{"id":"https://openalex.org/W2278336807","doi":"https://doi.org/10.1093/bib/bbv041","title":"Understanding tissue expression evolution: from expression phylogeny to phylogenetic network","display_name":"Understanding tissue expression evolution: from expression phylogeny to phylogenetic network","publication_year":2015,"publication_date":"2015-07-03","ids":{"openalex":"https://openalex.org/W2278336807","doi":"https://doi.org/10.1093/bib/bbv041","mag":"2278336807","pmid":"https://pubmed.ncbi.nlm.nih.gov/26141828"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbv041","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbv041","pdf_url":"https://academic.oup.com/bib/article-pdf/17/2/249/6685401/bbv041.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in 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/bib/article-pdf/17/2/249/6685401/bbv041.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5080712092","display_name":"Xun Gu","orcid":"https://orcid.org/0000-0001-9845-6986"},"institutions":[{"id":"https://openalex.org/I173911158","display_name":"Iowa State University","ror":"https://ror.org/04rswrd78","country_code":"US","type":"education","lineage":["https://openalex.org/I173911158"]},{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I4210087716","display_name":"Interuniversity Center for Social Science Theory and Methodology","ror":"https://ror.org/005rems48","country_code":"NL","type":"education","lineage":["https://openalex.org/I4210087716"]},{"id":"https://openalex.org/I4391768242","display_name":"State Key Laboratory of Genetic Engineering","ror":"https://ror.org/01n3rg866","country_code":null,"type":"facility","lineage":["https://openalex.org/I24943067","https://openalex.org/I4391768242"]}],"countries":["CN","NL","US"],"is_corresponding":true,"raw_author_name":"Xun Gu","raw_affiliation_strings":["Xun Gu is a professor of Fudan University and Iowa State University. His research interest has been focused on statistical theory and methods for evolutionary genomics","Iowa State University, Ames, IA 50011, USA","State Key Laboratory of Genetic Engineering, MOE Key Laboratory of Contemporary Anthropology, and Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China and Department of Genetics, Development and Cell Biology,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Xun Gu is a professor of Fudan University and Iowa State University. His research interest has been focused on statistical theory and methods for evolutionary genomics","institution_ids":["https://openalex.org/I4210087716"]},{"raw_affiliation_string":"Iowa State University, Ames, IA 50011, USA","institution_ids":["https://openalex.org/I173911158"]},{"raw_affiliation_string":"State Key Laboratory of Genetic Engineering, MOE Key Laboratory of Contemporary Anthropology, and Collaborative Innovation Center of Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, China and Department of Genetics, Development and Cell Biology,","institution_ids":["https://openalex.org/I24943067","https://openalex.org/I4391768242"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5080712092"],"corresponding_institution_ids":["https://openalex.org/I173911158","https://openalex.org/I24943067","https://openalex.org/I4210087716","https://openalex.org/I4391768242"],"apc_list":{"value":3885,"currency":"USD","value_usd":3885},"apc_paid":null,"fwci":0.8325,"has_fulltext":true,"cited_by_count":16,"citation_normalized_percentile":{"value":0.73264834,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"17","issue":"2","first_page":"249","last_page":"254"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9979000091552734,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9979000091552734,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9958999752998352,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9930999875068665,"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":0.8260332345962524},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.8164288401603699},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.7155288457870483},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.6597935557365417},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.5527396202087402},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.5387002825737},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4342975318431854},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2613659203052521},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2430073618888855},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.1157136857509613},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.08151009678840637}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.8260332345962524},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.8164288401603699},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.7155288457870483},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.6597935557365417},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.5527396202087402},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.5387002825737},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4342975318431854},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2613659203052521},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2430073618888855},