{"id":"https://openalex.org/W2142319534","doi":"https://doi.org/10.1093/bioinformatics/btg072","title":"Using multiple interdependencyto separate functional from phylogenetic correlations in protein alignments","display_name":"Using multiple interdependencyto separate functional from phylogenetic correlations in protein alignments","publication_year":2003,"publication_date":"2003-04-11","ids":{"openalex":"https://openalex.org/W2142319534","doi":"https://doi.org/10.1093/bioinformatics/btg072","mag":"2142319534","pmid":"https://pubmed.ncbi.nlm.nih.gov/12691987"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btg072","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg072","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/A5077733075","display_name":"Elisabeth R.M. Tillier","orcid":"https://orcid.org/0000-0003-2194-9058"},"institutions":[{"id":"https://openalex.org/I112260969","display_name":"Ontario Institute for Cancer Research","ror":"https://ror.org/043q8yx54","country_code":"CA","type":"funder","lineage":["https://openalex.org/I112260969"]},{"id":"https://openalex.org/I1325899441","display_name":"University Health Network","ror":"https://ror.org/042xt5161","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1325899441"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Elisabeth R.M. Tillier","raw_affiliation_strings":["Ontario Cancer Institute, University Health Network, Suite 703, 620 University Avenue, Toronto, Ontario, Canada M5G 2M9"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ontario Cancer Institute, University Health Network, Suite 703, 620 University Avenue, Toronto, Ontario, Canada M5G 2M9","institution_ids":["https://openalex.org/I112260969","https://openalex.org/I1325899441"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5103522709","display_name":"Thomas W.H. Lui","orcid":null},"institutions":[{"id":"https://openalex.org/I112260969","display_name":"Ontario Institute for Cancer Research","ror":"https://ror.org/043q8yx54","country_code":"CA","type":"funder","lineage":["https://openalex.org/I112260969"]},{"id":"https://openalex.org/I1325899441","display_name":"University Health Network","ror":"https://ror.org/042xt5161","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I1325899441"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Thomas W.H. Lui","raw_affiliation_strings":["Ontario Cancer Institute, University Health Network, Suite 703, 620 University Avenue, Toronto, Ontario, Canada M5G 2M9"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Ontario Cancer Institute, University Health Network, Suite 703, 620 University Avenue, Toronto, Ontario, Canada M5G 2M9","institution_ids":["https://openalex.org/I112260969","https://openalex.org/I1325899441"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.842,"has_fulltext":false,"cited_by_count":127,"citation_normalized_percentile":{"value":0.8503807,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"19","issue":"6","first_page":"750","last_page":"755"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.43630000948905945,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.43630000948905945,"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/T11162","display_name":"Enzyme Structure and Function","score":0.19699999690055847,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.13830000162124634,"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/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.858758270740509},{"id":"https://openalex.org/keywords/multiple-sequence-alignment","display_name":"Multiple sequence alignment","score":0.6203867197036743},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.6148450970649719},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6089983582496643},{"id":"https://openalex.org/keywords/substitution","display_name":"Substitution (logic)","score":0.549117922782898},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.5319721102714539},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.504682183265686},{"id":"https://openalex.org/keywords/sequence-alignment","display_name":"Sequence alignment","score":0.5034705996513367},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.5004982948303223},{"id":"https://openalex.org/keywords/protein-superfamily","display_name":"Protein superfamily","score":0.4633503556251526},{"id":"https://openalex.org/keywords/protein-sequencing","display_name":"Protein sequencing","score":0.44198864698410034},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.38710010051727295},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3566403090953827},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.34772616624832153},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.30169567465782166},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.16117733716964722},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1351603865623474}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.858758270740509},{"id":"https://openalex.org/C88031987","wikidata":"https://www.wikidata.org/wiki/Q1377767","display_name":"Multiple sequence alignment","level":5,"score":0.6203867197036743},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6148450970649719},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6089983582496643},{"id":"https://openalex.org/C2778220771","wikidata":"https://www.wikidata.org/wiki/Q1522579","display_name":"Substitution (logic)","level":2,"score":0.549117922782898},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.5319721102714539},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.504682183265686},{"id":"https://openalex.org/C45484198","wikidata":"https://www.wikidata.org/wiki/Q827246","display_name":"Sequence