{"id":"https://openalex.org/W2981475932","doi":"https://doi.org/10.1371/journal.pcbi.1007396","title":"Ancestral reconstruction of protein interaction networks","display_name":"Ancestral reconstruction of protein interaction networks","publication_year":2019,"publication_date":"2019-10-28","ids":{"openalex":"https://openalex.org/W2981475932","doi":"https://doi.org/10.1371/journal.pcbi.1007396","mag":"2981475932","pmid":"https://pubmed.ncbi.nlm.nih.gov/31658251"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1007396","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007396","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007396&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","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007396&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5025212281","display_name":"Benjamin J. Liebeskind","orcid":"https://orcid.org/0000-0002-8123-5260"},"institutions":[{"id":"https://openalex.org/I86519309","display_name":"The University of Texas at Austin","ror":"https://ror.org/00hj54h04","country_code":"US","type":"education","lineage":["https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Benjamin J. Liebeskind","raw_affiliation_strings":["Center for Systems and Synthetic Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America","Department of Neuroscience, University of Texas at Austin, Austin, Texas, United States of America"],"affiliations":[{"raw_affiliation_string":"Center for Systems and Synthetic Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America","institution_ids":["https://openalex.org/I86519309"]},{"raw_affiliation_string":"Department of Neuroscience, University of Texas at Austin, Austin, Texas, United States of America","institution_ids":["https://openalex.org/I86519309"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051410023","display_name":"Richard W. Aldrich","orcid":"https://orcid.org/0000-0001-7254-5876"},"institutions":[{"id":"https://openalex.org/I86519309","display_name":"The University of Texas at Austin","ror":"https://ror.org/00hj54h04","country_code":"US","type":"education","lineage":["https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Richard W. Aldrich","raw_affiliation_strings":["Department of Neuroscience, University of Texas at Austin, Austin, Texas, United States of America"],"affiliations":[{"raw_affiliation_string":"Department of Neuroscience, University of Texas at Austin, Austin, Texas, United States of America","institution_ids":["https://openalex.org/I86519309"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079751395","display_name":"Edward M. Marcotte","orcid":"https://orcid.org/0000-0001-8808-180X"},"institutions":[{"id":"https://openalex.org/I86519309","display_name":"The University of Texas at Austin","ror":"https://ror.org/00hj54h04","country_code":"US","type":"education","lineage":["https://openalex.org/I86519309"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Edward M. Marcotte","raw_affiliation_strings":["Center for Systems and Synthetic Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America"],"affiliations":[{"raw_affiliation_string":"Center for Systems and Synthetic Biology, Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas, United States of America","institution_ids":["https://openalex.org/I86519309"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5079751395"],"corresponding_institution_ids":["https://openalex.org/I86519309"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.0314,"has_fulltext":true,"cited_by_count":22,"citation_normalized_percentile":{"value":0.76506729,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"15","issue":"10","first_page":"e1007396","last_page":"e1007396"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9983999729156494,"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":0.9983999729156494,"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/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9894999861717224,"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":0.983299970626831,"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":0.6463233232498169},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5635839104652405},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5537996292114258},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.5135250687599182},{"id":"https://openalex.org/keywords/proteostasis","display_name":"Proteostasis","score":0.5104585886001587},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.5056571960449219},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.4811647832393646},{"id":"https://openalex.org/keywords/phylogenetics","display_name":"Phylogenetics","score":0.4577987492084503},{"id":"https://openalex.org/keywords/comparative-biology","display_name":"Comparative