{"id":"https://openalex.org/W4254712992","doi":"https://doi.org/10.1371/journal.pcbi.0010003","title":"Predicting Functional Gene Links from Phylogenetic-Statistical Analyses of Whole Genomes","display_name":"Predicting Functional Gene Links from Phylogenetic-Statistical Analyses of Whole Genomes","publication_year":2005,"publication_date":"2005-06-24","ids":{"openalex":"https://openalex.org/W4254712992","doi":"https://doi.org/10.1371/journal.pcbi.0010003"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.0010003","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.0010003","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0010003&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0010003&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5055008723","display_name":"Daniel Barker","orcid":"https://orcid.org/0000-0002-9255-8989"},"institutions":[{"id":"https://openalex.org/I71052956","display_name":"University of Reading","ror":"https://ror.org/05v62cm79","country_code":"GB","type":"education","lineage":["https://openalex.org/I71052956"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Daniel Barker","raw_affiliation_strings":["School of Animal and Microbial Sciences, University of Reading, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Animal and Microbial Sciences, University of Reading, United Kingdom","institution_ids":["https://openalex.org/I71052956"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5053582890","display_name":"Mark Pagel","orcid":"https://orcid.org/0000-0001-7287-8865"},"institutions":[{"id":"https://openalex.org/I71052956","display_name":"University of Reading","ror":"https://ror.org/05v62cm79","country_code":"GB","type":"education","lineage":["https://openalex.org/I71052956"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Mark Pagel","raw_affiliation_strings":["School of Animal and Microbial Sciences, University of Reading, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Animal and Microbial Sciences, University of Reading, United Kingdom","institution_ids":["https://openalex.org/I71052956"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I71052956"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":4.1506,"has_fulltext":true,"cited_by_count":168,"citation_normalized_percentile":{"value":0.94926577,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"1","issue":"1","first_page":"e3","last_page":"e3"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9975000023841858,"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":0.9975000023841858,"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":0.9973999857902527,"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/T10012","display_name":"Genetic diversity and population structure","score":0.9876000285148621,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.8500846028327942},{"id":"https://openalex.org/keywords/false-positive-paradox","display_name":"False positive paradox","score":0.8058895468711853},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6882671117782593},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5982264280319214},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.5891202092170715},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5870695114135742},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5762343406677246},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.43489181995391846},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.4234042465686798},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.1534382402896881},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.1049218475818634}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.8500846028327942},{"id":"https://openalex.org/C64869954","wikidata":"https://www.wikidata.org/wiki/Q1859747","display_name":"False positive paradox","level":2,"score":0.8058895468711853},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6882671117782593},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5982264280319214},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.5891202092170715},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5870695114135742},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5762343406677246},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.43489181995391846},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.4234042465686798},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.1534382402896881},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.1049218475818634}],"mesh":[],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.0010003","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.0010003","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0010003&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},{"id":"pmh:oai:centaur.reading.ac.uk:10271","is_oa":false,"landing_page_url":"https://centaur.reading.ac.uk/10271/","pdf_url":null,"source":{"id":"https://openalex.org/S4306402273","display_name":"CentAUR (University of Reading)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I71052956","host_organization_name":"University of Reading","host_organization_lineage":["https://openalex.org/I71052956"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Article"},{"id":"pmh:oai:doaj.org/article:4acc57f2792a4a26b5b7ad58926ecacf","is_oa":true,"landing_page_url":"https://doaj.org/article/4acc57f2792a4a26b5b7ad58926ecacf","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 1, Iss 1, p e3 (2005)","raw_type":"article"},{"id":"pmh:oai:doaj.org/article:aec9d8dc7b8c4e4887da8017e634520f","is_oa":true,"landing_page_url":"https://doaj.org/article/aec9d8dc7b8c4e4887da8017e634520f","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 1, Iss 1, p e3 (2005)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:1183509","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1183509","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":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:research-repository.st-andrews.ac.uk:10023/1588","is_oa":true,"landing_page_url":"http://www.scopus.com/inward/record.url?scp=55449127787&partnerID=8YFLogxK","pdf_url":null,"source":{"id":"https://openalex.org/S4306400230","display_name":"St Andrews Research Repository (St Andrews Research Repository)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I16835326","host_organization_name":"University of St Andrews","host_organization_lineage":["https://openalex.org/I16835326"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Journal article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.0010003","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.0010003","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.0010003&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land","score":0.5899999737739563}],"awards":[],"funders":[{"id":"https://openalex.org/F4320332167","display_name":"Directorate for Biological Sciences","ror":"https://ror.org/001xhss06"},{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4254712992.pdf","grobid_xml":"https://content.openalex.org/works/W4254712992.grobid-xml"},"referenced_works_count":40,"referenced_works":["https://openalex.org/W1516731772","https://openalex.org/W1945313450","https://openalex.org/W1980578041","https://openalex.org/W1991071802","https://openalex.org/W1996423252","https://openalex.org/W2001082957","https://openalex.org/W2010814032","https://openalex.org/W2013410948","https://openalex.org/W2041079361","https://openalex.org/W2057293816","https://openalex.org/W2057494903","https://openalex.org/W2068225247","https://openalex.org/W2072349904","https://openalex.org/W2079517933","https://openalex.org/W2095178364","https://openalex.org/W2095496907","https://openalex.org/W2095805667","https://openalex.org/W2096358531","https://openalex.org/W2096484952","https://openalex.org/W2097382368","https://openalex.org/W2101546326","https://openalex.org/W2102424972","https://openalex.org/W2113654464","https://openalex.org/W2114525641","https://openalex.org/W2116503869","https://openalex.org/W2130416410","https://openalex.org/W2134871125","https://openalex.org/W2136977855","https://openalex.org/W2137786672","https://openalex.org/W2141913814","https://openalex.org/W2144885342","https://openalex.org/W2150227862","https://openalex.org/W2150783480","https://openalex.org/W2152568394","https://openalex.org/W2158714788","https://openalex.org/W3103786587","https://openalex.org/W4236956086","https://openalex.org/W4239160012","https://openalex.org/W4252706339","https://openalex.org/W4388245928"],"related_works":["https://openalex.org/W2174809885","https://openalex.org/W2883025420","https://openalex.org/W2057191541","https://openalex.org/W2949296710","https://openalex.org/W1992658754","https://openalex.org/W2111939425","https://openalex.org/W2065083790","https://openalex.org/W2604174992","https://openalex.org/W2375383082","https://openalex.org/W1974895455"],"abstract_inverted_index":{"An":[0],"important":[1],"element":[2],"of":[3,7,42,49,68,74,76,85,105,141,163,190,201,221,228],"the":[4,29,69,82,110,161,188,219],"developing":[5],"field":[6],"proteomics":[8],"is":[9],"to":[10,37,116,137,225,232],"understand":[11],"protein-protein":[12],"interactions":[13],"and":[14,44,170,204,231],"other":[15,182],"functional":[16,25,60,175,191],"links":[17,26,230],"amongst":[18],"genes.":[19,183],"Across-species":[20],"correlation":[21],"methods":[22,92,213],"for":[23,58],"detecting":[24,206],"work":[27],"on":[28,78,118],"premise":[30],"that":[31,93,109,130,208],"functionally":[32,124,148],"linked":[33,125],"proteins":[34,77],"will":[35],"tend":[36],"show":[38],"a":[39,47,53,98,103,198],"common":[40],"pattern":[41],"presence":[43,156,162],"absence":[45,158],"across":[46],"range":[48],"genomes.":[50],"We":[51,100],"describe":[52],"maximum":[54],"likelihood":[55],"statistical":[56],"model":[57],"predicting":[59],"gene":[61,234],"linkages.":[62,192],"The":[63,127,193],"method":[64,112,128],"detects":[65],"independent":[66],"instances":[67],"correlated":[70,139],"gain":[71,142],"or":[72,143,157],"loss":[73,144],"pairs":[75,132],"phylogenetic":[79,111,185],"trees,":[80],"reducing":[81],"high":[83],"rates":[84],"false":[86,202],"positives":[87,203],"observed":[88],"in":[89,102,152],"conventional":[90],"across-species":[91,119,209],"do":[94],"not":[95],"explicitly":[96],"incorporate":[97],"phylogeny.":[99],"show,":[101],"dataset":[104],"10,551":[106],"protein":[107,131,229],"pairs,":[108],"improves":[113,187],"by":[114],"up":[115],"35%":[117],"analyses":[120,210],"at":[121,134],"identifying":[122],"known":[123],"proteins.":[126],"shows":[129],"with":[133,181],"least":[135],"two":[136],"three":[138],"events":[140],"are":[145],"almost":[146],"certainly":[147],"linked.":[149],"Contingent":[150],"evolution,":[151],"which":[153],"one":[154],"gene's":[155],"depends":[159,177],"upon":[160,178],"another,":[164],"can":[165,214],"also":[166],"be":[167,216],"detected":[168],"phylogenetically,":[169],"may":[171],"identify":[172,226],"genes":[173],"whose":[174],"significance":[176],"its":[179],"interaction":[180],"Incorporating":[184],"information":[186],"prediction":[189],"improvement":[194],"derives":[195],"from":[196,205],"having":[197],"lower":[199],"rate":[200],"trends":[207],"miss.":[211],"Phylogenetic":[212],"easily":[215],"incorporated":[217],"into":[218],"screening":[220],"large-scale":[222],"bioinformatics":[223],"datasets":[224],"sets":[227],"characterise":[233],"networks.":[235]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":7},{"year":2021,"cited_by_count":15},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":7},{"year":2018,"cited_by_count":5},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":7},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":7},{"year":2013,"cited_by_count":8},{"year":2012,"cited_by_count":18}],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2025-10-10T00:00:00"}
