{"id":"https://openalex.org/W2160246645","doi":"https://doi.org/10.1093/bioinformatics/btp676","title":"HIGEDA: a hierarchical gene-set genetics based algorithm for finding subtle motifs in biological sequences","display_name":"HIGEDA: a hierarchical gene-set genetics based algorithm for finding subtle motifs in biological sequences","publication_year":2009,"publication_date":"2009-12-08","ids":{"openalex":"https://openalex.org/W2160246645","doi":"https://doi.org/10.1093/bioinformatics/btp676","mag":"2160246645","pmid":"https://pubmed.ncbi.nlm.nih.gov/19996163"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp676","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp676","pdf_url":null,"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":["crossref","doaj","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5064952452","display_name":"Thanh Le","orcid":"https://orcid.org/0000-0002-2180-4222"},"institutions":[{"id":"https://openalex.org/I921990950","display_name":"University of Colorado Denver","ror":"https://ror.org/02hh7en24","country_code":"US","type":"education","lineage":["https://openalex.org/I921990950"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Thanh Le","raw_affiliation_strings":["1 Department of Computer Science and Engineering, 2 Department of Pediatrics, Computational Biosciences, Human Medical Genetics and Neuroscience Programs, University of Colorado, Denver, CO, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science and Engineering, 2 Department of Pediatrics, Computational Biosciences, Human Medical Genetics and Neuroscience Programs, University of Colorado, Denver, CO, USA","institution_ids":["https://openalex.org/I921990950"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047734445","display_name":"Tom Altman","orcid":null},"institutions":[{"id":"https://openalex.org/I921990950","display_name":"University of Colorado Denver","ror":"https://ror.org/02hh7en24","country_code":"US","type":"education","lineage":["https://openalex.org/I921990950"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tom Altman","raw_affiliation_strings":["1 Department of Computer Science and Engineering, 2 Department of Pediatrics, Computational Biosciences, Human Medical Genetics and Neuroscience Programs, University of Colorado, Denver, CO, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science and Engineering, 2 Department of Pediatrics, Computational Biosciences, Human Medical Genetics and Neuroscience Programs, University of Colorado, Denver, CO, USA","institution_ids":["https://openalex.org/I921990950"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5032439981","display_name":"Katheleen Gardiner","orcid":null},"institutions":[{"id":"https://openalex.org/I921990950","display_name":"University of Colorado Denver","ror":"https://ror.org/02hh7en24","country_code":"US","type":"education","lineage":["https://openalex.org/I921990950"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Katheleen Gardiner","raw_affiliation_strings":["1 Department of Computer Science and Engineering, 2 Department of Pediatrics, Computational Biosciences, Human Medical Genetics and Neuroscience Programs, University of Colorado, Denver, CO, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Computer Science and Engineering, 2 Department of Pediatrics, Computational Biosciences, Human Medical Genetics and Neuroscience Programs, University of Colorado, Denver, CO, USA","institution_ids":["https://openalex.org/I921990950"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5032439981"],"corresponding_institution_ids":["https://openalex.org/I921990950"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.2696,"has_fulltext":false,"cited_by_count":13,"citation_normalized_percentile":{"value":0.60960177,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"26","issue":"3","first_page":"302","last_page":"309"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9994000196456909,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9994000196456909,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9966999888420105,"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/T10015","display_name":"Genomics and Phylogenetic Studies","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"}}],"keywords":[{"id":"https://openalex.org/keywords/initialization","display_name":"Initialization","score":0.7993545532226562},{"id":"https://openalex.org/keywords/motif","display_name":"Motif (music)","score":0.749688446521759},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6366355419158936},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5692847371101379},{"id":"https://openalex.org/keywords/dynamic-programming","display_name":"Dynamic programming","score":0.4408451318740845},{"id":"https://openalex.org/keywords/sequence-motif","display_name":"Sequence motif","score":0.4354616403579712},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.42779844999313354},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.346916526556015},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.27521878480911255},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22554218769073486},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2151411771774292}],"concepts":[{"id":"https://openalex.org/C114466953","wikidata":"https://www.wikidata.org/wiki/Q6034165","display_name":"Initialization","level":2,"score":0.7993545532226562},{"id":"https://openalex.org/C32276052","wikidata":"https://www.wikidata.org/wiki/Q908349","display_name":"Motif (music)","level":2,"score":0.749688446521759},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6366355419158936},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5692847371101379},{"id":"https://openalex.org/C37404715","wikidata":"https://www.wikidata.org/wiki/Q380679","display_name":"Dynamic programming","level":2,"score":0.4408451318740845},{"id":"https://openalex.org/C117745874","wikidata":"https://www.wikidata.org/wiki/Q901612","display_name":"Sequence motif","level":3,"score":0.4354616403579712},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.42779844999313354},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.346916526556015},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.27521878480911255},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22554218769073486},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2151411771774292},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C24890656","wikidata":"https://www.wikidata.org/wiki/Q82811","display_name":"Acoustics","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017422","descriptor_name":"Sequence Analysis, DNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btp676","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp676","pdf_url":null,"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:19996163","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19996163","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}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W1214546200","https://openalex.org/W2004019212","https://openalex.org/W2050284387","https://openalex.org/W2079659879","https://openalex.org/W2087118127","https://openalex.org/W2108757877","https://openalex.org/W2111359483","https://openalex.org/W2118215072","https://openalex.org/W2142826891","https://openalex.org/W2145234224","https://openalex.org/W2149420772","https://openalex.org/W2156628505","https://openalex.org/W2157135462","https://openalex.org/W2167840024","https://openalex.org/W2423046776","https://openalex.org/W6628147189","https://openalex.org/W6681739218","https://openalex.org/W6682896526","https://openalex.org/W6683118431","https://openalex.org/W6684445230"],"related_works":["https://openalex.org/W2168642461","https://openalex.org/W3003818906","https://openalex.org/W2901786064","https://openalex.org/W2523750745","https://openalex.org/W2143837300","https://openalex.org/W2057508801","https://openalex.org/W2110403456","https://openalex.org/W2605190264","https://openalex.org/W2114066176","https://openalex.org/W2273834817"],"abstract_inverted_index":{"MOTIVATION:":[0],"Identification":[1],"of":[2,64,80,147],"motifs":[3,13,132],"in":[4,67,187],"biological":[5],"sequences":[6,152],"is":[7],"a":[8,134],"challenging":[9],"problem":[10],"because":[11],"such":[12],"are":[14,180],"often":[15],"short,":[16],"degenerate,":[17],"and":[18,48,89,116,138,162,169,177,189,193],"may":[19],"contain":[20],"gaps.":[21],"Most":[22],"algorithms":[23,38,66,165],"that":[24,76,90,104,158],"have":[25,99],"been":[26],"developed":[27,100],"for":[28,118,122,182],"motif-finding":[29,164],"use":[30],"the":[31,106,119,123,148,154],"expectation-maximization":[32],"(EM)":[33],"algorithm":[34,103,110],"iteratively.":[35],"Although":[36],"EM":[37,65,113],"can":[39,49,70,129],"converge":[40,50],"quickly,":[41],"they":[42,57],"depend":[43],"strongly":[44],"on":[45,166,191],"initialization":[46],"parameters":[47,82,121],"to":[51,83,114,141],"local":[52,87],"sub-optimal":[53],"solutions.":[54],"In":[55,126],"addition,":[56,127],"cannot":[58],"generate":[59,142],"gapped":[60,92,131,145],"motifs.":[61],"The":[62],"effectiveness":[63],"motif":[68,95,124,149],"finding":[69],"be":[71],"improved":[72],"by":[73],"incorporating":[74],"methods":[75],"choose":[77],"different":[78],"sets":[79],"initial":[81],"enable":[84],"escape":[85],"from":[86,153],"optima,":[88],"allow":[91],"alignments":[93],"within":[94],"models.":[96],"RESULTS:":[97],"We":[98,156],"HIGEDA,":[101],"an":[102,143],"uses":[105],"hierarchical":[107],"gene-set":[108],"genetic":[109],"(HGA)":[111],"with":[112,151],"initiate":[115],"search":[117],"best":[120],"model.":[125],"HIGEDA":[128,159],"identify":[130],"using":[133],"position":[135],"weight":[136],"matrix":[137],"dynamic":[139],"programming":[140],"optimal":[144],"alignment":[146],"model":[150],"dataset.":[155],"show":[157],"outperforms":[160],"MEME":[161],"other":[163],"both":[167],"DNA":[168],"protein":[170],"sequences.":[171],"AVAILABILITY":[172],"AND":[173],"IMPLEMENTATION:":[174],"Source":[175],"code":[176],"test":[178],"datasets":[179],"available":[181],"download":[183],"at":[184],"http://ouray.cudenver.edu/~tnle/,":[185],"implemented":[186],"C++":[188],"supported":[190],"Linux":[192],"MS":[194],"Windows.":[195]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":5},{"year":2012,"cited_by_count":1}],"updated_date":"2026-04-28T14:05:53.105641","created_date":"2025-10-10T00:00:00"}
