{"id":"https://openalex.org/W2061574900","doi":"https://doi.org/10.1186/1471-2105-10-130","title":"Willows: a memory efficient tree and forest construction package","display_name":"Willows: a memory efficient tree and forest construction package","publication_year":2009,"publication_date":"2009-05-05","ids":{"openalex":"https://openalex.org/W2061574900","doi":"https://doi.org/10.1186/1471-2105-10-130","mag":"2061574900","pmid":"https://pubmed.ncbi.nlm.nih.gov/19416535"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-10-130","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-130","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-130","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","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-130","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100775543","display_name":"Heping Zhang","orcid":"https://orcid.org/0000-0002-0688-4076"},"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":"Heping Zhang","raw_affiliation_strings":["Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT 06520-8034, USA. heping.zhang@yale.edu","Department of Epidemiology and Public Health, Yale University, School of Medicine, New Haven, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT 06520-8034, USA. heping.zhang@yale.edu","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Department of Epidemiology and Public Health, Yale University, School of Medicine, New Haven, USA","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100376896","display_name":"Minghui Wang","orcid":"https://orcid.org/0000-0001-9171-4962"},"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":false,"raw_author_name":"Minghui Wang","raw_affiliation_strings":["Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT, 06520-8034, USA","Department of Epidemiology and Public Health, Yale University, School of Medicine, New Haven, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT, 06520-8034, USA","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Department of Epidemiology and Public Health, Yale University, School of Medicine, New Haven, USA","institution_ids":["https://openalex.org/I32971472"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100441917","display_name":"Xiang Chen","orcid":"https://orcid.org/0000-0002-2499-8261"},"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":false,"raw_author_name":"Xiang Chen","raw_affiliation_strings":["Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT, 06520-8034, USA","Department of Epidemiology and Public Health, Yale University, School of Medicine, New Haven, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Epidemiology and Public Health, Yale University School of Medicine, New Haven, CT, 06520-8034, USA","institution_ids":["https://openalex.org/I32971472"]},{"raw_affiliation_string":"Department of Epidemiology and Public Health, Yale University, School of Medicine, New Haven, USA","institution_ids":["https://openalex.org/I32971472"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5100775543"],"corresponding_institution_ids":["https://openalex.org/I32971472"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":2.4685,"has_fulltext":true,"cited_by_count":32,"citation_normalized_percentile":{"value":0.89637179,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"10","issue":"1","first_page":"130","last_page":"130"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10261","display_name":"Genetic Associations and Epidemiology","score":0.7875000238418579,"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.7875000238418579,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.049300000071525574,"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/T10885","display_name":"Gene expression and cancer classification","score":0.039000000804662704,"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":0.7663308382034302},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.5847911238670349},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5284987092018127},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.46956634521484375},{"id":"https://openalex.org/keywords/r-package","display_name":"R package","score":0.45149916410446167},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.14577984809875488},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.12260603904724121}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7663308382034302},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.5847911238670349},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5284987092018127},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.46956634521484375},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.45149916410446167},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.14577984809875488},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.12260603904724121},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[{"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D055106","descriptor_name":"Genome-Wide Association Study","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055106","descriptor_name":"Genome-Wide Association Study","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055106","descriptor_name":"Genome-Wide Association Study","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055106","descriptor_name":"Genome-Wide