{"id":"https://openalex.org/W2171607324","doi":"https://doi.org/10.1093/bioinformatics/btq705","title":"A novel method for assigning functional linkages to proteins using enhanced phylogenetic trees","display_name":"A novel method for assigning functional linkages to proteins using enhanced phylogenetic trees","publication_year":2010,"publication_date":"2010-12-17","ids":{"openalex":"https://openalex.org/W2171607324","doi":"https://doi.org/10.1093/bioinformatics/btq705","mag":"2171607324","pmid":"https://pubmed.ncbi.nlm.nih.gov/21169380"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btq705","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq705","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/5/700/48865189/bioinformatics_27_5_700.pdf","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":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/27/5/700/48865189/bioinformatics_27_5_700.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5022000036","display_name":"Hung Xuan Ta","orcid":"https://orcid.org/0000-0002-1883-1190"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Hung Xuan Ta","raw_affiliation_strings":["1 Institute of Biotechnology and 2Division of Genetics, Faculty of Biological and Environmental Sciences, PO Box 56, 00014 University of Helsinki, Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Institute of Biotechnology and 2Division of Genetics, Faculty of Biological and Environmental Sciences, PO Box 56, 00014 University of Helsinki, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110295182","display_name":"Patrik Koskinen","orcid":null},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Patrik Koskinen","raw_affiliation_strings":["1 Institute of Biotechnology and 2Division of Genetics, Faculty of Biological and Environmental Sciences, PO Box 56, 00014 University of Helsinki, Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Institute of Biotechnology and 2Division of Genetics, Faculty of Biological and Environmental Sciences, PO Box 56, 00014 University of Helsinki, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064498279","display_name":"Liisa Holm","orcid":"https://orcid.org/0000-0002-7807-2966"},"institutions":[{"id":"https://openalex.org/I133731052","display_name":"University of Helsinki","ror":"https://ror.org/040af2s02","country_code":"FI","type":"education","lineage":["https://openalex.org/I133731052"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Liisa Holm","raw_affiliation_strings":["1 Institute of Biotechnology and 2Division of Genetics, Faculty of Biological and Environmental Sciences, PO Box 56, 00014 University of Helsinki, Helsinki, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Institute of Biotechnology and 2Division of Genetics, Faculty of Biological and Environmental Sciences, PO Box 56, 00014 University of Helsinki, Helsinki, Finland","institution_ids":["https://openalex.org/I133731052"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.4084,"has_fulltext":true,"cited_by_count":20,"citation_normalized_percentile":{"value":0.64372759,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"27","issue":"5","first_page":"700","last_page":"706"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.6906999945640564,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.6906999945640564,"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":0.10809999704360962,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.0851999968290329,"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":0.9271308183670044},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6760119199752808},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.6593010425567627},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.6369571089744568},{"id":"https://openalex.org/keywords/phylogenetic-network","display_name":"Phylogenetic network","score":0.5694044828414917},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.5238989591598511},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.518913984298706},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5187311768531799},{"id":"https://openalex.org/keywords/gene-duplication","display_name":"Gene duplication","score":0.47365009784698486},{"id":"https://openalex.org/keywords/protein-evolution","display_name":"Protein evolution","score":0.46205583214759827},{"id":"https://openalex.org/keywords/computational-phylogenetics","display_name":"Computational phylogenetics","score":0.4584048092365265},{"id":"https://openalex.org/keywords/protein-family","display_name":"Protein family","score":0.4573099613189697},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3538552522659302},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2987188696861267},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.13815683126449585},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.09706678986549377}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.9271308183670044},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6760119199752808},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.6593010425567627},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.6369571089744568},{"id":"https://openalex.org/C26619641","wikidata":"https://www.wikidata.org/wiki/Q3142246","display_name":"Phylogenetic network","level":4,"score":0.5694044828414917},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.5238989591598511},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.518913984298706},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5187311768531799},{"id":"https://openalex.org/C7602840","wikidata":"https://www.wikidata.org/wiki/Q746284","display_name":"Gene duplication","level":3,"score":0.47365009784698486},{"id":"https://openalex.org/C2992240565","wikidata":"https://www.wikidata.org/wiki/Q856529","display_name":"Protein