{"id":"https://openalex.org/W1983063320","doi":"https://doi.org/10.1093/nar/gkm764","title":"Human PAML browser: a database of positive selection on human genes using phylogenetic methods","display_name":"Human PAML browser: a database of positive selection on human genes using phylogenetic methods","publication_year":2007,"publication_date":"2007-10-25","ids":{"openalex":"https://openalex.org/W1983063320","doi":"https://doi.org/10.1093/nar/gkm764","mag":"1983063320","pmid":"https://pubmed.ncbi.nlm.nih.gov/17962310"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkm764","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkm764","pdf_url":"https://academic.oup.com/nar/article-pdf/36/suppl_1/D800/7625413/gkm764.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/36/suppl_1/D800/7625413/gkm764.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5006528347","display_name":"Gabrielle Nickel","orcid":null},"institutions":[{"id":"https://openalex.org/I58956616","display_name":"Case Western Reserve University","ror":"https://ror.org/051fd9666","country_code":"US","type":"education","lineage":["https://openalex.org/I58956616"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"G. C. Nickel","raw_affiliation_strings":["Department of Genetics, Case Western Reserve University, Cleveland, OH, USA","Department of Genetics, Case Western Reserve University, Cleveland, OH, USA;"],"affiliations":[{"raw_affiliation_string":"Department of Genetics, Case Western Reserve University, Cleveland, OH, USA","institution_ids":["https://openalex.org/I58956616"]},{"raw_affiliation_string":"Department of Genetics, Case Western Reserve University, Cleveland, OH, USA;","institution_ids":["https://openalex.org/I58956616"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039627313","display_name":"David L. Tefft","orcid":null},"institutions":[{"id":"https://openalex.org/I58956616","display_name":"Case Western Reserve University","ror":"https://ror.org/051fd9666","country_code":"US","type":"education","lineage":["https://openalex.org/I58956616"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"D. Tefft","raw_affiliation_strings":["Department of Genetics, Case Western Reserve University, Cleveland, OH, USA;"],"affiliations":[{"raw_affiliation_string":"Department of Genetics, Case Western Reserve University, Cleveland, OH, USA;","institution_ids":["https://openalex.org/I58956616"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5030017379","display_name":"Mark D. Adams","orcid":"https://orcid.org/0000-0003-3161-7460"},"institutions":[{"id":"https://openalex.org/I58956616","display_name":"Case Western Reserve University","ror":"https://ror.org/051fd9666","country_code":"US","type":"education","lineage":["https://openalex.org/I58956616"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"M. D. Adams","raw_affiliation_strings":["Department of Genetics, Case Western Reserve University, Cleveland, OH, USA;"],"affiliations":[{"raw_affiliation_string":"Department of Genetics, Case Western Reserve University, Cleveland, OH, USA;","institution_ids":["https://openalex.org/I58956616"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5006528347"],"corresponding_institution_ids":["https://openalex.org/I58956616"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":1.3397,"has_fulltext":false,"cited_by_count":24,"citation_normalized_percentile":{"value":0.7867947,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"36","issue":"Database","first_page":"D800","last_page":"D808"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998999834060669,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9998999834060669,"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":0.9969000220298767,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9925000071525574,"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/biology","display_name":"Biology","score":0.872226357460022},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.759591817855835},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6476665735244751},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.6468156576156616},{"id":"https://openalex.org/keywords/lineage","display_name":"Lineage (genetic)","score":0.606788158416748},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.5593568086624146},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5213807225227356},{"id":"https://openalex.org/keywords/negative-selection","display_name":"Negative selection","score":0.5105539560317993},{"id":"https://openalex.org/keywords/human-genome","display_name":"Human genome","score":0.45795688033103943},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.4354471266269684},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4145951569080353},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.32591915130615234},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.056837648153305054}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.872226357460022},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.759591817855835},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6476665735244751},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6468156576156616},{"id":"https://openalex.org/C2776817793","wikidata":"https://www.wikidata.org/wiki/Q6553369","display_name":"Lineage (genetic)","level":3,"score":0.606788158416748},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.5593568086624146},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5213807225227356},{"id":"https://openalex.org/C7386963","wikidata":"https://www.wikidata.org/wiki/Q3954859","display_name":"Negative