{"id":"https://openalex.org/W3045999237","doi":"https://doi.org/10.1093/bioinformatics/btaa661","title":"FANCY: fast estimation of privacy risk in functional genomics data","display_name":"FANCY: fast estimation of privacy risk in functional genomics data","publication_year":2020,"publication_date":"2020-07-22","ids":{"openalex":"https://openalex.org/W3045999237","doi":"https://doi.org/10.1093/bioinformatics/btaa661","mag":"3045999237","pmid":"https://pubmed.ncbi.nlm.nih.gov/32726397"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa661","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa661","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/21/5145/36150518/btaa661.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/36/21/5145/36150518/btaa661.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5040793469","display_name":"Gamze G\u00fcrsoy","orcid":"https://orcid.org/0000-0002-1352-8686"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Gamze G\u00fcrsoy","raw_affiliation_strings":["Computational Biology and Bioinformatics , New Haven, CT 06520, USA","Molecular Biophysics and Biochemistry , New Haven, CT 06520, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biology and Bioinformatics , New Haven, CT 06520, USA","institution_ids":[]},{"raw_affiliation_string":"Molecular Biophysics and Biochemistry , New Haven, CT 06520, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086627043","display_name":"Charlotte M. Brannon","orcid":"https://orcid.org/0000-0003-4390-2832"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Charlotte M Brannon","raw_affiliation_strings":["Computational Biology and Bioinformatics , New Haven, CT 06520, USA","Molecular Biophysics and Biochemistry , New Haven, CT 06520, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biology and Bioinformatics , New Haven, CT 06520, USA","institution_ids":[]},{"raw_affiliation_string":"Molecular Biophysics and Biochemistry , New Haven, CT 06520, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032592883","display_name":"F\u00e1bio C. P. Navarro","orcid":"https://orcid.org/0000-0002-5640-9070"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Fabio C P Navarro","raw_affiliation_strings":["Computational Biology and Bioinformatics , New Haven, CT 06520, USA","Molecular Biophysics and Biochemistry , New Haven, CT 06520, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biology and Bioinformatics , New Haven, CT 06520, USA","institution_ids":[]},{"raw_affiliation_string":"Molecular Biophysics and Biochemistry , New Haven, CT 06520, USA","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042321575","display_name":"Mark Gerstein","orcid":"https://orcid.org/0000-0002-9746-3719"},"institutions":[{"id":"https://openalex.org/I32971472","display_name":"Yale University","ror":"https://ror.org/03v76x132","country_code":"US","type":"education","lineage":["https://openalex.org/I32971472"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Mark Gerstein","raw_affiliation_strings":["Computational Biology and Bioinformatics , New Haven, CT 06520, USA","Computer Science, Yale University , New Haven, CT 06520, USA","Molecular Biophysics and Biochemistry , New Haven, CT 06520, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Biology and Bioinformatics , New Haven, CT 06520, USA","institution_ids":[]},{"raw_affiliation_string":"Computer Science, Yale University , New Haven, CT 06520, USA","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Molecular Biophysics and Biochemistry , New Haven, CT 06520, USA","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5042321575"],"corresponding_institution_ids":["https://openalex.org/I32971472"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.5137,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.70313094,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":95},"biblio":{"volume":"36","issue":"21","first_page":"5145","last_page":"5150"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.366100013256073,"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":0.366100013256073,"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/T10764","display_name":"Privacy-Preserving Technologies in Data","score":0.1664000004529953,"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/T10582","display_name":"Ethics in Clinical Research","score":0.07890000194311142,"subfield":{"id":"https://openalex.org/subfields/2739","display_name":"Public Health, Environmental and Occupational Health"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8160662651062012},{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.6915900707244873},{"id":"https://openalex.org/keywords/scripting-language","display_name":"Scripting language","score":0.6302083134651184},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5204358696937561},{"id":"https://openalex.org/keywords/raw-data","display_name":"Raw data","score":0.49783992767333984},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.470276415348053},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.44482123851776123},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.33020222187042236}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8160662651062012},{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.6915900707244873},{"id":"https://openalex.org/C61423126","wikidata":"https://www.wikidata.org/wiki/Q187432","display_name":"Scripting language","level":2,"score":0.6302083134651184},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5204358696937561},{"id":"https://openalex.org/C132964779","wikidata":"https://www.wikidata.org/wiki/Q2110223","display_name":"Raw data","level":2,"score":0.49783992767333984},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.470276415348053},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.44482123851776123},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.33020222187042236},{"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/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000073359","descriptor_name":"Exome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073359","descriptor_name":"Exome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000073359","descriptor_name":"Exome Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018907","descriptor_name":"Privacy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018907","descriptor_name":"Privacy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D018907","descriptor_name":"Privacy","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btaa661","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa661","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/21/5145/36150518/btaa661.