{"id":"https://openalex.org/W4413473546","doi":"https://doi.org/10.1093/bioinformatics/btaf468","title":"PRISM: privacy-preserving rare disease analysis using fully homomorphic encryption","display_name":"PRISM: privacy-preserving rare disease analysis using fully homomorphic encryption","publication_year":2025,"publication_date":"2025-08-23","ids":{"openalex":"https://openalex.org/W4413473546","doi":"https://doi.org/10.1093/bioinformatics/btaf468","pmid":"https://pubmed.ncbi.nlm.nih.gov/40848286"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaf468","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf468","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf468/64114782/btaf468.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf468/64114782/btaf468.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5119405181","display_name":"G\u00fcliz Akkaya","orcid":null},"institutions":[{"id":"https://openalex.org/I120217413","display_name":"Izmir Institute of Technology","ror":"https://ror.org/03stptj97","country_code":"TR","type":"education","lineage":["https://openalex.org/I120217413"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"G\u00fcliz Akkaya","raw_affiliation_strings":["Department of Computer Engineering, \u0130zmir Institute of Technology , Izmir, 35430,","\u0130zmir Institute of Technology Department of Computer Engineering, , Izmir,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, \u0130zmir Institute of Technology , Izmir, 35430,","institution_ids":["https://openalex.org/I120217413"]},{"raw_affiliation_string":"\u0130zmir Institute of Technology Department of Computer Engineering, , Izmir,","institution_ids":["https://openalex.org/I120217413"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107173641","display_name":"Nesli Erdo\u011fmu\u015f","orcid":"https://orcid.org/0000-0002-6875-2685"},"institutions":[{"id":"https://openalex.org/I120217413","display_name":"Izmir Institute of Technology","ror":"https://ror.org/03stptj97","country_code":"TR","type":"education","lineage":["https://openalex.org/I120217413"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Nesli Erdo\u011fmu\u015f","raw_affiliation_strings":["Department of Computer Engineering, \u0130zmir Institute of Technology , Izmir, 35430,","\u0130zmir Institute of Technology Department of Computer Engineering, , Izmir,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, \u0130zmir Institute of Technology , Izmir, 35430,","institution_ids":["https://openalex.org/I120217413"]},{"raw_affiliation_string":"\u0130zmir Institute of Technology Department of Computer Engineering, , Izmir,","institution_ids":["https://openalex.org/I120217413"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5037293831","display_name":"Mete Akg\u00fcn","orcid":"https://orcid.org/0000-0003-4088-2784"},"institutions":[{"id":"https://openalex.org/I8087733","display_name":"University of T\u00fcbingen","ror":"https://ror.org/03a1kwz48","country_code":"DE","type":"education","lineage":["https://openalex.org/I8087733"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Mete Akg\u00fcn","raw_affiliation_strings":["Department of Computer Science, University of T\u00fcbingen , T\u00fcbingen, 72076,","Institute for Bioinformatics and Medical Informatics, University of T\u00fcbingen , T\u00fcbingen, 72076,","University of T\u00fcbingen Department of Computer Science, , T\u00fcbingen,","Institute for Bioinformatics and Medical Informatics, University of T\u00fcbingen , T\u00fcbingen,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, University of T\u00fcbingen , T\u00fcbingen, 72076,","institution_ids":["https://openalex.org/I8087733"]},{"raw_affiliation_string":"Institute for Bioinformatics and Medical Informatics, University of T\u00fcbingen , T\u00fcbingen, 72076,","institution_ids":["https://openalex.org/I8087733"]},{"raw_affiliation_string":"University of T\u00fcbingen Department of Computer Science, , T\u00fcbingen,","institution_ids":["https://openalex.org/I8087733"]},{"raw_affiliation_string":"Institute for Bioinformatics and Medical Informatics, University of T\u00fcbingen , T\u00fcbingen,","institution_ids":["https://openalex.org/I8087733"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":3.5175,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.93264672,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":96},"biblio":{"volume":"41","issue":"10","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10237","display_name":"Cryptography