{"id":"https://openalex.org/W4225249012","doi":"https://doi.org/10.1186/s13015-022-00211-1","title":"Efficient privacy-preserving variable-length substring match for genome sequence","display_name":"Efficient privacy-preserving variable-length substring match for genome sequence","publication_year":2022,"publication_date":"2022-04-26","ids":{"openalex":"https://openalex.org/W4225249012","doi":"https://doi.org/10.1186/s13015-022-00211-1","pmid":"https://pubmed.ncbi.nlm.nih.gov/35473587"},"language":"en","primary_location":{"id":"doi:10.1186/s13015-022-00211-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-022-00211-1","pdf_url":"https://almob.biomedcentral.com/track/pdf/10.1186/s13015-022-00211-1","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"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":"Algorithms for Molecular Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://almob.biomedcentral.com/track/pdf/10.1186/s13015-022-00211-1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5009478047","display_name":"Yoshiki Nakagawa","orcid":null},"institutions":[{"id":"https://openalex.org/I150744194","display_name":"Waseda University","ror":"https://ror.org/00ntfnx83","country_code":"JP","type":"education","lineage":["https://openalex.org/I150744194"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yoshiki Nakagawa","raw_affiliation_strings":["Department of Computer Science and Engineering, Waseda University, Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Waseda University, Tokyo, Japan","institution_ids":["https://openalex.org/I150744194"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000871530","display_name":"Satsuya Ohata","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Satsuya Ohata","raw_affiliation_strings":["Self-employment, Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Self-employment, Tokyo, Japan","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5043657069","display_name":"Kana Shimizu","orcid":"https://orcid.org/0000-0001-6452-9091"},"institutions":[{"id":"https://openalex.org/I150744194","display_name":"Waseda University","ror":"https://ror.org/00ntfnx83","country_code":"JP","type":"education","lineage":["https://openalex.org/I150744194"]},{"id":"https://openalex.org/I73613424","display_name":"National Institute of Advanced Industrial Science and Technology","ror":"https://ror.org/01703db54","country_code":"JP","type":"government","lineage":["https://openalex.org/I73613424"]},{"id":"https://openalex.org/I74640424","display_name":"Advanced Institute of Industrial Technology","ror":"https://ror.org/04f9apy08","country_code":"JP","type":"education","lineage":["https://openalex.org/I74640424"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Kana Shimizu","raw_affiliation_strings":["Department of Computer Science and Engineering, Waseda University, Tokyo, Japan. shimizu.kana@waseda.jp","National Institute of Advanced Industrial Science and Technology, Tokyo, Japan. shimizu.kana@waseda.jp","National Institute of Advanced Industrial Science and Technology, Tokyo, Japan","Department of Computer Science and Engineering, Waseda University, Tokyo, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering, Waseda University, Tokyo, Japan. shimizu.kana@waseda.jp","institution_ids":["https://openalex.org/I150744194"]},{"raw_affiliation_string":"National Institute of Advanced Industrial Science and Technology, Tokyo, Japan. shimizu.kana@waseda.jp","institution_ids":["https://openalex.org/I74640424"]},{"raw_affiliation_string":"National Institute of Advanced Industrial Science and Technology, Tokyo, Japan","institution_ids":["https://openalex.org/I73613424"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, Waseda University, Tokyo, Japan","institution_ids":["https://openalex.org/I150744194"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5043657069"],"corresponding_institution_ids":["https://openalex.org/I150744194","https://openalex.org/I73613424","https://openalex.org/I74640424"],"apc_list":{"value":1490,"currency":"GBP","value_usd":1827},"apc_paid":{"value":1490,"currency":"GBP","value_usd":1827},"fwci":0.9185,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.7790924,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"17","issue":"1","first_page":"9","last_page":"9"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10237","display_name":"Cryptography and Data Security","score":0.9965000152587891,"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":0.9965000152587891,"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":0.9923999905586243,"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/T12009","display_name":"Hedgehog Signaling Pathway Studies","score":0.9628000259399414,"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/substring","display_name":"Substring","score":0.8937839269638062},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8150767087936401},{"id":"https://openalex.org/keywords/recursion","display_name":"Recursion (computer science)","score":0.6388295888900757},{"id":"https://openalex.org/keywords/table","display_name":"Table (database)","score":0.5272977352142334},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.4611608684062958},{"id":"https://openalex.org/keywords/bit-array","display_name":"Bit array","score":0.4582608640193939},{"id":"https://openalex.org/keywords/reference-genome","display_name":"Reference genome","score":0.44717806577682495},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.437224805355072},{"id":"https://openalex.org/keywords/lookup-table","display_name":"Lookup table","score":0.41589492559432983},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.37162622809410095},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3284221887588501},{"id":"https://openalex.org/keywords/data-structure","display_name":"Data structure","score":0.2890359163284302},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.1826452612876892},{"id":"https://openalex.org/keywords/type","display_name":"Type (biology)","score":0.09411132335662842}],"concepts":[{"id":"https://openalex.org/C182407805","wikidata":"https://www.wikidata.org/wiki/Q2626534","display_name":"Substring","level":3,"score":0.8937839269638062},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8150767087936401},{"id":"https://openalex.org/C168773036","wikidata":"https://www.wikidata.org/wiki/Q264164","display_name":"Recursion (computer science)","level":2,"score":0.6388295888900757},{"id":"https://openalex.org/C45235069","wikidata":"https://www.wikidata.org/wiki/Q278425","display_name":"Table (database)","level":2,"score":0.5272977352142334},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.4611608684062958},{"id":"https://openalex.org/C150807984","wikidata":"https://www.wikidata.org/wiki/Q1992074","display_name":"Bit array","level":3,"score":0.4582608640193939},{"id":"https://openalex.org/C192953774","wikidata":"https://www.wikidata.org/wiki/Q7307127","display_name":"Reference genome","level":4,"score":0.44717806577682495},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.437224805355072},{"id":"https://openalex.org/C134835016","wikidata":"https://www.wikidata.org/wiki/Q690265","display_name":"Lookup table","level":2,"score":0.41589492559432983},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.37162622809410095},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3284221887588501},{"id":"https://openalex.org/C162319229","wikidata":"https://www.wikidata.org/wiki/Q175263","display_name":"Data structure","level":2,"score":0.2890359163284302},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.1826452612876892},{"id":"https://openalex.org/C2777299769","wikidata":"https://www.wikidata.org/wiki/Q3707858","display_name":"Type (biology)","level":2,"score":0.09411132335662842},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13015-022-00211-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-022-00211-1","pdf_url":"https://almob.biomedcentral.com/track/pdf/10.1186/s13015-022-00211-1","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"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":"Algorithms for Molecular Biology","raw_type":"journal-article"},{"id":"pmid:35473587","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35473587","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":"Algorithms for molecular biology : AMB","raw_type":null},{"id":"pmh:oai:doaj.org/article:108657317ce04001baf4c1816de84486","is_oa":true,"landing_page_url":"https://doaj.org/article/108657317ce04001baf4c1816de84486","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":"Algorithms for Molecular Biology, Vol 17, Iss 1, Pp 1-22 (2022)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:9040336","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9040336","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":"Algorithms Mol Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13015-022-00211-1","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13015-022-00211-1","pdf_url":"https://almob.biomedcentral.com/track/pdf/10.1186/s13015-022-00211-1","source":{"id":"https://openalex.org/S205663195","display_name":"Algorithms for Molecular Biology","issn_l":"1748-7188","issn":["1748-7188"],"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":"Algorithms for Molecular Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2879543046","display_name":"Big Data Processing with Compressed Secure Computation","funder_award_id":"21H05052","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G5279269448","display_name":null,"funder_award_id":"JPMJCR19F6","funder_id":"https://openalex.org/F4320338075","funder_display_name":"Core Research for Evolutional Science and