{"id":"https://openalex.org/W1521732446","doi":"https://doi.org/10.1186/1471-2105-13-s18-a10","title":"Exact biclustering algorithm for the analysis of large gene expression data sets","display_name":"Exact biclustering algorithm for the analysis of large gene expression data sets","publication_year":2012,"publication_date":"2012-12-01","ids":{"openalex":"https://openalex.org/W1521732446","doi":"https://doi.org/10.1186/1471-2105-13-s18-a10","mag":"1521732446"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-13-s18-a10","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-s18-a10","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-13-S18-A10","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-13-S18-A10","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5059226899","display_name":"Oliver Voggenreiter","orcid":null},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Oliver Voggenreiter","raw_affiliation_strings":["Department of Biology, ETH Z\u00fcrich, Z\u00fcrich, Switzerland","Department of Biology, ETH Zurich Zurich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, ETH Z\u00fcrich, Z\u00fcrich, Switzerland","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"Department of Biology, ETH Zurich Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078315366","display_name":"Stefan Bleuler","orcid":"https://orcid.org/0000-0002-1680-4789"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Stefan Bleuler","raw_affiliation_strings":["Nebion AG, Z\u00fcrich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Nebion AG, Z\u00fcrich, Switzerland","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5006955632","display_name":"Wilhelm Gruissem","orcid":"https://orcid.org/0000-0002-1872-2998"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Wilhelm Gruissem","raw_affiliation_strings":["Department of Biology, ETH Z\u00fcrich, Z\u00fcrich, Switzerland","Department of Biology, ETH Zurich Zurich, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, ETH Z\u00fcrich, Z\u00fcrich, Switzerland","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"Department of Biology, ETH Zurich Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5059226899"],"corresponding_institution_ids":["https://openalex.org/I35440088"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.8813,"has_fulltext":true,"cited_by_count":31,"citation_normalized_percentile":{"value":0.84713383,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"13","issue":"S18","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9997000098228455,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9997000098228455,"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":0.994700014591217,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9925000071525574,"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/biclustering","display_name":"Biclustering","score":0.9697511196136475},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6391867995262146},{"id":"https://openalex.org/keywords/heuristic","display_name":"Heuristic","score":0.6330095529556274},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5053477883338928},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.49823760986328125},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.47579941153526306},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.47542980313301086},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.4632049798965454},{"id":"https://openalex.org/keywords/computational-complexity-theory","display_name":"Computational complexity theory","score":0.4520537555217743},{"id":"https://openalex.org/keywords/scope","display_name":"Scope (computer science)","score":0.4351329803466797},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.32396361231803894},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.26175379753112793},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.25914689898490906},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2205771505832672},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.17940852046012878},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17308610677719116},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.09077179431915283},{"id":"https://openalex.org/keywords/correlation-clustering","display_name":"Correlation clustering","score":0.07789137959480286}],"concepts":[{"id":"https://openalex.org/C144817290","wikidata":"https://www.wikidata.org/wiki/Q2976575","display_name":"Biclustering","level":5,"score":0.9697511196136475},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6391867995262146},{"id":"https://openalex.org/C173801870","wikidata":"https://www.wikidata.org/wiki/Q201413","display_name":"Heuristic","level":2,"score":0.6330095529556274},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5053477883338928},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.49823760986328125},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.47579941153526306},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.47542980313301086},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.4632049798965454},{"id":"https://openalex.org/C179799912","wikidata":"https://www.wikidata.org/wiki/Q205084","display_name":"Computational complexity theory","level":2,"score":0.4520537555217743},{"id":"https://openalex.org/C2778012447","wikidata":"https://www.wikidata.org/wiki/Q1034415","display_name":"Scope (computer science)","level":2,"score":0.4351329803466797},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32396361231803894},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.26175379753112793},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.25914689898490906},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2205771505832672},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.17940852046012878},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17308610677719116},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.09077179431915283},{"id":"https://openalex.org/C94641424","wikidata":"https://www.wikidata.org/wiki/Q5172845","display_name":"Correlation