and Data Security","score":0.4575999975204468,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10237","display_name":"Cryptography and Data Security","score":0.4575999975204468,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10764","display_name":"Privacy-Preserving Technologies in Data","score":0.1914999932050705,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10951","display_name":"Cryptographic Implementations and Security","score":0.05090000107884407,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/homomorphic-encryption","display_name":"Homomorphic encryption","score":0.9414424300193787},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6806093454360962},{"id":"https://openalex.org/keywords/encryption","display_name":"Encryption","score":0.6481543183326721},{"id":"https://openalex.org/keywords/prism","display_name":"Prism","score":0.5159919261932373},{"id":"https://openalex.org/keywords/computer-security","display_name":"Computer security","score":0.46480050683021545},{"id":"https://openalex.org/keywords/internet-privacy","display_name":"Internet privacy","score":0.36615628004074097}],"concepts":[{"id":"https://openalex.org/C158338273","wikidata":"https://www.wikidata.org/wiki/Q2154943","display_name":"Homomorphic encryption","level":3,"score":0.9414424300193787},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6806093454360962},{"id":"https://openalex.org/C148730421","wikidata":"https://www.wikidata.org/wiki/Q141090","display_name":"Encryption","level":2,"score":0.6481543183326721},{"id":"https://openalex.org/C67666897","wikidata":"https://www.wikidata.org/wiki/Q165896","display_name":"Prism","level":2,"score":0.5159919261932373},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.46480050683021545},{"id":"https://openalex.org/C108827166","wikidata":"https://www.wikidata.org/wiki/Q175975","display_name":"Internet privacy","level":1,"score":0.36615628004074097},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"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":"D016494","descriptor_name":"Computer Security","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016494","descriptor_name":"Computer Security","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016494","descriptor_name":"Computer Security","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016494","descriptor_name":"Computer Security","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016494","descriptor_name":"Computer Security","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D030661","descriptor_name":"Genetic Privacy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030661","descriptor_name":"Genetic Privacy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030661","descriptor_name":"Genetic Privacy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030661","descriptor_name":"Genetic Privacy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030661","descriptor_name":"Genetic Privacy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D035583","descriptor_name":"Rare Diseases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D035583","descriptor_name":"Rare Diseases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D035583","descriptor_name":"Rare Diseases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D035583","descriptor_name":"Rare Diseases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D035583","descriptor_name":"Rare Diseases","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btaf468","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf468","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf468/64114782/btaf468.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40848286","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40848286","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:europepmc.org:11319909","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12512125","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:gcris.iyte.edu.tr:11147/18533","is_oa":true,"landing_page_url":"https://hdl.handle.net/11147/18533","pdf_url":null,"source":{"id":"https://openalex.org/S4306400894","display_name":"\u0130YTE (\u0130ZM\u0130R Y\u00dcKSEK TEKNOLOJ\u0130 ENST\u0130T\u00dcS\u00dc)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I120217413","host_organization_name":"Izmir Institute of Technology","host_organization_lineage":["https://openalex.org/I120217413"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaf468","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaf468","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btaf468/64114782/btaf468.