{"id":"https://openalex.org/W7126092500","doi":"https://doi.org/10.1109/bibm66473.2025.11356528","title":"From Reads to Reports: A Vision for a GFM-Powered Genomic Diagnostic Platform","display_name":"From Reads to Reports: A Vision for a GFM-Powered Genomic Diagnostic Platform","publication_year":2025,"publication_date":"2025-12-15","ids":{"openalex":"https://openalex.org/W7126092500","doi":"https://doi.org/10.1109/bibm66473.2025.11356528"},"language":null,"primary_location":{"id":"doi:10.1109/bibm66473.2025.11356528","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356528","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/A5030927255","display_name":"Thomas Krause","orcid":"https://orcid.org/0000-0003-4912-1703"},"institutions":[{"id":"https://openalex.org/I120691247","display_name":"FernUniversit\u00e4t in Hagen","ror":"https://ror.org/04tkkr536","country_code":"DE","type":"education","lineage":["https://openalex.org/I120691247"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Thomas Krause","raw_affiliation_strings":["University of Hagen,Germany"],"affiliations":[{"raw_affiliation_string":"University of Hagen,Germany","institution_ids":["https://openalex.org/I120691247"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002175542","display_name":"Philippe Tamla","orcid":"https://orcid.org/0000-0002-0786-4253"},"institutions":[{"id":"https://openalex.org/I120691247","display_name":"FernUniversit\u00e4t in Hagen","ror":"https://ror.org/04tkkr536","country_code":"DE","type":"education","lineage":["https://openalex.org/I120691247"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Philippe Tamla","raw_affiliation_strings":["University of Hagen,Germany"],"affiliations":[{"raw_affiliation_string":"University of Hagen,Germany","institution_ids":["https://openalex.org/I120691247"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124163633","display_name":"Andrea Leoni","orcid":null},"institutions":[{"id":"https://openalex.org/I4210125264","display_name":"R2M Solution (Italy)","ror":"https://ror.org/0385et328","country_code":"IT","type":"company","lineage":["https://openalex.org/I4210125264"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Andrea Leoni","raw_affiliation_strings":["OKKAM S.r.l.,Italy"],"affiliations":[{"raw_affiliation_string":"OKKAM S.r.l.,Italy","institution_ids":["https://openalex.org/I4210125264"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039169968","display_name":"F. Monti","orcid":null},"institutions":[{"id":"https://openalex.org/I861853513","display_name":"Sapienza University of Rome","ror":"https://ror.org/02be6w209","country_code":"IT","type":"education","lineage":["https://openalex.org/I861853513"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Flavia Monti","raw_affiliation_strings":["Sapienza University,Rome,Italy"],"affiliations":[{"raw_affiliation_string":"Sapienza University,Rome,Italy","institution_ids":["https://openalex.org/I861853513"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056500931","display_name":"Francesca De Luzi","orcid":"https://orcid.org/0000-0002-9896-2528"},"institutions":[{"id":"https://openalex.org/I861853513","display_name":"Sapienza University of Rome","ror":"https://ror.org/02be6w209","country_code":"IT","type":"education","lineage":["https://openalex.org/I861853513"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Francesca De Luzi","raw_affiliation_strings":["Sapienza University,Rome,Italy"],"affiliations":[{"raw_affiliation_string":"Sapienza University,Rome,Italy","institution_ids":["https://openalex.org/I861853513"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124232624","display_name":"Jamie Fitz Gerald","orcid":null},"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":"Jamie Fitz Gerald","raw_affiliation_strings":["Munster Technological University (MTU),Ireland"],"affiliations":[{"raw_affiliation_string":"Munster Technological University (MTU),Ireland","institution_ids":["https://openalex.org/I4210100923"]}]},{"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 (MTU),Ireland"],"affiliations":[{"raw_affiliation_string":"Munster Technological University (MTU),Ireland","institution_ids":["https://openalex.org/I4210100923"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053439775","display_name":"Haithem Alfi","orcid":null},"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":"Haithem Afli","raw_affiliation_strings":["Munster Technological University (MTU),Ireland"],"affiliations":[{"raw_affiliation_string":"Munster Technological University (MTU),Ireland","institution_ids":["https://openalex.org/I4210100923"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068425882","display_name":"Massimo Mecella","orcid":"https://orcid.org/0000-0002-9730-8882"},"institutions":[{"id":"https://openalex.org/I861853513","display_name":"Sapienza University of