{"id":"https://openalex.org/W1987940107","doi":"https://doi.org/10.1186/1471-2105-10-242","title":"R/BHC: fast Bayesian hierarchical clustering for microarray data","display_name":"R/BHC: fast Bayesian hierarchical clustering for microarray data","publication_year":2009,"publication_date":"2009-08-06","ids":{"openalex":"https://openalex.org/W1987940107","doi":"https://doi.org/10.1186/1471-2105-10-242","mag":"1987940107","pmid":"https://pubmed.ncbi.nlm.nih.gov/19660130","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/2736174"},"language":"en","primary_location":{"is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-242","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-242","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/P4310319965","https://openalex.org/P4310320256"],"host_organization_lineage_names":["Springer Nature","BioMed Central"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true},"type":"article","type_crossref":"journal-article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-242","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5086506904","display_name":"Richard S. Savage","orcid":"https://orcid.org/0000-0001-6025-1571"},"institutions":[{"id":"https://openalex.org/I39555362","display_name":"University of Warwick","ror":"https://ror.org/01a77tt86","country_code":"GB","type":"education","lineage":["https://openalex.org/I39555362"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Richard S Savage","raw_affiliation_strings":["Systems Biology Centre, University of Warwick, Coventry House, Coventry, CV4 7AL, UK"],"affiliations":[{"raw_affiliation_string":"Systems Biology Centre, University of Warwick, Coventry House, Coventry, CV4 7AL, UK","institution_ids":["https://openalex.org/I39555362"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014018142","display_name":"Katherine Heller","orcid":"https://orcid.org/0000-0002-4848-7466"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Katherine Heller","raw_affiliation_strings":["Department of Engineering, University of Cambridge, Cambridge, CB2 1PZ, UK"],"affiliations":[{"raw_affiliation_string":"Department of Engineering, University of Cambridge, Cambridge, CB2 1PZ, UK","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101407572","display_name":"Yang Xu","orcid":"https://orcid.org/0000-0003-3068-8793"},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Yang Xu","raw_affiliation_strings":["Department of Engineering, University of Cambridge, Cambridge, CB2 1PZ, UK"],"affiliations":[{"raw_affiliation_string":"Department of Engineering, University of Cambridge, Cambridge, CB2 1PZ, UK","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010820865","display_name":"Zoubin Ghahramani","orcid":null},"institutions":[{"id":"https://openalex.org/I241749","display_name":"University of Cambridge","ror":"https://ror.org/013meh722","country_code":"GB","type":"education","lineage":["https://openalex.org/I241749"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Zoubin Ghahramani","raw_affiliation_strings":["Department of Engineering, University of Cambridge, Cambridge, CB2 1PZ, UK"],"affiliations":[{"raw_affiliation_string":"Department of Engineering, University of Cambridge, Cambridge, CB2 1PZ, UK","institution_ids":["https://openalex.org/I241749"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062672304","display_name":"William Truman","orcid":"https://orcid.org/0000-0002-9840-2539"},"institutions":[{"id":"https://openalex.org/I23923803","display_name":"University of Exeter","ror":"https://ror.org/03yghzc09","country_code":"GB","type":"education","lineage":["https://openalex.org/I23923803"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"William M Truman","raw_affiliation_strings":["School of Biosciences, University of Exeter, Exeter, EX4 4QD, UK"],"affiliations":[{"raw_affiliation_string":"School of Biosciences, University of Exeter, Exeter, EX4 4QD, UK","institution_ids":["https://openalex.org/I23923803"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037813372","display_name":"Murray Grant","orcid":"https://orcid.org/0000-0003-3357-0264"},"institutions":[{"id":"https://openalex.org/I23923803","display_name":"University of Exeter","ror":"https://ror.org/03yghzc09","country_code":"GB","type":"education","lineage":["https://openalex.org/I23923803"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Murray Grant","raw_affiliation_strings":["School of Biosciences, University of Exeter, Exeter, EX4 4QD, UK"],"affiliations":[{"raw_affiliation_string":"School of Biosciences, University of Exeter, Exeter, EX4 4QD, UK","institution_ids":["https://openalex.org/I23923803"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051420519","display_name":"Katherine Denby","orcid":"https://orcid.org/0000-0002-7857-6814"},"institutions":[{"id":"https://openalex.org/I39555362","display_name":"University