{"id":"https://openalex.org/W7126037363","doi":"https://doi.org/10.1109/bibm66473.2025.11356536","title":"Genomic Foundation Models for SNP Analysis","display_name":"Genomic Foundation Models for SNP Analysis","publication_year":2025,"publication_date":"2025-12-15","ids":{"openalex":"https://openalex.org/W7126037363","doi":"https://doi.org/10.1109/bibm66473.2025.11356536"},"language":null,"primary_location":{"id":"doi:10.1109/bibm66473.2025.11356536","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356536","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5124208023","display_name":"Johanna Pethke","orcid":null},"institutions":[{"id":"https://openalex.org/I120691247","display_name":"University of Hagen","ror":"https://ror.org/04tkkr536","country_code":"DE","type":"education","lineage":["https://openalex.org/I120691247"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Johanna Pethke","raw_affiliation_strings":["FernUniversit&#x00E4;t Hagen, Universit&#x00E4;tsstr. 1,Hagen,Germany,58097"],"affiliations":[{"raw_affiliation_string":"FernUniversit&#x00E4;t Hagen, Universit&#x00E4;tsstr. 1,Hagen,Germany,58097","institution_ids":["https://openalex.org/I120691247"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5030927255","display_name":"Thomas Krause","orcid":"https://orcid.org/0000-0003-4912-1703"},"institutions":[{"id":"https://openalex.org/I120691247","display_name":"University of Hagen","ror":"https://ror.org/04tkkr536","country_code":"DE","type":"education","lineage":["https://openalex.org/I120691247"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Thomas Krause","raw_affiliation_strings":["FernUniversit&#x00E4;t Hagen, Universit&#x00E4;tsstr. 1,Hagen,Germany,58097"],"affiliations":[{"raw_affiliation_string":"FernUniversit&#x00E4;t Hagen, Universit&#x00E4;tsstr. 1,Hagen,Germany,58097","institution_ids":["https://openalex.org/I120691247"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013968607","display_name":"Bruno B. Andrade","orcid":"https://orcid.org/0000-0001-6833-3811"},"institutions":[{"id":"https://openalex.org/I4210100923","display_name":"Munster Technological University","ror":"https://ror.org/013xpqh61","country_code":"IE","type":"facility","lineage":["https://openalex.org/I4210100923"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"Bruno Andrade","raw_affiliation_strings":["Munster Technological University, Bishopstown,Cork,Ireland"],"affiliations":[{"raw_affiliation_string":"Munster Technological University, Bishopstown,Cork,Ireland","institution_ids":["https://openalex.org/I4210100923"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124268162","display_name":"Michael Kramer","orcid":null},"institutions":[{"id":"https://openalex.org/I2799978770","display_name":"X-Fab (Germany)","ror":"https://ror.org/030bh9196","country_code":"DE","type":"company","lineage":["https://openalex.org/I2799978770"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Michael Kramer","raw_affiliation_strings":["ImmBioMed Business Consultants GmbH &#x0026; Co. KG, Bergstr. 85,Pfungstadt,64319"],"affiliations":[{"raw_affiliation_string":"ImmBioMed Business Consultants GmbH &#x0026; Co. KG, Bergstr. 85,Pfungstadt,64319","institution_ids":["https://openalex.org/I2799978770"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5124244466","display_name":"Matthias Hemmje","orcid":null},"institutions":[{"id":"https://openalex.org/I120691247","display_name":"University of Hagen","ror":"https://ror.org/04tkkr536","country_code":"DE","type":"education","lineage":["https://openalex.org/I120691247"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Matthias Hemmje","raw_affiliation_strings":["FernUniversit&#x00E4;t Hagen, Universit&#x00E4;tsstr. 1,Hagen,Germany,58097"],"affiliations":[{"raw_affiliation_string":"FernUniversit&#x00E4;t Hagen, Universit&#x00E4;tsstr. 1,Hagen,Germany,58097","institution_ids":["https://openalex.org/I120691247"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5124208023"],"corresponding_institution_ids":["https://openalex.org/I120691247"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.79545641,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"7214","last_page":"7218"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.7846999764442444,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.7846999764442444,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.08749999850988388,"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.049400001764297485,"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/workflow","display_name":"Workflow","score":0.7858999967575073},{"id":"https://openalex.org/keywords/complement","display_name":"Complement (music)","score":0.6212999820709229},{"id":"https://openalex.org/keywords/snp","display_name":"SNP","score":0.4577000141143799},{"id":"https://openalex.org/keywords/foundation","display_name":"Foundation (evidence)","score":0.43369999527931213},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.42080000042915344},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.36809998750686646},{"id":"https://openalex.org/keywords/human-genome","display_name":"Human