biology","score":0.4168015122413635},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4122338891029358},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.27194809913635254},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.21006202697753906},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1498497724533081}],"concepts":[{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.6463233232498169},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5635839104652405},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5537996292114258},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.5135250687599182},{"id":"https://openalex.org/C2781452922","wikidata":"https://www.wikidata.org/wiki/Q2892805","display_name":"Proteostasis","level":2,"score":0.5104585886001587},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.5056571960449219},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.4811647832393646},{"id":"https://openalex.org/C90132467","wikidata":"https://www.wikidata.org/wiki/Q171184","display_name":"Phylogenetics","level":3,"score":0.4577987492084503},{"id":"https://openalex.org/C39234202","wikidata":"https://www.wikidata.org/wiki/Q2904159","display_name":"Comparative biology","level":2,"score":0.4168015122413635},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4122338891029358},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.27194809913635254},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.21006202697753906},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1498497724533081}],"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":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005075","descriptor_name":"Biological Evolution","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":"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":"D010802","descriptor_name":"Phylogeny","qualifier_ui":null,"qualifier_name":null,"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019143","descriptor_name":"Evolution, Molecular","qualifier_ui":null,"qualifier_name":null,"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},{"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":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1371/journal.pcbi.1007396","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007396","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007396&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":"pmid:31658251","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31658251","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:e680c1ffb4034675aa2471e91e48f37d","is_oa":true,"landing_page_url":"https://doaj.org/article/e680c1ffb4034675aa2471e91e48f37d","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"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 15, Iss 10, p e1007396 (2019)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:6837550","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6837550","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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1007396","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007396","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1007396&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":[{"score":0.5400000214576721,"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land"}],"awards":[{"id":"https://openalex.org/G1002378658","display_name":null,"funder_award_id":"GM1224","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G1346015802","display_name":null,"funder_award_id":"F-1515","funder_id":"https://openalex.org/F4320306196","funder_display_name":"Welch Foundation"},{"id":"https://openalex.org/G1666390221","display_name":null,"funder_award_id":"R01 HD085901","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2366074401","display_name":null,"funder_award_id":"R01 DK110520","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3667756519","display_name":null,"funder_award_id":"R01 HD085901","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3899806454","display_name":null,"funder_award_id":"F-1515","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G4429919288","display_name":null,"funder_award_id":"HD085901","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4714635365","display_name":null,"funder_award_id":"IOS-1237975","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4914405554","display_name":null,"funder_award_id":"1237975","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G565896766","display_name":null,"funder_award_id":"R35 GM122480","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6094793950","display_name":null,"funder_award_id":"IOS-1237975","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G6135638177","display_name":null,"funder_award_id":"F-1515","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6401715999","display_name":null,"funder_award_id":"DK110520","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8275225545","display_name":null,"funder_award_id":"R01 DK110520","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G8557659522","display_name":null,"funder_award_id":"GM122480","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306196","display_name":"Welch