of Warwick","ror":"https://ror.org/01a77tt86","country_code":"GB","type":"education","lineage":["https://openalex.org/I39555362"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Katherine J Denby","raw_affiliation_strings":["Warwick HRI, University of Warwick, Wellesbourne, CV35 9EF, UK"],"affiliations":[{"raw_affiliation_string":"Warwick HRI, University of Warwick, Wellesbourne, CV35 9EF, UK","institution_ids":["https://openalex.org/I39555362"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5112596370","display_name":"David L. Wild","orcid":null},"institutions":[{"id":"https://openalex.org/I39555362","display_name":"University of Warwick","ror":"https://ror.org/01a77tt86","country_code":"GB","type":"education","lineage":["https://openalex.org/I39555362"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"David L Wild","raw_affiliation_strings":["Systems Biology Centre, University of Warwick, Coventry House, Coventry, CV4 7AL, UK"],"affiliations":[{"raw_affiliation_string":"Systems Biology Centre, University of Warwick, Coventry House, Coventry, CV4 7AL, UK","institution_ids":["https://openalex.org/I39555362"]}]}],"institution_assertions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072,"provenance":"doaj"},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072,"provenance":"doaj"},"fwci":1.993,"has_fulltext":true,"fulltext_origin":"pdf","cited_by_count":56,"citation_normalized_percentile":{"value":0.86538,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":96},"biblio":{"volume":"10","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9994,"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":0.9994,"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/T11901","display_name":"Bayesian Methods and Mixture Models","score":0.9944,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9808,"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/hierarchical-clustering","display_name":"Hierarchical clustering","score":0.61045},{"id":"https://openalex.org/keywords/microarray-databases","display_name":"Microarray databases","score":0.45553777}],"concepts":[{"id":"https://openalex.org/C92835128","wikidata":"https://www.wikidata.org/wiki/Q1277447","display_name":"Hierarchical clustering","level":3,"score":0.61045},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6013178},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.5830721},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.55419433},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.52800155},{"id":"https://openalex.org/C8415881","wikidata":"https://www.wikidata.org/wiki/Q6839217","display_name":"Microarray analysis techniques","level":4,"score":0.4728601},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4649369},{"id":"https://openalex.org/C548314002","wikidata":"https://www.wikidata.org/wiki/Q6839218","display_name":"Microarray databases","level":5,"score":0.45553777},{"id":"https://openalex.org/C186836561","wikidata":"https://www.wikidata.org/wiki/Q1931516","display_name":"Microarray","level":4,"score":0.4301151},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4123538},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2591343},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.24794051},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12952739},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.09442502},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.071146935}],"mesh":[{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D012985","descriptor_name":"Software Design","qualifier_ui":"","qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017360","descriptor_name":"Arabidopsis","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013997","descriptor_name":"Time Factors","qualifier_ui":"","qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-242","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-242","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/P4310319965","https://openalex.org/P4310320256"],"host_organization_lineage_names":["Springer Nature","BioMed Central"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true},{"is_oa":true,"landing_page_url":"https://europepmc.org/articles/pmc2736174","pdf_url":"https://europepmc.org/articles/pmc2736174?pdf=render","source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":true,"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":["European Bioinformatics Institute"],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true},{"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2736174","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":["National Institutes of Health"],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true},{"is_oa":true,"landing_page_url":"http://wrap.warwick.ac.uk/2463/1/WRAP_Savage_hr-151209-bmc_article_june09.pdf","pdf_url":"http://wrap.warwick.ac.uk/2463/1/WRAP_Savage_hr-151209-bmc_article_june09.pdf","source":{"id":"https://openalex.org/S4306400665","display_name":"Warwick