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2622353380","display_name":null,"funder_award_id":"545857928","funder_id":"https://openalex.org/F4320308022","funder_display_name":"California Department of Fish and Game"}],"funders":[{"id":"https://openalex.org/F4320308022","display_name":"California Department of Fish and Game","ror":"https://ror.org/02v6w2r95"},{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"},{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4413473546.pdf","grobid_xml":"https://content.openalex.org/works/W4413473546.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4408218896","https://openalex.org/W2539930818","https://openalex.org/W4406779505","https://openalex.org/W4403623784","https://openalex.org/W4393118461","https://openalex.org/W4390664647","https://openalex.org/W3012147850","https://openalex.org/W4313300189","https://openalex.org/W2949835517","https://openalex.org/W4407007798"],"abstract_inverted_index":{"MOTIVATION:":[0],"Rare":[1],"diseases":[2],"affect":[3],"millions":[4,189],"of":[5,43,83,149,190,198],"people":[6],"worldwide,":[7],"yet":[8],"their":[9],"genomic":[10,44,77],"foundations":[11],"remain":[12],"poorly":[13],"understood":[14],"due":[15],"to":[16,155,171,187],"limited":[17],"patient":[18],"data":[19,45,235],"and":[20,102,120,138,164,183,221,233],"strict":[21],"privacy":[22],"regulations,":[23],"such":[24],"as":[25],"the":[26,40,81,147,196,203,234],"General":[27],"Data":[28],"Protection":[29],"Regulation":[30],"(GDPR)":[31],"(https://gdpr.eu/tag/gdpr/)":[32],"in":[33,159,192,223,237,243],"March":[34],"2025.":[35],"These":[36],"restrictions":[37],"can":[38,107,240],"hinder":[39],"collaborative":[41],"analysis":[42,70,213],"necessary":[46],"for":[47,161,166,209],"uncovering":[48],"disease-causing":[49,115],"variants.":[50],"RESULTS:":[51],"We":[52,129],"present":[53],"PRISM,":[54],"a":[55,90,134,156,224],"novel":[56],"privacy-preserving":[57,210],"framework":[58],"based":[59],"on":[60,126],"fully":[61],"homomorphic":[62],"encryption":[63],"(FHE)":[64],"that":[65,206],"facilitates":[66],"rare":[67,211],"disease":[68,212],"variant":[69],"across":[71,99,214],"multiple":[72,215],"institutions":[73,101],"without":[74],"exposing":[75],"sensitive":[76,110],"information.":[78],"To":[79,195],"address":[80],"challenges":[82],"centralized":[84],"trust,":[85],"PRISM":[86],"is":[87,202],"built":[88],"upon":[89],"Threshold":[91],"FHE":[92,208],"scheme.":[93],"This":[94],"approach":[95,137],"decentralizes":[96],"key":[97],"management":[98],"participating":[100],"ensures":[103],"no":[104],"single":[105],"entity":[106],"unilaterally":[108],"decrypt":[109],"data.":[111,128],"Our":[112],"method":[113],"filters":[114],"variants":[116,191],"under":[117],"recessive,":[118],"dominant,":[119],"de":[121,167],"novo":[122,168],"inheritance":[123,216],"models":[124],"entirely":[125],"encrypted":[127],"propose":[130],"two":[131],"algorithmic":[132],"variants:":[133],"multiplication-intensive":[135],"(MUL-IN)":[136],"an":[139],"addition-intensive":[140],"(ADD-IN)":[141],"approach.":[142],"The":[143,230],"ADD-IN":[144,175],"algorithms":[145],"minimize":[146],"number":[148],"costly":[150],"multiplication":[151],"operations,":[152],"enabling":[153],"up":[154],"17\u00d7":[157],"improvement":[158],"runtime":[160],"recessive/dominant":[162],"filtering":[163],"22\u00d7":[165],"filtering,":[169],"compared":[170],"MUL-IN":[172],"methods.":[173],"While":[174],"produces":[176],"larger":[177],"ciphertexts,":[178],"efficient":[179],"parallelization":[180],"via":[181],"SIMD":[182],"multithreading":[184],"allows":[185],"it":[186],"handle":[188],"reasonable":[193],"time.":[194],"best":[197],"our":[199],"knowledge,":[200],"this":[201,238],"first":[204],"study":[205],"utilizes":[207],"models,":[217],"demonstrating":[218],"its":[219],"practicality":[220],"scalability":[222],"single-cloud":[225],"setting.":[226],"AVAILABILITY":[227],"AND":[228],"IMPLEMENTATION:":[229],"source":[231],"code":[232],"used":[236],"work":[239],"be":[241],"found":[242],"https://github.com/mdppml/PRISM.git.":[244]},"counts_by_year":[{"year":2025,"cited_by_count":2}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