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:32726397","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32726397","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:pubmedcentral.nih.gov:7850135","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7850135","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:europepmc.org:6763456","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC7850135","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaa661","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa661","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/21/5145/36150518/btaa661.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4399076203","display_name":null,"funder_award_id":"R01 HG010749","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4441724675","display_name":null,"funder_award_id":"K99 HG010909","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5748368319","display_name":null,"funder_award_id":"K99 HG010909","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"},{"id":"https://openalex.org/G674878520","display_name":null,"funder_award_id":"R01 HG010749","funder_id":"https://openalex.org/F4320337348","funder_display_name":"National Human Genome Research Institute"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337348","display_name":"National Human Genome Research Institute","ror":"https://ror.org/00baak391"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3045999237.pdf","grobid_xml":"https://content.openalex.org/works/W3045999237.grobid-xml"},"referenced_works_count":22,"referenced_works":["https://openalex.org/W1479918017","https://openalex.org/W1746819321","https://openalex.org/W1919257374","https://openalex.org/W1966711026","https://openalex.org/W2025943989","https://openalex.org/W2077499594","https://openalex.org/W2102729801","https://openalex.org/W2103441770","https://openalex.org/W2104116111","https://openalex.org/W2108234281","https://openalex.org/W2121984048","https://openalex.org/W2168133698","https://openalex.org/W2169456326","https://openalex.org/W2171777347","https://openalex.org/W2254169419","https://openalex.org/W2806277159","https://openalex.org/W2808838971","https://openalex.org/W2885727518","https://openalex.org/W2904763455","https://openalex.org/W3102229796","https://openalex.org/W4211049957","https://openalex.org/W6669930439"],"related_works":["https://openalex.org/W3023169329","https://openalex.org/W4389470870","https://openalex.org/W2782165897","https://openalex.org/W1582950852","https://openalex.org/W4300438041","https://openalex.org/W2054104202","https://openalex.org/W2139703748","https://openalex.org/W2761254753","https://openalex.org/W1024825291","https://openalex.org/W2188981919"],"abstract_inverted_index":{"MOTIVATION:":[0],"Functional":[1],"genomics":[2],"data":[3,71,194],"are":[4,195],"becoming":[5],"clinically":[6],"actionable,":[7],"raising":[8],"privacy":[9,13,68],"concerns.":[10],"However,":[11],"quantifying":[12],"leakage":[14],"via":[15],"genotyping":[16],"is":[17,106,130],"difficult":[18],"due":[19],"to":[20,147],"the":[21,36,66,77,95,101,115,125,149,166,169],"heterogeneous":[22],"nature":[23],"of":[24,38,65,80,97,103,114,127,140],"sequencing":[25,57],"techniques.":[26],"Thus,":[27,108],"we":[28,109],"present":[29],"FANCY,":[30,141],"a":[31,111],"tool":[32],"that":[33,162,180],"rapidly":[34],"estimates":[35],"number":[37,79,102,126],"leaking":[39,81,128],"variants":[40,105,129],"from":[41],"raw":[42],"RNA-Seq,":[43],"ATAC-Seq":[44],"and":[45,61,137,183],"ChIP-Seq":[46],"reads,":[47],"without":[48],"explicit":[49],"genotyping.":[50],"FANCY":[51,74],"employs":[52],"supervised":[53],"regression":[54,170],"using":[55],"overall":[56,67],"statistics":[58],"as":[59,142,144],"features":[60,150],"provides":[62],"an":[63,84],"estimate":[64],"risk":[69],"before":[70],"release.":[72],"RESULTS:":[73],"can":[75,118,151,164,186],"predict":[76],"cumulative":[78],"SNVs":[82],"with":[83,121],"average":[85],"0.95":[86],"R2":[87],"for":[88],"all":[89],"independent":[90],"test":[91],"sets.":[92],"We":[93,156],"realize":[94],"importance":[96],"accurate":[98],"prediction":[99],"when":[100,124],"leaked":[104],"low.":[107,131],"develop":[110],"special":[112],"version":[113],"model,":[116],"which":[117],"make":[119],"predictions":[120],"higher":[122],"accuracy":[123],"AVAILABILITY":[132],"AND":[133],"IMPLEMENTATION:":[134],"A":[135],"python":[136],"MATLAB":[138],"implementation":[139],"well":[143],"custom":[145],"scripts":[146],"generate":[148],"be":[152,187],"found":[153,188],"at":[154,189,197],"https://github.com/gersteinlab/FANCY.":[155],"also":[157],"provide":[158],"jupyter":[159],"notebooks":[160],"so":[161],"users":[163],"optimize":[165],"parameters":[167],"in":[168],"model":[171],"based":[172],"on":[173],"their":[174],"own":[175],"data.":[176],"An":[177],"easy-to-use":[178],"webserver":[179],"takes":[181],"inputs":[182],"displays":[184],"results":[185],"fancy.gersteinlab.org.":[190],"SUPPLEMENTARY":[191],"INFORMATION:":[192],"Supplementary":[193],"available":[196],"Bioinformatics":[198],"online.":[199]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