Technology"},{"id":"https://openalex.org/G6718509927","display_name":null,"funder_award_id":"CREST","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G6884664920","display_name":"\u5727\u7e2e\u79d8\u533f\u8a08\u7b97\u306b\u3088\u308b\u5927\u898f\u6a21\u30c7\u30fc\u30bf\u51e6\u7406","funder_award_id":"21H04871","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G7879866177","display_name":null,"funder_award_id":"CREST","funder_id":"https://openalex.org/F4320320912","funder_display_name":"Ministry of Education, Culture, Sports, Science and Technology"},{"id":"https://openalex.org/G868272877","display_name":null,"funder_award_id":"JPMJCR19F6","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G8962319651","display_name":"Development of privacy-preserving technology for genome information analysis","funder_award_id":"19K12209","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320320912","display_name":"Ministry of Education, Culture, Sports, Science and Technology","ror":"https://ror.org/048rj2z13"},{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"},{"id":"https://openalex.org/F4320338075","display_name":"Core Research for Evolutional Science and Technology","ror":"https://ror.org/00097mb19"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4225249012.pdf","grobid_xml":"https://content.openalex.org/works/W4225249012.grobid-xml"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W190228621","https://openalex.org/W1524288918","https://openalex.org/W1599991662","https://openalex.org/W1980132682","https://openalex.org/W1987521207","https://openalex.org/W2060238632","https://openalex.org/W2087135382","https://openalex.org/W2136068515","https://openalex.org/W2141420453","https://openalex.org/W2147477044","https://openalex.org/W2161360183","https://openalex.org/W2166971704","https://openalex.org/W2233233025","https://openalex.org/W2284068942","https://openalex.org/W2408443837","https://openalex.org/W2536058570","https://openalex.org/W2584293206","https://openalex.org/W2604552141","https://openalex.org/W2615471603","https://openalex.org/W2701059868","https://openalex.org/W2767257195","https://openalex.org/W2790563985","https://openalex.org/W2805670944","https://openalex.org/W2919288702","https://openalex.org/W2949524341","https://openalex.org/W2956528105","https://openalex.org/W3014302928","https://openalex.org/W3043831752","https://openalex.org/W3044359607","https://openalex.org/W3123552000","https://openalex.org/W4255046826"],"related_works":["https://openalex.org/W1583922594","https://openalex.org/W1542422837","https://openalex.org/W1974038726","https://openalex.org/W2998448420","https://openalex.org/W1598224733","https://openalex.org/W4280502676","https://openalex.org/W2000769876","https://openalex.org/W4387216472","https://openalex.org/W3005884313","https://openalex.org/W4304891330"],"abstract_inverted_index":{"The":[0,100],"development":[1],"of":[2,73,103,170,182,191,199],"a":[3,21,26,29,36,43,55,61,70,86,128,163,177,203],"privacy-preserving":[4],"technology":[5],"is":[6,67,79,85,108,151],"important":[7],"for":[8,42,69,94],"accelerating":[9],"genome":[10,165],"data":[11],"sharing.":[12],"This":[13],"study":[14],"proposes":[15],"an":[16,50,80,160],"algorithm":[17,51],"that":[18,38,52,63,109,186],"securely":[19],"searches":[20],"variable-length":[22],"substring":[23,129],"match":[24,130],"between":[25],"query":[27,125,178,188],"and":[28,83,112,146,176,184],"database":[30,144,175,205],"sequence.":[31],"Our":[32],"concept":[33],"hinges":[34],"on":[35,98,118],"technique":[37],"efficiently":[39],"applies":[40],"FM-index":[41],"secret-sharing":[44],"scheme.":[45],"More":[46],"precisely,":[47],"we":[48],"developed":[49],"can":[53,137],"achieve":[54],"secure":[56,91,105],"table":[57,92,106,120,136],"lookup":[58,93,107],"in":[59],"such":[60],"way":[62],"[Formula:":[64,76],"see":[65,77],"text]":[66,78],"computed":[68],"given":[71],"depth":[72],"recursion":[74],"where":[75],"initial":[81],"position,":[82],"V":[84],"vector.":[87],"We":[88,158],"used":[89],"the":[90,104,119,124,134,143,147,168,174,180,187,209],"vectors":[95],"created":[96],"based":[97],"FM-index.":[99],"notable":[101],"feature":[102],"time,":[110],"communication,":[111],"round":[113],"complexities":[114],"are":[115],"not":[116],"dependent":[117],"length":[121,169,181],"N,":[122],"after":[123],"input.":[126],"Therefore,":[127],"by":[131],"reference":[132],"to":[133,155],"FM-index-based":[135],"also":[138],"be":[139],"conducted":[140,159],"independently":[141],"against":[142],"length,":[145],"entire":[148],"search":[149,206],"time":[150,190],"dramatically":[152],"improved":[153],"compared":[154],"previous":[156],"approaches.":[157],"experiment":[161],"using":[162],"human":[164],"sequence":[166],"with":[167,179],"10":[171],"million":[172],"as":[173],"100":[183],"found":[185],"response":[189],"our":[192],"protocol":[193,207],"was":[194],"at":[195],"least":[196],"three":[197],"orders":[198],"magnitude":[200],"faster":[201],"than":[202],"non-indexed":[204],"under":[208],"realistic":[210],"computation/network":[211],"environment.":[212]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