alignment","level":4,"score":0.5034705996513367},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.5004982948303223},{"id":"https://openalex.org/C178180057","wikidata":"https://www.wikidata.org/wiki/Q7251477","display_name":"Protein superfamily","level":3,"score":0.4633503556251526},{"id":"https://openalex.org/C10010492","wikidata":"https://www.wikidata.org/wiki/Q3142557","display_name":"Protein sequencing","level":4,"score":0.44198864698410034},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.38710010051727295},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3566403090953827},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.34772616624832153},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.30169567465782166},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.16117733716964722},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1351603865623474},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"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":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008958","descriptor_name":"Models, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011487","descriptor_name":"Protein Conformation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000145","qualifier_name":"classification","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":"D011786","descriptor_name":"Quality Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011786","descriptor_name":"Quality Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011786","descriptor_name":"Quality Control","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017386","descriptor_name":"Sequence Homology, Amino Acid","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"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}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btg072","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btg072","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:12691987","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/12691987","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":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":19,"referenced_works":["https://openalex.org/W1970655212","https://openalex.org/W2033806446","https://openalex.org/W2072325671","https://openalex.org/W2096279929","https://openalex.org/W2100271852","https://openalex.org/W2115217810","https://openalex.org/W2116503869","https://openalex.org/W2120549641","https://openalex.org/W2129586683","https://openalex.org/W2130479394","https://openalex.org/W2132520255","https://openalex.org/W2141885858","https://openalex.org/W2151538750","https://openalex.org/W2154131901","https://openalex.org/W2159409048","https://openalex.org/W2325276118","https://openalex.org/W2331052961","https://openalex.org/W2947000318","https://openalex.org/W3199943451"],"related_works":["https://openalex.org/W2009133913","https://openalex.org/W2015399150","https://openalex.org/W2061567716","https://openalex.org/W2275032899","https://openalex.org/W2498689255","https://openalex.org/W2032757954","https://openalex.org/W2804480386","https://openalex.org/W2075451741","https://openalex.org/W3186624150","https://openalex.org/W2505756865"],"abstract_inverted_index":{"Abstract":[0],"Motivation:":[1],"Multiple":[2],"sequence":[3],"alignments":[4],"of":[5,30,74,112,127,146,168],"homologous":[6],"proteins":[7],"are":[8,177],"useful":[9],"for":[10],"inferring":[11],"their":[12],"phylogenetic":[13,80,105],"history":[14],"and":[15,154,173],"to":[16,28,58,84,93,109,157],"reveal":[17],"functionally":[18],"important":[19],"regions":[20],"in":[21,36,65,118,164],"the":[22,37,60,66,72,103,110,119,125,128,138,141,147,165,180],"proteins.":[23],"Functional":[24],"constraints":[25],"may":[26,70],"lead":[27,83],"co-variation":[29],"two":[31],"or":[32,140],"more":[33],"amino":[34,162],"acids":[35,163],"sequence,":[38],"such":[39],"that":[40,107],"a":[41],"substitution":[42,142],"at":[43,51],"one":[44],"site":[45,114,181],"is":[46,55,91],"accompanied":[47],"by":[48,101],"compensatory":[49],"substitutions":[50],"another":[52],"site.":[53],"It":[54],"not":[56,133],"sufficient":[57],"find":[59],"statistical":[61,95],"correlations":[62,96,111],"between":[63,161],"sites":[64],"alignment":[67,129],"because":[68],"these":[69],"be":[71,190],"result":[73],"several":[75],"undetermined":[76],"causes.":[77],"In":[78],"particular,":[79],"clustering":[81],"will":[82],"many":[85,116],"strong":[86,104],"correlations.":[87],"Results:":[88],"A":[89],"procedure":[90],"developed":[92],"detect":[94],"stemming":[97],"from":[98,179],"functional":[99,159],"interaction":[100],"removing":[102],"signal":[106],"leads":[108],"each":[113],"with":[115],"others":[117],"sequence.":[120],"Our":[121],"method":[122,148],"relies":[123],"upon":[124],"accuracy":[126],"but":[130],"it":[131],"does":[132],"require":[134],"any":[135],"assumptions":[136],"about":[137],"phylogeny":[139],"process.":[143],"The":[144,171],"effectiveness":[145],"was":[149],"verified":[150],"using":[151],"computer":[152],"simulations":[153],"then":[155],"applied":[156],"predict":[158],"interactions":[160],"Pfam":[166],"database":[167],"alignments.":[169],"Availability:":[170],"program":[172],"supplementary":[174],"figures":[175],"tables":[176],"available":[178],"http://www.uhnres.utoronto.ca/tillier/depend2/dependency.html.":[182],"Contact:":[183],"e.tillier@utoronto.ca":[184],"*":[185],"To":[186],"whom":[187],"correspondence":[188],"should":[189],"addressed.":[191]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":6},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":5},{"year":2014,"cited_by_count":5},{"year":2013,"cited_by_count":7},{"year":2012,"cited_by_count":11}],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2025-10-10T00:00:00"}