evolution","level":3,"score":0.46205583214759827},{"id":"https://openalex.org/C41168302","wikidata":"https://www.wikidata.org/wiki/Q3772859","display_name":"Computational phylogenetics","level":5,"score":0.4584048092365265},{"id":"https://openalex.org/C171897839","wikidata":"https://www.wikidata.org/wiki/Q417841","display_name":"Protein family","level":3,"score":0.4573099613189697},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3538552522659302},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2987188696861267},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.13815683126449585},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.09706678986549377}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","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":"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":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","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}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btq705","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq705","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/5/700/48865189/bioinformatics_27_5_700.pdf","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:21169380","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21169380","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":{"id":"doi:10.1093/bioinformatics/btq705","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btq705","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/27/5/700/48865189/bioinformatics_27_5_700.pdf","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"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2171607324.pdf","grobid_xml":"https://content.openalex.org/works/W2171607324.grobid-xml"},"referenced_works_count":47,"referenced_works":["https://openalex.org/W1542454955","https://openalex.org/W1863042168","https://openalex.org/W1958476169","https://openalex.org/W1973434492","https://openalex.org/W1979770219","https://openalex.org/W1980578041","https://openalex.org/W1995117714","https://openalex.org/W1995409416","https://openalex.org/W2032506253","https://openalex.org/W2037753747","https://openalex.org/W2039950254","https://openalex.org/W2040660680","https://openalex.org/W2044514479","https://openalex.org/W2050331566","https://openalex.org/W2050721857","https://openalex.org/W2054187015","https://openalex.org/W2057885377","https://openalex.org/W2063026923","https://openalex.org/W2080922074","https://openalex.org/W2084619201","https://openalex.org/W2095957046","https://openalex.org/W2096358531","https://openalex.org/W2102379149","https://openalex.org/W2103017472","https://openalex.org/W2107424557","https://openalex.org/W2107717979","https://openalex.org/W2109715166","https://openalex.org/W2116117181","https://openalex.org/W2116447934","https://openalex.org/W2117436816","https://openalex.org/W2119603641","https://openalex.org/W2124354935","https://openalex.org/W2127839728","https://openalex.org/W2128049108","https://openalex.org/W2137464714","https://openalex.org/W2142510328","https://openalex.org/W2146312020","https://openalex.org/W2148043260","https://openalex.org/W2151831732","https://openalex.org/W2152568394","https://openalex.org/W2154139219","https://openalex.org/W2160697532","https://openalex.org/W2167188257","https://openalex.org/W2170190415","https://openalex.org/W2171430493","https://openalex.org/W4252706339","https://openalex.org/W4254712992"],"related_works":["https://openalex.org/W85430217","https://openalex.org/W4389053046","https://openalex.org/W2800044728","https://openalex.org/W2363720861","https://openalex.org/W2607237371","https://openalex.org/W3088015816","https://openalex.org/W2534129866","https://openalex.org/W2950925648","https://openalex.org/W227783133","https://openalex.org/W1600112846"],"abstract_inverted_index":{"MOTIVATION:":[0],"Functional":[1],"linkages":[2,161],"implicate":[3],"pairwise":[4],"relationships":[5],"between":[6,128],"proteins":[7,19,163],"that":[8,50,82],"work":[9],"together":[10],"to":[11,22,44,135],"implement":[12],"biological":[13],"tasks.":[14],"During":[15],"evolution,":[16],"functionally":[17,138],"linked":[18],"are":[20,133],"likely":[21],"be":[23],"preserved":[24],"or":[25,78],"eliminated":[26],"across":[27,76,91],"a":[28,33,60,66,106,114],"range":[29],"of":[30,47,59,69,73,86,88,110,113,151],"genomes":[31],"in":[32],"correlated":[34],"fashion.":[35],"Based":[36],"on":[37],"this":[38,74,89],"hypothesis,":[39],"phylogenetic":[40,104,130,145],"profiling-based":[41],"approaches":[42],"try":[43],"detect":[45,136],"pairs":[46],"protein":[48,61,75,90,100,115,140],"families":[49],"show":[51],"similar":[52],"evolutionary":[53,57,149],"patterns.":[54],"Traditionally,":[55],"the":[56,84,111,137,143,168],"pattern":[58],"is":[62],"encoded":[63],"by":[64,101,120],"either":[65],"binary":[67],"profile":[68,81],"presence":[70],"and":[71,122,158],"absence":[72],"species":[77],"an":[79],"occurrence":[80],"indicates":[83],"distribution":[85],"copies":[87],"species.":[92],"RESULTS:":[93],"In":[94],"our":[95,153],"study,":[96],"we":[97,132],"characterize":[98],"each":[99],"its":[102],"enhanced":[103,129,144],"tree,":[105],"novel":[107],"graphical":[108],"model":[109],"evolution":[112],"family":[116],"with":[117,167],"explicitly":[118],"marked":[119],"speciation":[121],"duplication":[123],"events.":[124],"By":[125],"topological":[126],"comparison":[127],"trees,":[131],"able":[134],"associated":[139],"pairs.":[141],"Because":[142],"trees":[146],"contain":[147],"more":[148,164],"information":[150],"proteins,":[152],"method":[154],"shows":[155],"greater":[156],"performance":[157],"discovers":[159],"functional":[160],"among":[162],"reliably":[165],"compared":[166],"conventional":[169],"approaches.":[170]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2026-06-17T08:01:34.144755","created_date":"2025-10-10T00:00:00"}
