid.org/0000-0002-3307-5549","affiliations":[{"raw_affiliation_string":"Biostatistics Program, School of Public Health, Louisiana State University Health Sciences Center, New Orleans, LA, 70112, USA. hlin1@lsuhsc.edu","institution_ids":["https://openalex.org/I75420490"]},{"raw_affiliation_string":"Biostatistics Program, School of Public Health, Louisiana State University Health Sciences Center, New Orleans, LA, 70112, USA","institution_ids":["https://openalex.org/I75420490"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021227488","display_name":"Po\u2010Yu Huang","orcid":"https://orcid.org/0000-0002-8682-1322"},"institutions":[{"id":"https://openalex.org/I4210148468","display_name":"Industrial Technology Research Institute","ror":"https://ror.org/05szzwt63","country_code":"TW","type":"nonprofit","lineage":["https://openalex.org/I4210148468"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Po-Yu Huang","raw_affiliation_strings":["Computational Intelligence Technology Center, Industrial Technology Research Institute, Hsinchu City, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Intelligence Technology Center, Industrial Technology Research Institute, Hsinchu City, Taiwan","institution_ids":["https://openalex.org/I4210148468"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090998977","display_name":"Tung\u2010Sung Tseng","orcid":"https://orcid.org/0000-0001-6266-9891"},"institutions":[{"id":"https://openalex.org/I75420490","display_name":"Louisiana State University Health Sciences Center New Orleans","ror":"https://ror.org/01qv8fp92","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I75420490"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tung-Sung Tseng","raw_affiliation_strings":["Behavioral and Community Health Sciences Program, School of Public Health, Louisiana State University Health Sciences Center, New Orleans, LA, 70112, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Behavioral and Community Health Sciences Program, School of Public Health, Louisiana State University Health Sciences Center, New Orleans, LA, 70112, USA","institution_ids":["https://openalex.org/I75420490"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5069824664","display_name":"Jong Y. Park","orcid":"https://orcid.org/0000-0002-6384-6447"},"institutions":[{"id":"https://openalex.org/I3019308854","display_name":"Moffitt Cancer Center","ror":"https://ror.org/01xf75524","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I3019308854"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jong Y. Park","raw_affiliation_strings":["Department of Cancer Epidemiology, Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Cancer Epidemiology, Moffitt Cancer Center and Research Institute, Tampa, FL, 33612, USA","institution_ids":["https://openalex.org/I3019308854"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5030129271"],"corresponding_institution_ids":["https://openalex.org/I75420490"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.4826,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.70020226,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"22","issue":"1","first_page":"425","last_page":"425"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10261","display_name":"Genetic Associations and Epidemiology","score":0.9789999723434448,"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"}},"topics":[{"id":"https://openalex.org/T10261","display_name":"Genetic Associations and Epidemiology","score":0.9789999723434448,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.006500000134110451,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.0015999999595806003,"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/snp","display_name":"SNP","score":0.7446780800819397},{"id":"https://openalex.org/keywords/gene\u2013environment-interaction","display_name":"Gene\u2013environment interaction","score":0.6242780685424805},{"id":"https://openalex.org/keywords/categorical-variable","display_name":"Categorical variable","score":0.6230310797691345},{"id":"https://openalex.org/keywords/single-nucleotide-polymorphism","display_name":"Single-nucleotide polymorphism","score":0.5308371782302856},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.49036669731140137},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.42006099224090576},{"id":"https://openalex.org/keywords/tag-snp","display_name":"Tag SNP","score":0.4199434220790863},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4066523313522339},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3704230785369873},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.17005014419555664},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.16135725378990173},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.07419580221176147}],"concepts":[{"id":"https://openalex.org/C139275648","wikidata":"https://www.wikidata.org/wiki/Q17134011","display_name":"SNP","level":5,"score":0.7446780800819397},{"id":"https://openalex.org/C130947863","wikidata":"https://www.wikidata.org/wiki/Q5533121","display_name":"Gene\u2013environment interaction","level":4,"score":0.6242780685424805},{"id":"https://openalex.org/C5274069","wikidata":"https://www.wikidata.org/wiki/Q2285707","display_name":"Categorical variable","level":2,"score":0.6230310797691345},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.5308371782302856},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.49036669731140137},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.42006099224090576},{"id":"https://openalex.org/C55060382","wikidata":"https://www.wikidata.org/wiki/Q7675093","display_name":"Tag SNP","level":5,"score":0.4199434220790863},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4066523313522339},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3704230785369873},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.17005014419555664},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.16135725378990173},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07419580221176147}],"mesh":[{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","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":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},{"descriptor_ui":"D059647","descriptor_name":"Gene-Environment