Rome","ror":"https://ror.org/02be6w209","country_code":"IT","type":"education","lineage":["https://openalex.org/I861853513"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Massimo Mecella","raw_affiliation_strings":["Sapienza University,Rome,Italy"],"affiliations":[{"raw_affiliation_string":"Sapienza University,Rome,Italy","institution_ids":["https://openalex.org/I861853513"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064219476","display_name":"Paolo Buono","orcid":"https://orcid.org/0000-0002-1421-3686"},"institutions":[{"id":"https://openalex.org/I5561750","display_name":"University of Bari Aldo Moro","ror":"https://ror.org/027ynra39","country_code":"IT","type":"education","lineage":["https://openalex.org/I5561750"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Paolo Buono","raw_affiliation_strings":["University of Bari,Italy"],"affiliations":[{"raw_affiliation_string":"University of Bari,Italy","institution_ids":["https://openalex.org/I5561750"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Andrea Molinari","orcid":null},"institutions":[{"id":"https://openalex.org/I193223587","display_name":"University of Trento","ror":"https://ror.org/05trd4x28","country_code":"IT","type":"education","lineage":["https://openalex.org/I193223587"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Andrea Molinari","raw_affiliation_strings":["University of Trento,Italy"],"affiliations":[{"raw_affiliation_string":"University of Trento,Italy","institution_ids":["https://openalex.org/I193223587"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5124244466","display_name":"Matthias Hemmje","orcid":null},"institutions":[{"id":"https://openalex.org/I120691247","display_name":"FernUniversit\u00e4t in 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":["University of Hagen,Germany"],"affiliations":[{"raw_affiliation_string":"University of Hagen,Germany","institution_ids":["https://openalex.org/I120691247"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":12,"corresponding_author_ids":["https://openalex.org/A5030927255"],"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":0.78643651,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"7207","last_page":"7213"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.12449999898672104,"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":0.12449999898672104,"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.09889999777078629,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10885","display_name":"Gene expression and cancer classification","score":0.07530000060796738,"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/cloud-computing","display_name":"Cloud computing","score":0.4878999888896942},{"id":"https://openalex.org/keywords/big-data","display_name":"Big data","score":0.4092000126838684},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.39719998836517334},{"id":"https://openalex.org/keywords/data-sharing","display_name":"Data sharing","score":0.3928000032901764},{"id":"https://openalex.org/keywords/personalized-medicine","display_name":"Personalized medicine","score":0.388700008392334},{"id":"https://openalex.org/keywords/bridge","display_name":"Bridge (graph theory)","score":0.3723999857902527},{"id":"https://openalex.org/keywords/architecture","display_name":"Architecture","score":0.36250001192092896},{"id":"https://openalex.org/keywords/precision-medicine","display_name":"Precision medicine","score":0.35420000553131104}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.538100004196167},{"id":"https://openalex.org/C79974875","wikidata":"https://www.wikidata.org/wiki/Q483639","display_name":"Cloud computing","level":2,"score":0.4878999888896942},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.43389999866485596},{"id":"https://openalex.org/C75684735","wikidata":"https://www.wikidata.org/wiki/Q858810","display_name":"Big data","level":2,"score":0.4092000126838684},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.39719998836517334},{"id":"https://openalex.org/C2779965156","wikidata":"https://www.wikidata.org/wiki/Q5227350","display_name":"Data sharing","level":3,"score":0.3928000032901764},{"id":"https://openalex.org/C32220436","wikidata":"https://www.wikidata.org/wiki/Q2072214","display_name":"Personalized medicine","level":2,"score":0.388700008392334},{"id":"https://openalex.org/C100776233","wikidata":"https://www.wikidata.org/wiki/Q2532492","display_name":"Bridge (graph theory)","level":2,"score":0.3723999857902527},{"id":"https://openalex.org/C123657996","wikidata":"https://www.wikidata.org/wiki/Q12271","display_name":"Architecture","level":2,"score":0.36250001192092896},{"id":"https://openalex.org/C163763905","wikidata":"https://www.wikidata.org/wiki/Q17075943","display_name":"Precision medicine","level":2,"score":0.35420000553131104},{"id":"https://openalex.org/C1668388","wikidata":"https://www.wikidata.org/wiki/Q1149776","display_name":"Data