{"id":"https://openalex.org/W2165533101","doi":"https://doi.org/10.1093/bioinformatics/btl039","title":"CFinder: locating cliques and overlapping modules in biological networks","display_name":"CFinder: locating cliques and overlapping modules in biological networks","publication_year":2006,"publication_date":"2006-02-10","ids":{"openalex":"https://openalex.org/W2165533101","doi":"https://doi.org/10.1093/bioinformatics/btl039","mag":"2165533101","pmid":"https://pubmed.ncbi.nlm.nih.gov/16473872"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btl039","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl039","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/8/1021/48841370/bioinformatics_22_8_1021.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["arxiv","crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/22/8/1021/48841370/bioinformatics_22_8_1021.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5043156655","display_name":"Bal\u00e1zs Adamcsek","orcid":null},"institutions":[{"id":"https://openalex.org/I106118109","display_name":"E\u00f6tv\u00f6s Lor\u00e1nd University","ror":"https://ror.org/01jsq2704","country_code":"HU","type":"education","lineage":["https://openalex.org/I106118109"]}],"countries":["HU"],"is_corresponding":false,"raw_author_name":"Bal\u00e1zs Adamcsek","raw_affiliation_strings":["Department of Biological Physics, E\u00f6tv\u00f6s University 1 \u00a0 1 \u00a0 \u00a0 P\u00e1zm\u00e1ny P. stny. 1A, H-1117 Budapest, Hungary"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Physics, E\u00f6tv\u00f6s University 1 \u00a0 1 \u00a0 \u00a0 P\u00e1zm\u00e1ny P. stny. 1A, H-1117 Budapest, Hungary","institution_ids":["https://openalex.org/I106118109"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035349918","display_name":"Gergely Palla","orcid":"https://orcid.org/0000-0002-3406-4200"},"institutions":[{"id":"https://openalex.org/I7597260","display_name":"Hungarian Academy of Sciences","ror":"https://ror.org/02ks8qq67","country_code":"HU","type":"government","lineage":["https://openalex.org/I7597260"]}],"countries":["HU"],"is_corresponding":false,"raw_author_name":"Gergely Palla","raw_affiliation_strings":["Biological Physics Research Group of the Hungarian Academy of Sciences 2 \u00a0 2 \u00a0 \u00a0 P\u00e1zm\u00e1ny P. stny. 1A, H-1117 Budapest, Hungary"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biological Physics Research Group of the Hungarian Academy of Sciences 2 \u00a0 2 \u00a0 \u00a0 P\u00e1zm\u00e1ny P. stny. 1A, H-1117 Budapest, Hungary","institution_ids":["https://openalex.org/I7597260"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5000251403","display_name":"Ill\u00e9s J. Farkas","orcid":"https://orcid.org/0000-0001-5341-5582"},"institutions":[{"id":"https://openalex.org/I7597260","display_name":"Hungarian Academy of Sciences","ror":"https://ror.org/02ks8qq67","country_code":"HU","type":"government","lineage":["https://openalex.org/I7597260"]}],"countries":["HU"],"is_corresponding":false,"raw_author_name":"Ill\u00e9s J. Farkas","raw_affiliation_strings":["Biological Physics Research Group of the Hungarian Academy of Sciences 2 \u00a0 2 \u00a0 \u00a0 P\u00e1zm\u00e1ny P. stny. 1A, H-1117 Budapest, Hungary"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biological Physics Research Group of the Hungarian Academy of Sciences 2 \u00a0 2 \u00a0 \u00a0 P\u00e1zm\u00e1ny P. stny. 1A, H-1117 Budapest, Hungary","institution_ids":["https://openalex.org/I7597260"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013747794","display_name":"Imre Der\u00e9nyi","orcid":"https://orcid.org/0000-0003-1171-1214"},"institutions":[{"id":"https://openalex.org/I106118109","display_name":"E\u00f6tv\u00f6s Lor\u00e1nd University","ror":"https://ror.org/01jsq2704","country_code":"HU","type":"education","lineage":["https://openalex.org/I106118109"]}],"countries":["HU"],"is_corresponding":false,"raw_author_name":"Imre Der\u00e9nyi","raw_affiliation_strings":["Department of Biological Physics, E\u00f6tv\u00f6s University 1 \u00a0 1 \u00a0 \u00a0 P\u00e1zm\u00e1ny P. stny. 1A, H-1117 Budapest, Hungary"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Physics, E\u00f6tv\u00f6s University 1 \u00a0 1 \u00a0 \u00a0 P\u00e1zm\u00e1ny P. stny. 1A, H-1117 Budapest, Hungary","institution_ids":["https://openalex.org/I106118109"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066728847","display_name":"Tam\u00e1s Vicsek","orcid":"https://orcid.org/0000-0003-1431-2884"},"institutions":[{"id":"https://openalex.org/I106118109","display_name":"E\u00f6tv\u00f6s Lor\u00e1nd University","ror":"https://ror.org/01jsq2704","country_code":"HU","type":"education","lineage":["https://openalex.org/I106118109"]},{"id":"https://openalex.org/I7597260","display_name":"Hungarian Academy of Sciences","ror":"https://ror.org/02ks8qq67","country_code":"HU","type":"government","lineage":["https://openalex.org/I7597260"]}],"countries":["HU"],"is_corresponding":true,"raw_author_name":"Tam\u00e1s Vicsek","raw_affiliation_strings":["Biological Physics Research Group of the Hungarian Academy of Sciences 2 \u00a0 2 \u00a0 \u00a0 P\u00e1zm\u00e1ny P. stny. 1A, H-1117 Budapest, Hungary","Department of Biological Physics, E\u00f6tv\u00f6s University 1 \u00a0 1 \u00a0 \u00a0 P\u00e1zm\u00e1ny P. stny. 1A, H-1117 Budapest, Hungary"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biological Physics Research Group of the Hungarian Academy of Sciences 2 \u00a0 2 \u00a0 \u00a0 P\u00e1zm\u00e1ny P. stny. 1A, H-1117 Budapest, Hungary","institution_ids":["https://openalex.org/I7597260"]},{"raw_affiliation_string":"Department of Biological Physics, E\u00f6tv\u00f6s University 1 \u00a0 1 \u00a0 \u00a0 P\u00e1zm\u00e1ny P. stny. 1A, H-1117 