Foundation","ror":"https://ror.org/00np6vq88"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2981475932.pdf","grobid_xml":"https://content.openalex.org/works/W2981475932.grobid-xml"},"referenced_works_count":64,"referenced_works":["https://openalex.org/W373793162","https://openalex.org/W562286511","https://openalex.org/W1496815279","https://openalex.org/W1594994360","https://openalex.org/W1611787727","https://openalex.org/W1777916189","https://openalex.org/W1828269311","https://openalex.org/W1965307886","https://openalex.org/W1966716734","https://openalex.org/W1967814055","https://openalex.org/W1987682645","https://openalex.org/W2012847399","https://openalex.org/W2013410948","https://openalex.org/W2032140335","https://openalex.org/W2041704188","https://openalex.org/W2046550649","https://openalex.org/W2051001559","https://openalex.org/W2071501030","https://openalex.org/W2089616676","https://openalex.org/W2097805330","https://openalex.org/W2101234009","https://openalex.org/W2102212449","https://openalex.org/W2102424972","https://openalex.org/W2102878257","https://openalex.org/W2104266030","https://openalex.org/W2116117181","https://openalex.org/W2118978333","https://openalex.org/W2122082385","https://openalex.org/W2123685783","https://openalex.org/W2124790653","https://openalex.org/W2127589936","https://openalex.org/W2135021437","https://openalex.org/W2135611147","https://openalex.org/W2139736670","https://openalex.org/W2146835130","https://openalex.org/W2148043260","https://openalex.org/W2150681269","https://openalex.org/W2152605077","https://openalex.org/W2160011794","https://openalex.org/W2160586365","https://openalex.org/W2161224111","https://openalex.org/W2162579346","https://openalex.org/W2165733650","https://openalex.org/W2166444569","https://openalex.org/W2171111703","https://openalex.org/W2198514005","https://openalex.org/W2345206408","https://openalex.org/W2604308930","https://openalex.org/W2616561032","https://openalex.org/W2620130100","https://openalex.org/W2620381443","https://openalex.org/W2624282460","https://openalex.org/W2755483397","https://openalex.org/W2788361091","https://openalex.org/W2794609805","https://openalex.org/W2802012092","https://openalex.org/W2809189453","https://openalex.org/W2809507176","https://openalex.org/W2933507162","https://openalex.org/W2949841808","https://openalex.org/W2951375998","https://openalex.org/W2952523648","https://openalex.org/W4254518620","https://openalex.org/W6675354045"],"related_works":["https://openalex.org/W2174809885","https://openalex.org/W2057191541","https://openalex.org/W2949296710","https://openalex.org/W2883025420","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":{"The":[0],"molecular":[1,103],"and":[2,37,60,105,110,132,144,169,190,210],"cellular":[3,23,99],"basis":[4],"of":[5,11,22,33,43,87,98,119,135,180,186,196],"novelty":[6],"is":[7,57,114],"an":[8,177],"active":[9],"area":[10],"research":[12],"in":[13,51,164,199],"evolutionary":[14,133],"biology.":[15],"Until":[16],"very":[17],"recently,":[18],"the":[19,41,75,96,129,181],"vast":[20],"majority":[21],"phenomena":[24],"were":[25,35],"so":[26],"difficult":[27],"to":[28,94,127,205],"sample":[29],"that":[30,64,89,113],"cross-species":[31],"studies":[32],"biochemistry":[34],"rare":[36],"comparative":[38,61,117],"analysis":[39],"at":[40],"level":[42],"biochemical":[44,120],"systems":[45,52],"was":[46],"almost":[47],"impossible.":[48],"Recent":[49],"advances":[50],"biology":[53],"are":[54,70],"changing":[55],"what":[56],"possible,":[58],"however,":[59],"phylogenetic":[62],"methods":[63],"can":[65],"handle":[66],"this":[67,124],"new":[68,108,125],"data":[69],"wanted.":[71],"Here,":[72],"we":[73,153,175],"introduce":[74],"term":[76],"\"phylogenetic":[77],"latent":[78],"variable":[79],"models\"":[80],"(PLVMs,":[81],"pronounced":[82],"\"plums\")":[83],"for":[84,116],"a":[85,107],"class":[86],"models":[88],"has":[90],"recently":[91],"been":[92],"used":[93],"infer":[95,128],"evolution":[97],"states":[100,131],"from":[101],"systems-level":[102],"data,":[104,152],"develop":[106,206],"parameterization":[109],"fitting":[111,208],"strategy":[112],"useful":[115],"inference":[118],"networks.":[121],"We":[122,201],"deploy":[123],"framework":[126],"ancestral":[130,155],"dynamics":[134],"protein-interaction":[136],"networks":[137],"by":[138],"analyzing":[139],">16,000":[140],"predominantly":[141],"metazoan":[142],"co-fractionation":[143],"affinity-purification":[145],"mass":[146],"spectrometry":[147],"experiments.":[148],"Based":[149],"on":[150],"these":[151,173],"estimate":[154],"interactions":[156],"across":[157],"unikonts,":[158],"broadly":[159],"recovering":[160],"protein":[161],"complexes":[162],"involved":[163],"translation,":[165],"transcription,":[166],"proteostasis,":[167],"transport,":[168],"membrane":[170],"trafficking.":[171],"Using":[172],"results,":[174],"predict":[176],"ancient":[178],"core":[179],"Commander":[182],"complex":[183],"made":[184],"up":[185],"CCDC22,":[187],"CCDC93,":[188],"C16orf62,":[189],"DSCR3,":[191],"with":[192],"more":[193],"recent":[194],"additions":[195],"COMMD-containing":[197],"proteins":[198],"tetrapods.":[200],"also":[202],"use":[203],"simulations":[204],"model":[207,213],"strategies":[209],"discuss":[211],"future":[212],"developments.":[214]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":7},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":1}],"updated_date":"2026-04-04T08:04:53.788161","created_date":"2025-10-10T00:00:00"}