clustering","level":3,"score":0.07789137959480286},{"id":"https://openalex.org/C33704608","wikidata":"https://www.wikidata.org/wiki/Q5014717","display_name":"CURE data clustering algorithm","level":4,"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":[],"locations_count":2,"locations":[{"id":"doi:10.1186/1471-2105-13-s18-a10","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-s18-a10","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-13-S18-A10","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:europepmc.org:2521771","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3522044","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"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-13-s18-a10","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-13-s18-a10","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-13-S18-A10","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"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":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1521732446.pdf","grobid_xml":"https://content.openalex.org/works/W1521732446.grobid-xml"},"referenced_works_count":3,"referenced_works":["https://openalex.org/W1972791615","https://openalex.org/W2105883975","https://openalex.org/W2116007667"],"related_works":["https://openalex.org/W1974340769","https://openalex.org/W2900595096","https://openalex.org/W4289277241","https://openalex.org/W2979322793","https://openalex.org/W2765801824","https://openalex.org/W2188068678","https://openalex.org/W2157302779","https://openalex.org/W4236723217","https://openalex.org/W4226363062","https://openalex.org/W2795952052"],"abstract_inverted_index":{"Biclustering":[0],"of":[1,10,18,28,56,63,84,113,126,136,152,161,206,226,277,327],"gene":[2,115,131,186,193],"expression":[3,116,132],"data":[4,67,89,320,326],"is":[5,23,297,315],"used":[6],"to":[7,24,31,42,81,86,122,216,255,269,317],"discover":[8,123],"groups":[9],"genes":[11,129,178,329],"that":[12,91,97,118,198,281,293],"are":[13,71,77,98,177],"co-expressed":[14],"over":[15,337,343],"a":[16,37,44,110,149,171,182,185,202,212,244,306],"subset":[17],"tested":[19,243],"conditions.":[20],"The":[21,103],"objective":[22],"maximize":[25],"the":[26,54,61,114,143,158,164,175,192,218,227,247,259,267,278,294,318,336,347],"detection":[27],"significant":[29],"biclusters;":[30],"do":[32],"so,":[33],"most":[34],"approaches":[35],"employ":[36],"heuristic":[38],"approximation":[39],"in":[40,79,130,170,197,310,341],"order":[41,80,215],"avoid":[43],"non-polynomial":[45],"computational":[46],"complexity.":[47],"Previous":[48],"algorithms":[49,76],"have":[50,239],"focused":[51],"on":[52,148,210,261],"enabling":[53],"discovery":[55],"biologically":[57,127],"relevant":[58,128],"results":[59],"within":[60],"scope":[62],"single":[64],"studies,":[65],"where":[66,174],"size":[68,151],"and":[69,75,96,181,187,241,330],"complexity":[70],"limited.":[72],"New":[73],"methods":[74],"required":[78],"enable":[82],"applications":[83],"biclustering":[85,137,159],"larger":[87],"scale":[88],"sets":[90],"can":[92,156],"span":[93],"multiple":[94],"experiments":[95,180],"potentially":[99],"far":[100],"more":[101],"heterogenous.":[102],"BiMax":[104,144,162,333],"[":[105,231],"1":[106,290],"]":[107,233],"algorithm":[108,145,204,230,268,296,350],"uses":[109,252],"binary":[111],"representation":[112],"matrix":[117],"has":[119],"been":[120],"proven":[121],"enriched":[124],"modules":[125],"data.":[133,154],"This":[134,264],"model":[135],"allows":[138],"for":[139,166,234,335],"exact":[140],"solutions,":[141],"however,":[142],"performs":[146],"best":[147],"restricted":[150],"input":[153,319,325],"We":[155,200,238],"view":[157],"formulation":[160],"as":[163],"search":[165,279],"all":[167,208,271],"maximal":[168,219,235,272],"bicliques":[169,260,273],"bipartite":[172,262],"graph;":[173],"nodes":[176],"or":[179],"connection":[183],"between":[184],"an":[188],"experiment":[189],"exists":[190],"if":[191],"was":[194],"significantly":[195,298],"expressed":[196],"experiment.":[199],"propose":[201],"new":[203,245,295],"capable":[205],"enumerating":[207],"biclusters":[209,340],"such":[211],"graph.":[213],"In":[214],"solve":[217],"biclique":[220],"enumeration":[221],"problem,":[222],"we":[223],"make":[224],"use":[225],"backtracking":[228],"Bron-Kerbosch":[229,249,256,349],"2":[232],"clique":[236],"enumeration.":[237],"developed":[240],"successfully":[242],"algorithm,":[246,250],"Bipartite":[248,348],"which":[251],"similar":[253],"principles":[254],"but":[257],"traverses":[258],"graphs.":[263],"approach":[265],"enables":[266],"explore":[270],"without":[274],"visiting":[275],"branches":[276],"tree":[280],"contain":[282],"previously":[283],"discovered":[284],"biclusters.":[285],"Our":[286],"results,":[287],"see":[288],"Table":[289],",":[291],"conclude":[292],"faster":[299],"at":[300],"bicluster":[301],"exploration":[302],"than":[303],"BiMax,":[304],"demonstrating":[305],"factor":[307],"n":[308,314],"improvement":[309],"running":[311],"time":[312],"(where":[313],"proportional":[316],"size).":[321],"For":[322],"instance,":[323],"with":[324],"800":[328,331],"experiments,":[332],"solved":[334],"500":[338],"thousand":[339],"just":[342],"three":[344],"minutes":[345],"whereas":[346],"takes":[351],"approximately":[352],"3":[353],"seconds.":[354]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":8},{"year":2014,"cited_by_count":5},{"year":2012,"cited_by_count":1}],"updated_date":"2026-06-15T08:34:33.830935","created_date":"2025-10-10T00:00:00"}