{"id":"https://openalex.org/W2159693571","doi":"https://doi.org/10.1093/bioinformatics/btr203","title":"RINQ: Reference-based Indexing for Network Queries","display_name":"RINQ: Reference-based Indexing for Network Queries","publication_year":2011,"publication_date":"2011-06-14","ids":{"openalex":"https://openalex.org/W2159693571","doi":"https://doi.org/10.1093/bioinformatics/btr203","mag":"2159693571","pmid":"https://pubmed.ncbi.nlm.nih.gov/21685064"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btr203","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr203","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/13/i149/48876782/bioinformatics_27_13_i149.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/27/13/i149/48876782/bioinformatics_27_13_i149.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000929673","display_name":"G\u00fcnhan G\u00fclsoy","orcid":"https://orcid.org/0000-0001-8482-2930"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"G\u00fcnhan G\u00fclsoy","raw_affiliation_strings":["Computer and Information Sciences and Engineering Department, University of Florida, Gainesville, FL 32611, USA"],"affiliations":[{"raw_affiliation_string":"Computer and Information Sciences and Engineering Department, University of Florida, Gainesville, FL 32611, USA","institution_ids":["https://openalex.org/I33213144"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5091769289","display_name":"Tamer Kahveci","orcid":"https://orcid.org/0000-0002-4403-8612"},"institutions":[{"id":"https://openalex.org/I33213144","display_name":"University of Florida","ror":"https://ror.org/02y3ad647","country_code":"US","type":"education","lineage":["https://openalex.org/I33213144"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tamer Kahveci","raw_affiliation_strings":["Computer and Information Sciences and Engineering Department, University of Florida, Gainesville, FL 32611, USA"],"affiliations":[{"raw_affiliation_string":"Computer and Information Sciences and Engineering Department, University of Florida, Gainesville, FL 32611, USA","institution_ids":["https://openalex.org/I33213144"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5000929673"],"corresponding_institution_ids":["https://openalex.org/I33213144"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.2606,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.58983685,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"27","issue":"13","first_page":"i149","last_page":"i158"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998000264167786,"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"}},"topics":[{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998000264167786,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.995199978351593,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9872999787330627,"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/computer-science","display_name":"Computer science","score":0.8227730989456177},{"id":"https://openalex.org/keywords/search-engine-indexing","display_name":"Search engine indexing","score":0.6481521129608154},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.5699113011360168},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.5591177344322205},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.5543950796127319},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5197588801383972},{"id":"https://openalex.org/keywords/view","display_name":"View","score":0.5111568570137024},{"id":"https://openalex.org/keywords/database-index","display_name":"Database index","score":0.4908321499824524},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.48509037494659424},{"id":"https://openalex.org/keywords/query-optimization","display_name":"Query optimization","score":0.4817793071269989},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3846392333507538},{"id":"https://openalex.org/keywords/database-design","display_name":"Database design","score":0.2162553369998932},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.11751028895378113}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8227730989456177},{"id":"https://openalex.org/C75165309","wikidata":"https://www.wikidata.org/wiki/Q2258979","display_name":"Search engine indexing","level":2,"score":0.6481521129608154},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.5699113011360168},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.5591177344322205},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.5543950796127319},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5197588801383972},{"id":"https://openalex.org/C54239708","wikidata":"https://www.wikidata.org/wiki/Q1329910","display_name":"View","level":3,"score":0.5111568570137024},{"id":"https://openalex.org/C59276292","wikidata":"https://www.wikidata.org/wiki/Q580427","display_name":"Database index","level":3,"score":0.4908321499824524},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.48509037494659424},{"id":"https://openalex.org/C157692150","wikidata":"https://www.wikidata.org/wiki/Q2919848","display_name":"Query optimization","level":2,"score":0.4817793071269989},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3846392333507538},{"id":"https://openalex.org/C148840519","wikidata":"https://www.wikidata.org/wiki/Q1049878","display_name":"Database design","level":2,"score":0.2162553369998932},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.11751028895378113},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"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":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016208","descriptor_name":"Databases, Factual","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btr203","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr203","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/13/i149/48876782/bioinformatics_27_13_i149.