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.1157136857509613},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.08151009678840637},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":"Q000235","qualifier_name":"genetics","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":false},{"descriptor_ui":"D010802","descriptor_name":"Phylogeny","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":false},{"descriptor_ui":"D014781","descriptor_name":"Viscera","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D014781","descriptor_name":"Viscera","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D014781","descriptor_name":"Viscera","qualifier_ui":"Q000502","qualifier_name":"physiology","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":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbv041","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbv041","pdf_url":"https://academic.oup.com/bib/article-pdf/17/2/249/6685401/bbv041.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26141828","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26141828","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":"Briefings in bioinformatics","raw_type":"Journal Article"},{"id":"pmh:oai:open-archive.highwire.org:bib:17/2/249","is_oa":false,"landing_page_url":"http://bib.oxfordjournals.org/cgi/content/short/17/2/249","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bib/bbv041","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbv041","pdf_url":"https://academic.oup.com/bib/article-pdf/17/2/249/6685401/bbv041.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"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":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321851","display_name":"Fudan University","ror":"https://ror.org/013q1eq08"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2278336807.pdf","grobid_xml":"https://content.openalex.org/works/W2278336807.grobid-xml"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W1966517214","https://openalex.org/W1969499963","https://openalex.org/W1971977350","https://openalex.org/W1983275320","https://openalex.org/W1986849266","https://openalex.org/W1996222640","https://openalex.org/W2014279841","https://openalex.org/W2022756254","https://openalex.org/W2028018367","https://openalex.org/W2029747645","https://openalex.org/W2037594820","https://openalex.org/W2040618467","https://openalex.org/W2044621597","https://openalex.org/W2063593640","https://openalex.org/W2065172786","https://openalex.org/W2072977772","https://openalex.org/W2080510309","https://openalex.org/W2086433728","https://openalex.org/W2087684630","https://openalex.org/W2088014737","https://openalex.org/W2093477772","https://openalex.org/W2095178364","https://openalex.org/W2098063592","https://openalex.org/W2103320667","https://openalex.org/W2110225946","https://openalex.org/W2110511835","https://openalex.org/W2116888053","https://openalex.org/W2120920194","https://openalex.org/W2123384627","https://openalex.org/W2128969076","https://openalex.org/W2150926065","https://openalex.org/W2150989284","https://openalex.org/W2154681634","https://openalex.org/W2157274247","https://openalex.org/W2164242630","https://openalex.org/W2164683872","https://openalex.org/W4243261323"],"related_works":["https://openalex.org/W4229549692","https://openalex.org/W3161267193","https://openalex.org/W2417800113","https://openalex.org/W2387199019","https://openalex.org/W1967807546","https://openalex.org/W2991335786","https://openalex.org/W2968219990","https://openalex.org/W2111939425","https://openalex.org/W2375383082","https://openalex.org/W1789273902"],"abstract_inverted_index":{"Our":[0],"understanding":[1,114],"of":[2,17,35,57,75,86,115],"tissue":[3,36,58,76],"expression":[4,39,59,77,84],"evolution":[5,78],"in":[6,79],"multi-cellular":[7,80],"model":[8],"organisms":[9],"has":[10],"been":[11],"considerably":[12],"advanced":[13],"with":[14],"the":[15,32,73,83,87,99,116,123],"help":[16],"high-throughput":[18],"technologies":[19],"from":[20,31,91],"EST,":[21],"microarray":[22],"to":[23,38,50],"RNA-seq.":[24],"Yet,":[25],"many":[26],"controversies":[27],"remained":[28],"unsolved,":[29],"ranging":[30],"evolutionary":[33,120],"patterns":[34],"expressions":[37],"phylogenetic":[40,105],"analysis.":[41],"Moreover,":[42],"despite":[43],"numerous":[44],"reports":[45],"published,":[46],"it":[47],"is":[48],"desirable":[49],"have":[51],"a":[52],"general":[53],"framework":[54],"for":[55,72,112],"study":[56,74],"evolution.":[60,125],"In":[61],"this":[62],"article,":[63],"we":[64,102],"first":[65],"provide":[66],"an":[67],"up-to-date":[68],"and":[69,119],"concise":[70],"review":[71],"organisms.":[81],"While":[82],"phylogeny":[85],"same":[88],"tissues":[89],"sampled":[90],"closely":[92],"or":[93],"intermediately":[94],"related":[95],"species":[96,100],"largely":[97],"reflects":[98],"phylogeny,":[101],"demonstrate":[103],"that":[104],"network":[106],"approach":[107],"may":[108],"shed":[109],"some":[110],"lights":[111],"our":[113],"developmental":[117],"similarity":[118],"relatedness":[121],"during":[122],"multi-tissue":[124]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":3},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2}],"updated_date":"2026-08-26T07:47:46.906454","created_date":"2025-10-10T00:00:00"}