selection","level":4,"score":0.5105539560317993},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.45795688033103943},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.4354471266269684},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4145951569080353},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.32591915130615234},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.056837648153305054},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D005796","descriptor_name":"Genes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005796","descriptor_name":"Genes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D005796","descriptor_name":"Genes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"D012641","descriptor_name":"Selection, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012641","descriptor_name":"Selection, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012641","descriptor_name":"Selection, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016013","descriptor_name":"Likelihood Functions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016415","descriptor_name":"Sequence Alignment","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","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":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/nar/gkm764","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkm764","pdf_url":"https://academic.oup.com/nar/article-pdf/36/suppl_1/D800/7625413/gkm764.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:17962310","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17962310","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:2238824","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2238824","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gkm764","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkm764","pdf_url":"https://academic.oup.com/nar/article-pdf/36/suppl_1/D800/7625413/gkm764.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"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":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Life in Land","score":0.5099999904632568,"id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1983063320.pdf","grobid_xml":"https://content.openalex.org/works/W1983063320.grobid-xml"},"referenced_works_count":50,"referenced_works":["https://openalex.org/W1689369637","https://openalex.org/W1920973730","https://openalex.org/W1968002146","https://openalex.org/W1972673599","https://openalex.org/W1982603712","https://openalex.org/W1990144966","https://openalex.org/W2002854942","https://openalex.org/W2015292449","https://openalex.org/W2016314379","https://openalex.org/W2025484566","https://openalex.org/W2027938985","https://openalex.org/W2029549914","https://openalex.org/W2044992198","https://openalex.org/W2045391589","https://openalex.org/W2055043387","https://openalex.org/W2055543630","https://openalex.org/W2057456873","https://openalex.org/W2057538311","https://openalex.org/W2061646232","https://openalex.org/W2064322162","https://openalex.org/W2088769441","https://openalex.org/W2091203297","https://openalex.org/W2096525273","https://openalex.org/W2097040991","https://openalex.org/W2101671848","https://openalex.org/W2102424972","https://openalex.org/W2104306559","https://openalex.org/W2104878392","https://openalex.org/W2112132489","https://openalex.org/W2114611642","https://openalex.org/W2115650522","https://openalex.org/W2117790117","https://openalex.org/W2119632499","https://openalex.org/W2125548284","https://openalex.org/W2127230663","https://openalex.org/W2128969076","https://openalex.org/W2130687290","https://openalex.org/W2135123683","https://openalex.org/W2138245520","https://openalex.org/W2138578706","https://openalex.org/W2139084975","https://openalex.org/W2151464048","https://openalex.org/W2165460636","https://openalex.org/W2168909179","https://openalex.org/W2170565120","https://openalex.org/W2612812586","https://openalex.org/W4205911826","https://openalex.org/W4210241463","https://openalex.org/W4236236547","https://openalex.org/W4245543257"],"related_works":["https://openalex.org/W4229549692","https://openalex.org/W2177037579","https://openalex.org/W3161267193","https://openalex.org/W2809244473","https://openalex.org/W1576057203","https://openalex.org/W2765286129","https://openalex.org/W2387199019","https://openalex.org/W2033694563","https://openalex.org/W2130436157","https://openalex.org/W2042929965"],"abstract_inverted_index":{"With":[0],"the":[1,5,31,67,84,92,101,137,150],"recent":[2],"increase":[3],"in":[4,95,100],"number":[6],"of":[7,33,44,58,86,121,125,146],"mammalian":[8],"genomes":[9],"being":[10],"sequenced,":[11],"large-scale":[12],"genome":[13,104],"scans":[14],"for":[15,88,118,136],"human-specific":[16],"positive":[17,89,147],"selection":[18,90,148],"are":[19,70],"now":[20],"possible.":[21],"Selection":[22],"can":[23,48,116],"be":[24,49],"inferred":[25],"through":[26,113],"phylogenetic":[27],"analysis":[28,43],"by":[29,127,155],"comparing":[30],"rates":[32],"silent":[34],"and":[35,73,131,139],"replacement":[36],"substitution":[37,46,61],"between":[38],"related":[39],"species.":[40],"Maximum-likelihood":[41],"(ML)":[42],"codon":[45],"models":[47],"used":[50],"to":[51,75],"identify":[52],"genes":[53,97,126],"with":[54,98],"an":[55],"accelerated":[56],"pattern":[57],"amino":[59],"acid":[60],"on":[62],"a":[63,80,111,119],"particular":[64],"lineage.":[65],"However,":[66],"ML":[68],"methods":[69],"computationally":[71],"intensive":[72],"awkward":[74],"configure.":[76],"We":[77],"have":[78],"created":[79],"database":[81],"that":[82],"contains":[83],"results":[85,143],"tests":[87,145],"along":[91],"human":[93],"lineage":[94],"13,721":[96],"orthologs":[99],"UCSC":[102],"multispecies":[103],"alignments.":[105],"The":[106,158],"Human":[107,159],"PAML":[108,160],"Browser":[109,161],"is":[110,162],"resource":[112],"which":[114],"researchers":[115],"search":[117],"gene":[120,138],"interest":[122],"or":[123],"groups":[124],"Gene":[128],"Ontology":[129],"category,":[130],"obtain":[132],"coding":[133],"sequence":[134],"alignments":[135],"as":[140,142],"well":[141],"from":[144,149],"software":[151],"package":[152],"Phylogenetic":[153],"Analysis":[154],"Maximum":[156],"Likelihood.":[157],"available":[163],"at":[164],"http://mendel.gene.cwru.edu/adamslab/pbrowser.py.":[165]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2014,"cited_by_count":4},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":3}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}