Budapest, Hungary","institution_ids":["https://openalex.org/I106118109"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5066728847"],"corresponding_institution_ids":["https://openalex.org/I106118109","https://openalex.org/I7597260"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":10.3591,"has_fulltext":true,"cited_by_count":941,"citation_normalized_percentile":{"value":0.98988645,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"22","issue":"8","first_page":"1021","last_page":"1023"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9805999994277954,"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":0.9805999994277954,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.0015999999595806003,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.0015999999595806003,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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":0.7797715663909912},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.544640064239502},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4869297742843628},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.44672006368637085},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2139272391796112}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7797715663909912},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.544640064239502},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4869297742843628},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.44672006368637085},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2139272391796112}],"mesh":[{"descriptor_ui":"D001695","descriptor_name":"Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D001695","descriptor_name":"Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D001695","descriptor_name":"Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btl039","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl039","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/8/1021/48841370/bioinformatics_22_8_1021.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:16473872","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16473872","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:arXiv.org:q-bio/0602004","is_oa":true,"landing_page_url":"http://arxiv.org/abs/q-bio/0602004","pdf_url":"https://arxiv.org/pdf/q-bio/0602004","source":{"id":"https://openalex.org/S4393918464","display_name":"ArXiv.org","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"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":null,"raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.242.9120","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.242.9120","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://arxiv.org/pdf/q-bio/0602004v1.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btl039","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl039","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/8/1021/48841370/bioinformatics_22_8_1021.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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321994","display_name":"Hungarian Scientific Research Fund","ror":"https://ror.org/00v349e63"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2165533101.pdf","grobid_xml":"https://content.openalex.org/works/W2165533101.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W1513501940","https://openalex.org/W1980578041","https://openalex.org/W2081931663","https://openalex.org/W2109278577","https://openalex.org/W2123500593","https://openalex.org/W2125050594","https://openalex.org/W2130687290","https://openalex.org/W2136850043","https://openalex.org/W2159675211","https://openalex.org/W2164928285","https://openalex.org/W2166574880","https://openalex.org/W2169404653","https://openalex.org/W6676698813"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W4391913857","https://openalex.org/W2350741829"],"abstract_inverted_index":{"UNLABELLED:":[0],"Most":[1],"cellular":[2],"tasks":[3],"are":[4,154],"performed":[5],"not":[6],"by":[7,11],"individual":[8],"proteins,":[9,16],"but":[10],"groups":[12,30,74],"of":[13,31,51,75,94,113,131],"functionally":[14],"associated":[15],"often":[17,42],"referred":[18],"to":[19,84,109,118],"as":[20,29],"modules.":[21,121],"In":[22],"a":[23,49,65,114],"protein":[24,116],"association":[25,103],"network":[26,50],"modules":[27,41,60],"appear":[28],"densely":[32,72],"interconnected":[33,73],"nodes,":[34],"also":[35,124],"called":[36],"communities":[37],"or":[38],"clusters.":[39],"These":[40],"overlap":[43],"with":[44],"each":[45],"other":[46],"and":[47,69,80,91,117,140,142],"form":[48],"their":[52],"own,":[53],"in":[54,77,100],"which":[55],"nodes":[56,76],"(links)":[57],"represent":[58],"the":[59,82,88,92,111,129],"(overlaps).":[61],"We":[62,97],"introduce":[63],"CFinder,":[64],"fast":[66],"program":[67],"locating":[68,128],"visualizing":[70],"overlapping,":[71],"undirected":[78],"graphs,":[79],"allowing":[81],"user":[83],"easily":[85],"navigate":[86],"between":[87],"original":[89],"graph":[90],"web":[93],"these":[95],"groups.":[96],"show":[98],"that":[99],"gene":[101],"(protein)":[102],"networks":[104],"CFinder":[105,122,136],"can":[106,145],"be":[107,146],"used":[108],"predict":[110],"function(s)":[112],"single":[115],"discover":[119],"novel":[120],"is":[123],"very":[125],"efficient":[126],"for":[127],"cliques":[130],"large":[132],"sparse":[133],"graphs.":[134],"AVAILABILITY:":[135],"(for":[137],"Windows,":[138],"Linux":[139],"Macintosh)":[141],"its":[143],"manual":[144],"downloaded":[147],"from":[148],"http://angel.elte.hu/clustering.":[149],"SUPPLEMENTARY":[150],"INFORMATION:":[151],"Supplementary":[152],"data":[153],"available":[155],"on":[156],"Bioinformatics":[157],"online.":[158]},"counts_by_year":[{"year":2026,"cited_by_count":5},{"year":2025,"cited_by_count":19},{"year":2024,"cited_by_count":25},{"year":2023,"cited_by_count":22},{"year":2022,"cited_by_count":54},{"year":2021,"cited_by_count":59},{"year":2020,"cited_by_count":41},{"year":2019,"cited_by_count":38},{"year":2018,"cited_by_count":73},{"year":2017,"cited_by_count":85},{"year":2016,"cited_by_count":65},{"year":2015,"cited_by_count":64},{"year":2014,"cited_by_count":77},{"year":2013,"cited_by_count":76},{"year":2012,"cited_by_count":65}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