management","level":2,"score":0.33340001106262207},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.33250001072883606},{"id":"https://openalex.org/C128544194","wikidata":"https://www.wikidata.org/wiki/Q474859","display_name":"Translational research","level":2,"score":0.3237000107765198},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.32190001010894775},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.30649998784065247},{"id":"https://openalex.org/C143121216","wikidata":"https://www.wikidata.org/wiki/Q1330402","display_name":"Microbiome","level":2,"score":0.2994999885559082},{"id":"https://openalex.org/C47487241","wikidata":"https://www.wikidata.org/wiki/Q5227230","display_name":"Data access","level":2,"score":0.2994000017642975},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.2939999997615814},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.27219998836517334},{"id":"https://openalex.org/C98025372","wikidata":"https://www.wikidata.org/wiki/Q477538","display_name":"Systems architecture","level":3,"score":0.2720000147819519},{"id":"https://openalex.org/C2778464652","wikidata":"https://www.wikidata.org/wiki/Q309849","display_name":"Open research","level":2,"score":0.25290000438690186},{"id":"https://openalex.org/C2988867146","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Human disease","level":3,"score":0.25200000405311584}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm66473.2025.11356528","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356528","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":0.44845643639564514,"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":11,"referenced_works":["https://openalex.org/W43120215","https://openalex.org/W2142678478","https://openalex.org/W2158342889","https://openalex.org/W2302501749","https://openalex.org/W2917207851","https://openalex.org/W2963276645","https://openalex.org/W4220973461","https://openalex.org/W4281490401","https://openalex.org/W4297340531","https://openalex.org/W4412730473","https://openalex.org/W7126013078"],"related_works":[],"abstract_inverted_index":{"Microbiome":[0],"sequencing":[1],"offers":[2],"significant":[3],"potential":[4],"for":[5,141,164],"advancing":[6],"clinical":[7,29,84,180,201],"diagnostics,":[8],"but":[9],"its":[10,108,117],"adoption":[11],"is":[12,69],"hindered":[13],"by":[14,37,51],"challenges":[15,36],"in":[16],"data":[17,26,81,143],"processing,":[18],"standardization,":[19],"and":[20,58,76,112,130,137,152,169,179,186,199],"the":[21,60,113,193],"translation":[22],"of":[23,62,104,116],"complex":[24],"genomic":[25,197],"into":[27],"actionable":[28],"insights.":[30],"The":[31,65,120],"GenDAI":[32,189],"project":[33],"addresses":[34],"these":[35],"developing":[38],"a":[39,72,127,135,184],"novel,":[40],"integrated":[41],"medical":[42],"diagnostics":[43,132],"platform":[44,140],"that":[45],"leverages":[46],"Artificial":[47],"Intelligence":[48],"(AI),":[49],"powered":[50],"Genomic":[52],"Foundation":[53],"Models":[54],"(GFMs),":[55],"to":[56,70,83,86,176,191],"accelerate":[57],"improve":[59],"analysis":[61],"microbiome":[63],"data.":[64],"platform's":[66],"primary":[67],"goal":[68],"provide":[71],"fully":[73,128],"automated,":[74],"reproducible,":[75],"compliant":[77,138],"end-to-end":[78],"solution,":[79],"from":[80],"ingestion":[82],"reporting,":[85],"support":[87],"personalized":[88],"medicine,":[89],"with":[90],"an":[91,102,160],"initial":[92],"focus":[93],"on":[94,146],"Inflammatory":[95],"Bowel":[96],"Disease":[97],"(IBD).":[98],"This":[99],"paper":[100],"presents":[101],"overview":[103],"GenDAI's":[105],"vision,":[106],"outlining":[107],"user-centered":[109],"methodological":[110],"approach":[111],"conceptual":[114],"architecture":[115,121],"core":[118],"components.":[119],"integrates":[122],"four":[123],"key":[124],"pillars:":[125],"(1)":[126],"automated":[129],"auditable":[131],"workflow,":[133],"(2)":[134],"secure":[136],"cloud":[139],"long-term":[142],"management":[144],"based":[145],"Open":[147],"Archival":[148],"Information":[149],"System":[150],"(OAIS)":[151],"Findable,":[153],"Accessible,":[154],"Interoperable,":[155],"Reusable":[156],"(FAIR)":[157],"principles,":[158],"(3)":[159],"advanced":[161,196],"AI":[162],"engine":[163],"biomarker":[165],"discovery":[166],"using":[167],"GFMs,":[168],"(4)":[170],"interactive,":[171],"usercentered":[172],"reporting":[173],"tools":[174],"designed":[175],"enhance":[177],"explainability":[178],"trust.":[181],"By":[182],"providing":[183],"holistic":[185],"ethically-grounded":[187],"framework,":[188],"aims":[190],"bridge":[192],"gap":[194],"between":[195],"research":[198],"practical":[200],"application.":[202]},"counts_by_year":[],"updated_date":"2026-03-25T23:56:10.502304","created_date":"2026-01-30T00:00:00"}