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:21685064","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21685064","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:open-archive.highwire.org:bioinfo:27/13/i149","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/27/13/i149","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"},{"id":"pmh:oai:pubmedcentral.nih.gov:3117351","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3117351","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btr203","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btr203","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/13/i149/48876782/bioinformatics_27_13_i149.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":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2159693571.pdf","grobid_xml":"https://content.openalex.org/works/W2159693571.grobid-xml"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W1518994209","https://openalex.org/W1598875832","https://openalex.org/W1788277699","https://openalex.org/W1964321121","https://openalex.org/W1966893452","https://openalex.org/W1974024530","https://openalex.org/W1976511318","https://openalex.org/W1994303884","https://openalex.org/W1995070820","https://openalex.org/W2055043387","https://openalex.org/W2097917188","https://openalex.org/W2101511590","https://openalex.org/W2102057828","https://openalex.org/W2104009289","https://openalex.org/W2104315543","https://openalex.org/W2110017370","https://openalex.org/W2110034858","https://openalex.org/W2112200469","https://openalex.org/W2121773288","https://openalex.org/W2122144032","https://openalex.org/W2142965177","https://openalex.org/W2145631416","https://openalex.org/W2148312898","https://openalex.org/W2148944713","https://openalex.org/W2153929049","https://openalex.org/W2159482845","https://openalex.org/W2167222948","https://openalex.org/W6634440281","https://openalex.org/W6635675104","https://openalex.org/W6638011265","https://openalex.org/W6677726879","https://openalex.org/W6680870402"],"related_works":["https://openalex.org/W2379847823","https://openalex.org/W2554271401","https://openalex.org/W2889903446","https://openalex.org/W2363222923","https://openalex.org/W2372649518","https://openalex.org/W2371929047","https://openalex.org/W1505866794","https://openalex.org/W2374912898","https://openalex.org/W2003701127","https://openalex.org/W2375340541"],"abstract_inverted_index":{"We":[0,109,187,204,213],"consider":[1],"the":[2,20,56,95,113,117,121,131,136,153,161,165,174,177,184,202,210,229,242,268,271],"problem":[3],"of":[4,14,42,54,86,94,115,156,167,176,194,227,245,252,270,281],"similarity":[5,16,24,38],"queries":[6],"in":[7],"biological":[8,107],"network":[9,32,103,133,159],"databases.":[10],"Given":[11],"a":[12,29,36,46,60,69,84,91,105,144,191,216,224,246,250,279],"database":[13,21,57,96,122,126,158,178,231,251],"networks,":[15],"query":[17,31,61,132,162,185,248],"returns":[18],"all":[19,55,116,120,135],"networks":[22,44,58,88,179,255,297],"whose":[23],"(i.e.":[25],"alignment":[26,154,207],"score)":[27],"to":[28,89,152,183,198,201,219,260],"given":[30],"is":[33,45,104,127],"at":[34],"least":[35],"specified":[37],"cutoff":[39],"value.":[40],"Alignment":[41],"two":[43],"very":[47],"costly":[48],"operation,":[49],"which":[50],"makes":[51],"exhaustive":[52],"comparison":[53],"with":[59,119,134,160],"impractical.":[62],"To":[63],"tackle":[64],"this":[65],"problem,":[66],"we":[67,129,142,172],"develop":[68],"novel":[70],"indexing":[71],"method,":[72],"named":[73],"RINQ":[74],"(Reference-based":[75],"Indexing":[76],"for":[77,98,209],"Biological":[78],"Network":[79],"Queries).":[80],"Our":[81],"method":[82,218,240,266,273,288],"uses":[83],"set":[85],"reference":[87,102,137],"eliminate":[90,173],"large":[92,225],"portion":[93,193],"quickly":[97,189],"each":[99,157],"query.":[100,203],"A":[101],"small":[106,192],"network.":[108,163,186],"precompute":[110],"and":[111,147,169,276,285,292,298],"store":[112],"alignments":[114],"references":[118,221],"networks.":[123,138,212,232],"When":[124],"our":[125,239,265,287],"queried,":[128],"align":[130],"Using":[139],"these":[140,195],"alignments,":[141],"calculate":[143],"lower":[145,170],"bound":[146,151],"an":[148],"approximate":[149],"upper":[150,168],"score":[155],"With":[164],"help":[166],"bounds,":[171],"majority":[175],"without":[180],"aligning":[181],"them":[182],"also":[188,214],"identify":[190],"as":[196],"guaranteed":[197],"be":[199],"similar":[200],"perform":[205],"pairwise":[206],"only":[208,261],"remaining":[211],"propose":[215],"supervised":[217],"pick":[220],"that":[222,237],"have":[223],"chance":[226],"filtering":[228],"unpromising":[230],"Extensive":[233],"experimental":[234],"evaluation":[235],"suggests":[236],"(i)":[238],"reduced":[241],"running":[243],"time":[244],"single":[247],"on":[249],"around":[253],"300":[254],"from":[256],"over":[257],"2":[258],"days":[259],"8":[262],"h;":[263],"(ii)":[264],"outperformed":[267],"state":[269],"art":[272],"Closure":[274],"Tree":[275],"SAGA":[277],"by":[278],"factor":[280],"three":[282],"or":[283],"more;":[284],"(iii)":[286],"successfully":[289],"identified":[290],"statistically":[291],"biologically":[293],"significant":[294],"relationships":[295],"across":[296],"organisms.":[299]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":3},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