Interaction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059647","descriptor_name":"Gene-Environment Interaction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059647","descriptor_name":"Gene-Environment Interaction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/s12859-021-04326-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04326-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04326-x","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:34493206","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34493206","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:7d9bc30f57db4c4187e7f44de2ad1a73","is_oa":true,"landing_page_url":"https://doaj.org/article/7d9bc30f57db4c4187e7f44de2ad1a73","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 22, Iss 1, Pp 1-9 (2021)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8425112","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8425112","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-021-04326-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04326-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-021-04326-x","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6200000047683716,"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land"}],"awards":[{"id":"https://openalex.org/G2814595813","display_name":null,"funder_award_id":"R21 CA202417","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G2934950977","display_name":null,"funder_award_id":"P20 GM121288","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G4594693215","display_name":null,"funder_award_id":"R21CA202417","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6636757183","display_name":null,"funder_award_id":"P20 GM121288","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320310395","display_name":"Louisiana State University","ror":"https://ror.org/05ect4e57"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3197597699.pdf","grobid_xml":"https://content.openalex.org/works/W3197597699.grobid-xml"},"referenced_works_count":24,"referenced_works":["https://openalex.org/W1490453899","https://openalex.org/W1966360257","https://openalex.org/W1998977949","https://openalex.org/W2028197440","https://openalex.org/W2063575312","https://openalex.org/W2104605543","https://openalex.org/W2146841033","https://openalex.org/W2416985086","https://openalex.org/W2515572166","https://openalex.org/W2567343548","https://openalex.org/W2598124616","https://openalex.org/W2619186549","https://openalex.org/W2806504012","https://openalex.org/W2806521756","https://openalex.org/W2894991738","https://openalex.org/W2911032740","https://openalex.org/W2948515282","https://openalex.org/W2969879921","https://openalex.org/W3037100096","https://openalex.org/W3040338113","https://openalex.org/W3087564393","https://openalex.org/W3111412003","https://openalex.org/W3139106591","https://openalex.org/W3157359833"],"related_works":["https://openalex.org/W2164855536","https://openalex.org/W1997352593","https://openalex.org/W1978000554","https://openalex.org/W2583457094","https://openalex.org/W2415959690","https://openalex.org/W2745006295","https://openalex.org/W2057218249","https://openalex.org/W2329144129","https://openalex.org/W2258660676","https://openalex.org/W2388756488"],"abstract_inverted_index":{"BACKGROUND:":[0],"Interactions":[1],"of":[2,22,170,203,213,244],"single":[3],"nucleotide":[4],"polymorphisms":[5],"(SNPs)":[6],"and":[7,120,144,181,194,228],"environmental":[8,182],"factors":[9,183],"play":[10],"an":[11,53,116],"important":[12],"role":[13],"in":[14,28],"understanding":[15],"complex":[16],"diseases'":[17],"pathogenesis.":[18],"A":[19],"growing":[20],"number":[21],"SNP-environment":[23,38,86,94,108,130,215,226],"studies":[24],"have":[25],"been":[26],"conducted":[27],"the":[29,33,63,149,153,162,167,171,174,179,204,211,229,237],"past":[30],"decade;":[31],"however,":[32],"statistical":[34,45,80],"methods":[35],"for":[36,106,115,123,210,223,235,249],"evaluating":[37],"interactions":[39],"are":[40],"still":[41],"underdeveloped.":[42],"The":[43,241],"conventional":[44],"approach":[46,67],"with":[47,52,103],"a":[48,79,93,104,124,201,214,220],"full":[49,64],"interaction":[50,60,65,87,95,100,113,155],"model":[51,66,138],"additive":[54],"SNP":[55],"mode":[56],"tests":[57,98],"one":[58],"specific":[59],"type,":[61],"so":[62],"tends":[68],"to":[69,71,82,191],"lead":[70],"false-negative":[72],"findings.":[73],"To":[74],"increase":[75],"detection":[76],"accuracy,":[77],"developing":[78],"tool":[81,222],"effectively":[83],"detect":[84],"various":[85],"patterns":[88,101,114,122],"is":[89,219,246],"necessary.":[90],"RESULTS:":[91],"SNPxE,":[92],"pattern":[96,156],"identifier,":[97],"multiple":[99,150],"associated":[102],"phenotype":[105],"each":[107],"pair.":[109,216],"SNPxE":[110,132,187,218,230,245],"evaluates":[111],"27":[112],"ordinal":[117],"environment":[118,126],"factor":[119],"18":[121],"categorical":[125],"factor.":[127],"For":[128,197],"detecting":[129],"interactions,":[131,227],"considers":[133],"three":[134],"major":[135],"components:":[136],"(1)":[137],"structure,":[139],"(2)":[140],"SNP's":[141],"inheritance":[142],"mode,":[143],"(3)":[145],"risk":[146,175],"direction.":[147],"Among":[148],"testing":[151],"patterns,":[152],"best":[154],"will":[157],"be":[158,185,189,208],"identified":[159],"based":[160,177],"on":[161,178],"Bayesian":[163],"information":[164],"criterion":[165],"or":[166],"smallest":[168],"p-value":[169],"interaction.":[172],"Furthermore,":[173],"sub-groups":[176,212],"SNPs":[180],"can":[184,188,207,232],"identified.":[186],"applied":[190],"both":[192],"numeric":[193],"binary":[195],"phenotypes.":[196],"better":[198],"results":[199],"interpretation,":[200],"heat-table":[202],"outcome":[205],"proportions":[206],"generated":[209],"CONCLUSIONS:":[217],"valuable":[221],"intensively":[224],"evaluate":[225],"findings":[231],"provide":[233],"insights":[234],"solving":[236],"missing":[238],"heritability":[239],"issue.":[240],"R":[242],"function":[243],"freely":[247],"available":[248],"download":[250],"at":[251],"GitHub":[252],"(":[253],"https://github.com/LinHuiyi/SIPI":[254],").":[255]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