Association Study","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-10-130","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-130","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-130","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":"pmid:19416535","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19416535","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:c75be9ef8c3b4ee884ece34441e2a3ac","is_oa":false,"landing_page_url":"https://doaj.org/article/c75be9ef8c3b4ee884ece34441e2a3ac","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"BMC Bioinformatics, Vol 10, Iss 1, p 130 (2009)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2683818","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2683818","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-10-130","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-130","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-130","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":[{"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15","score":0.6000000238418579}],"awards":[{"id":"https://openalex.org/G5576253517","display_name":null,"funder_award_id":"N01 HC25195","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G6551497379","display_name":null,"funder_award_id":"K02 DA017713","funder_id":"https://openalex.org/F4320337347","funder_display_name":"National Institute on Drug Abuse"},{"id":"https://openalex.org/G7657004681","display_name":null,"funder_award_id":"N01 HC025195","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G8157898008","display_name":null,"funder_award_id":"R01 DA016750","funder_id":"https://openalex.org/F4320337347","funder_display_name":"National Institute on Drug Abuse"}],"funders":[{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"},{"id":"https://openalex.org/F4320337347","display_name":"National Institute on Drug Abuse","ror":"https://ror.org/00fq5cm18"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2061574900.pdf","grobid_xml":"https://content.openalex.org/works/W2061574900.grobid-xml"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W1499959019","https://openalex.org/W1553500812","https://openalex.org/W1594031697","https://openalex.org/W1975899243","https://openalex.org/W1995751421","https://openalex.org/W2002666062","https://openalex.org/W2006423274","https://openalex.org/W2022110382","https://openalex.org/W2034349070","https://openalex.org/W2036198235","https://openalex.org/W2050063758","https://openalex.org/W2086099578","https://openalex.org/W2113784410","https://openalex.org/W2118921994","https://openalex.org/W2120451046","https://openalex.org/W2134783591","https://openalex.org/W2148023821","https://openalex.org/W2161633633","https://openalex.org/W2168894308","https://openalex.org/W2330820318","https://openalex.org/W2341346562","https://openalex.org/W2911964244","https://openalex.org/W3085162807"],"related_works":["https://openalex.org/W2365333639","https://openalex.org/W2347219288","https://openalex.org/W2366221835","https://openalex.org/W2365371251","https://openalex.org/W2355247546","https://openalex.org/W2379488605","https://openalex.org/W3157478955","https://openalex.org/W2566205467","https://openalex.org/W4244646660","https://openalex.org/W1588921741"],"abstract_inverted_index":{"BACKGROUND:":[0],"Existing":[1],"tree":[2],"and":[3,44,70,90,93,114,116,155],"forest":[4],"methods":[5,84],"are":[6],"powerful":[7],"bioinformatics":[8],"tools":[9],"to":[10,37,62,74],"explore":[11],"high":[12,16],"dimensional":[13],"data":[14,26,43],"including":[15],"throughput":[17],"genomic":[18,147],"data.":[19,78,102,148],"However,":[20],"they":[21],"cannot":[22],"deal":[23],"with":[24,132],"the":[25,38,42,51,64,67,97,118,133,137],"generated":[27],"by":[28],"recent":[29],"genotyping":[30],"platforms":[31],"for":[32,144],"single":[33],"nucleotide":[34],"polymorphisms":[35],"due":[36],"massive":[39,76,98],"size":[40],"of":[41,66,100,120,135,139,146],"its":[45],"excessive":[46],"memory":[47,69],"demand.":[48],"RESULTS:":[49],"Using":[50],"recursive":[52],"partitioning":[53],"technique,":[54],"we":[55],"developed":[56,125],"a":[57,128],"new":[58],"software":[59],"package,":[60],"Willows,":[61],"maximize":[63],"utility":[65],"computer":[68],"make":[71],"it":[72],"feasible":[73],"analyze":[75],"genotype":[77],"This":[79],"package":[80,106,151],"includes":[81],"three":[82],"tree-based":[83],"--":[85],"classification":[86],"tree,":[87],"random":[88],"forest,":[89,92],"deterministic":[91],"can":[94,107],"efficiently":[95],"handle":[96],"amount":[99],"SNP":[101],"In":[103],"addition,":[104],"this":[105],"easily":[108],"set":[109],"different":[110],"options":[111],"(e.g.,":[112],"algorithms":[113],"specifications)":[115],"predict":[117],"class":[119],"test":[121],"samples.":[122],"CONCLUSION:":[123],"We":[124],"Willows":[126,150],"in":[127],"user":[129],"friendly":[130],"interface":[131],"goal":[134],"maximizing":[136],"use":[138],"memory,":[140],"which":[141],"is":[142,152],"critical":[143],"analysis":[145],"The":[149],"well":[153],"documented":[154],"publicly":[156],"available":[157],"at":[158],"(http://c2s2.yale.edu/software/Willows).":[159]},"counts_by_year":[{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":5}],"updated_date":"2026-06-15T08:34:33.830935","created_date":"2025-10-10T00:00:00"}