genome","score":0.36149999499320984},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.36000001430511475}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7858999967575073},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6297000050544739},{"id":"https://openalex.org/C112313634","wikidata":"https://www.wikidata.org/wiki/Q7886648","display_name":"Complement (music)","level":5,"score":0.6212999820709229},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.560699999332428},{"id":"https://openalex.org/C139275648","wikidata":"https://www.wikidata.org/wiki/Q17134011","display_name":"SNP","level":5,"score":0.4577000141143799},{"id":"https://openalex.org/C2780966255","wikidata":"https://www.wikidata.org/wiki/Q5474306","display_name":"Foundation (evidence)","level":2,"score":0.43369999527931213},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.42080000042915344},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.40720000863075256},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.36809998750686646},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.36579999327659607},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.36149999499320984},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.36000001430511475},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.3116999864578247},{"id":"https://openalex.org/C64502627","wikidata":"https://www.wikidata.org/wiki/Q170065","display_name":"Pathogenicity","level":2,"score":0.30079999566078186},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2815000116825104},{"id":"https://openalex.org/C61053724","wikidata":"https://www.wikidata.org/wiki/Q1154615","display_name":"Sequence analysis","level":3,"score":0.2797999978065491},{"id":"https://openalex.org/C24432333","wikidata":"https://www.wikidata.org/wiki/Q2068526","display_name":"Whole genome sequencing","level":4,"score":0.2662000060081482},{"id":"https://openalex.org/C47042493","wikidata":"https://www.wikidata.org/wiki/Q265799","display_name":"Human genetics","level":3,"score":0.2624000012874603},{"id":"https://openalex.org/C120567893","wikidata":"https://www.wikidata.org/wiki/Q1582085","display_name":"Knowledge extraction","level":2,"score":0.2621999979019165},{"id":"https://openalex.org/C16671776","wikidata":"https://www.wikidata.org/wiki/Q5420592","display_name":"Exome sequencing","level":4,"score":0.2621000111103058},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2556000053882599},{"id":"https://openalex.org/C2994067223","wikidata":"https://www.wikidata.org/wiki/Q380546","display_name":"Genomic sequencing","level":4,"score":0.2535000145435333},{"id":"https://openalex.org/C18762648","wikidata":"https://www.wikidata.org/wiki/Q42213","display_name":"Work (physics)","level":2,"score":0.2526000142097473}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm66473.2025.11356536","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356536","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.40997347235679626,"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":12,"referenced_works":["https://openalex.org/W2120336373","https://openalex.org/W2143452407","https://openalex.org/W2158342889","https://openalex.org/W2168610667","https://openalex.org/W2417483443","https://openalex.org/W2770026599","https://openalex.org/W4251439403","https://openalex.org/W4377205902","https://openalex.org/W4401933237","https://openalex.org/W4404282917","https://openalex.org/W4404821554","https://openalex.org/W4411006009"],"related_works":[],"abstract_inverted_index":{"This":[0],"paper":[1,69],"presents":[2,35],"SnipFlow,":[3],"a":[4,30,40,83],"workflow":[5,51],"for":[6],"knowledge-based":[7],"analysis":[8,101],"of":[9,95],"single":[10],"nucleotide":[11],"polymorphisms":[12],"in":[13,29,82,98],"personalised":[14],"medicine.":[15],"SnipFlow":[16],"combines":[17],"structured":[18],"knowledge":[19,28,41],"derived":[20],"from":[21],"the":[22,36,50,91,99],"genome":[23],"sequence":[24],"with":[25],"unstructured":[26],"literaturebased":[27],"common":[31],"data":[32],"model":[33],"and":[34,60,86,93],"results":[37],"transparently":[38],"via":[39],"management":[42],"system.":[43],"By":[44],"integrating":[45],"Genomic":[46],"Foundation":[47],"Models":[48],"(GFMs),":[49],"can":[52,79],"be":[53],"extended":[54],"to":[55],"predict":[56],"functional":[57],"effects,":[58],"pathogenicity":[59],"context-dependent":[61],"relationships":[62],"even":[63],"without":[64],"existing":[65],"database":[66],"entries.":[67],"The":[68],"shows":[70],"that":[71],"GFMs":[72],"do":[73],"not":[74],"replace":[75],"classical":[76],"approaches,":[77],"but":[78],"complement":[80],"them":[81],"targeted":[84],"manner,":[85],"outlines":[87],"future":[88],"work":[89],"on":[90],"integration":[92],"evaluation":[94],"different":[96],"models":[97],"SNP":[100],"process.":[102]},"counts_by_year":[],"updated_date":"2026-02-01T03:34:12.195049","created_date":"2026-01-30T00:00:00"}