Research Archive Portal (University of Warwick)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I39555362","host_organization_name":"University of Warwick","host_organization_lineage":["https://openalex.org/I39555362"],"host_organization_lineage_names":["University of Warwick"],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false},{"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19660130","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":["National Institutes of Health"],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false}],"best_oa_location":{"is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-242","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-242","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/P4310319965","https://openalex.org/P4310320256"],"host_organization_lineage_names":["Springer Nature","BioMed Central"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true},"sustainable_development_goals":[],"grants":[],"datasets":[],"versions":[],"referenced_works_count":37,"referenced_works":["https://openalex.org/W1513910506","https://openalex.org/W1533133806","https://openalex.org/W1607198972","https://openalex.org/W1964735403","https://openalex.org/W1973249296","https://openalex.org/W1973614663","https://openalex.org/W1994181640","https://openalex.org/W2019997982","https://openalex.org/W2033403400","https://openalex.org/W2071217865","https://openalex.org/W2087684630","https://openalex.org/W2092870907","https://openalex.org/W2115876683","https://openalex.org/W2119410461","https://openalex.org/W2120636621","https://openalex.org/W2128999403","https://openalex.org/W2131456395","https://openalex.org/W2135945534","https://openalex.org/W2137784044","https://openalex.org/W2138255346","https://openalex.org/W2140422929","https://openalex.org/W2146264532","https://openalex.org/W2150926065","https://openalex.org/W2151646205","https://openalex.org/W2152012752","https://openalex.org/W2162460645","https://openalex.org/W2162721377","https://openalex.org/W2164628006","https://openalex.org/W2168846334","https://openalex.org/W2492794003","https://openalex.org/W2583838264","https://openalex.org/W2913066018","https://openalex.org/W3121318964","https://openalex.org/W3140968660","https://openalex.org/W4238306122","https://openalex.org/W4239973457","https://openalex.org/W4252521233"],"related_works":["https://openalex.org/W3152114242","https://openalex.org/W3023720143","https://openalex.org/W2796636403","https://openalex.org/W2490137852","https://openalex.org/W2151007749","https://openalex.org/W2074092657","https://openalex.org/W2028324514","https://openalex.org/W170658859","https://openalex.org/W1547158732","https://openalex.org/W1483316219"],"abstract_inverted_index":{"Abstract":[0],"Background":[1],"Although":[2],"the":[3,13,18,34,79],"use":[4,56],"of":[5,12,20,43,108,115,125],"clustering":[6,52,58],"methods":[7],"has":[8,28],"rapidly":[9],"become":[10],"one":[11],"standard":[14],"computational":[15],"approaches":[16],"in":[17,33,57,78],"literature":[19],"microarray":[21,61],"gene":[22,59],"expression":[23,60,106],"data":[24,80,104],"analysis,":[25],"little":[26],"attention":[27],"been":[29],"paid":[30],"to":[31,75,85,92,112,138],"uncertainty":[32,77],"results":[35,97],"obtained.":[36],"Results":[37],"We":[38],"present":[39],"an":[40],"R/Bioconductor":[41],"port":[42],"a":[44,70,101,113,140],"fast":[45],"novel":[46],"algorithm":[47],"for":[48,128],"Bayesian":[49,82],"agglomerative":[50],"hierarchical":[51,67],"and":[53,81,117,136],"demonstrate":[54],"its":[55],"data.":[62],"The":[63],"method":[64,121],"performs":[65],"bottom-up":[66],"clustering,":[68],"using":[69],"Dirichlet":[71],"Process":[72],"(infinite":[73],"mixture)":[74],"model":[76,83],"selection":[84],"decide":[86],"at":[87],"each":[88],"step":[89],"which":[90],"clusters":[91,132],"merge.":[93],"Conclusion":[94],"Biologically":[95],"plausible":[96],"are":[98],"presented":[99],"from":[100],"well":[102],"studied":[103],"set:":[105],"profiles":[107],"A.":[109],"thaliana":[110],"subjected":[111],"variety":[114],"biotic":[116],"abiotic":[118],"stresses.":[119],"Our":[120],"avoids":[122],"several":[123],"limitations":[124],"traditional":[126],"methods,":[127],"example":[129],"how":[130,137],"many":[131],"there":[133],"should":[134],"be":[135],"choose":[139],"principled":[141],"distance":[142],"metric.":[143]},"cited_by_api_url":"https://api.openalex.org/works?filter=cites:W1987940107","counts_by_year":[{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":3},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":6},{"year":2012,"cited_by_count":8}],"updated_date":"2024-12-14T06:21:33.185457","created_date":"2016-06-24"}