{"id":"https://openalex.org/W3042573861","doi":"https://doi.org/10.1093/bioinformatics/btaa468","title":"The ortholog conjecture revisited: the value of orthologs and paralogs in function prediction","display_name":"The ortholog conjecture revisited: the value of orthologs and paralogs in function prediction","publication_year":2020,"publication_date":"2020-06-04","ids":{"openalex":"https://openalex.org/W3042573861","doi":"https://doi.org/10.1093/bioinformatics/btaa468","mag":"3042573861","pmid":"https://pubmed.ncbi.nlm.nih.gov/32657391"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btaa468","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa468","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/Supplement_1/i219/33489095/btaa468.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/36/Supplement_1/i219/33489095/btaa468.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5074353601","display_name":"Moses Stamboulian","orcid":"https://orcid.org/0000-0003-4212-0548"},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Moses Stamboulian","raw_affiliation_strings":["Department of Computer Science, Indiana University , Bloomington, IN 47405, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Indiana University , Bloomington, IN 47405, USA","institution_ids":["https://openalex.org/I4210119109"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075645165","display_name":"Rafael F. Guerrero","orcid":"https://orcid.org/0000-0002-8451-3609"},"institutions":[{"id":"https://openalex.org/I137902535","display_name":"North Carolina State University","ror":"https://ror.org/04tj63d06","country_code":"US","type":"education","lineage":["https://openalex.org/I137902535"]},{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rafael F Guerrero","raw_affiliation_strings":["Department of Biological Sciences, North Carolina State University , Raleigh, NC 27695, USA","Department of Computer Science, Indiana University , Bloomington, IN 47405, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Sciences, North Carolina State University , Raleigh, NC 27695, USA","institution_ids":["https://openalex.org/I137902535"]},{"raw_affiliation_string":"Department of Computer Science, Indiana University , Bloomington, IN 47405, USA","institution_ids":["https://openalex.org/I4210119109"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038671526","display_name":"Matthew W. Hahn","orcid":"https://orcid.org/0000-0002-5731-8808"},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Matthew W Hahn","raw_affiliation_strings":["Department of Biology, Indiana University , Bloomington, IN 47405, USA","Department of Computer Science, Indiana University , Bloomington, IN 47405, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biology, Indiana University , Bloomington, IN 47405, USA","institution_ids":["https://openalex.org/I4210119109"]},{"raw_affiliation_string":"Department of Computer Science, Indiana University , Bloomington, IN 47405, USA","institution_ids":["https://openalex.org/I4210119109"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5051324698","display_name":"Predrag Radivojac","orcid":"https://orcid.org/0000-0002-6769-0793"},"institutions":[{"id":"https://openalex.org/I12912129","display_name":"Northeastern University","ror":"https://ror.org/04t5xt781","country_code":"US","type":"education","lineage":["https://openalex.org/I12912129"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Predrag Radivojac","raw_affiliation_strings":["Khoury College of Computer Sciences, Northeastern University , Boston, MA 02115, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Khoury College of Computer Sciences, Northeastern University , Boston, MA 02115, USA","institution_ids":["https://openalex.org/I12912129"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5038671526","https://openalex.org/A5051324698"],"corresponding_institution_ids":["https://openalex.org/I12912129","https://openalex.org/I4210119109"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.1733,"has_fulltext":true,"cited_by_count":72,"citation_normalized_percentile":{"value":0.92979855,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"36","issue":"Supplement_1","first_page":"i219","last_page":"i226"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.4097000062465668,"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":0.4097000062465668,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.19480000436306,"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":0.14830000698566437,"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/conjecture","display_name":"Conjecture","score":0.6959580779075623},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.6958777904510498},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5842549800872803},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5472235083580017},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5414116978645325},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5058503150939941},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5004706382751465},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.45139074325561523},{"id":"https://openalex.org/keywords/homologous-chromosome","display_name":"Homologous chromosome","score":0.4391374886035919},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4272151589393616},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4155365824699402},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.34867870807647705},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1417590081691742},{"id":"https://openalex.org/keywords/combinatorics","display_name":"Combinatorics","score":0.11593928933143616}],"concepts":[{"id":"https://openalex.org/C2780990831","wikidata":"https://www.wikidata.org/wiki/Q319141","display_name":"Conjecture","level":2,"score":0.6959580779075623},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.6958777904510498},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5842549800872803},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5472235083580017},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5414116978645325},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5058503150939941},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5004706382751465},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.45139074325561523},{"id":"https://openalex.org/C64894306","wikidata":"https://www.wikidata.org/wiki/Q849622","display_name":"Homologous chromosome","level":3,"score":0.4391374886035919},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4272151589393616},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4155365824699402},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.34867870807647705},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1417590081691742},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.11593928933143616},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C187736073","wikidata":"https://www.wikidata.org/wiki/Q2920921","display_name":"Management","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":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","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":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":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btaa468","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa468","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/Supplement_1/i219/33489095/btaa468.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:32657391","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32657391","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:7355290","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7355290","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btaa468","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btaa468","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/36/Supplement_1/i219/33489095/btaa468.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4054019331","display_name":null,"funder_award_id":"DBI-1458477","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5814771522","display_name":"ABI Development: CAFE for very large comparative genomic datasets","funder_award_id":"1564611","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5884611877","display_name":null,"funder_award_id":"DBI-1564611","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G7156484112","display_name":"Bilateral BBSRC-NSF/BIO Collaborative Research: ABI Development: A Critical Assessment of Protein Function Annotation","funder_award_id":"1458477","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3042573861.pdf","grobid_xml":"https://content.openalex.org/works/W3042573861.grobid-xml"},"referenced_works_count":67,"referenced_works":["https://openalex.org/W1821527815","https://openalex.org/W1968637495","https://openalex.org/W1969745832","https://openalex.org/W1976952616","https://openalex.org/W1986367828","https://openalex.org/W1990453950","https://openalex.org/W1995245082","https://openalex.org/W2002604364","https://openalex.org/W2041386815","https://openalex.org/W2045534443","https://openalex.org/W2057119643","https://openalex.org/W2060797027","https://openalex.org/W2068886104","https://openalex.org/W2074231493","https://openalex.org/W2081741335","https://openalex.org/W2097542211","https://openalex.org/W2098127859","https://openalex.org/W2098432760","https://openalex.org/W2099641023","https://openalex.org/W2103017472","https://openalex.org/W2108984616","https://openalex.org/W2113275510","https://openalex.org/W2117486996","https://openalex.org/W2117602634","https://openalex.org/W2121343862","https://openalex.org/W2126045294","https://openalex.org/W2127204815","https://openalex.org/W2132985118","https://openalex.org/W2141879010","https://openalex.org/W2142055410","https://openalex.org/W2143210482","https://openalex.org/W2145100181","https://openalex.org/W2145189015","https://openalex.org/W2145225004","https://openalex.org/W2146771637","https://openalex.org/W2151859071","https://openalex.org/W2151970555","https://openalex.org/W2152810365","https://openalex.org/W2157585454","https://openalex.org/W2159266221","https://openalex.org/W2161955763","https://openalex.org/W2168156479","https://openalex.org/W2227395312","https://openalex.org/W2514044079","https://openalex.org/W2547533409","https://openalex.org/W2549666150","https://openalex.org/W2604808360","https://openalex.org/W2782262419","https://openalex.org/W2806467350","https://openalex.org/W2905265174","https://openalex.org/W2950147502","https://openalex.org/W2950847261","https://openalex.org/W2963418189","https://openalex.org/W2982258968","https://openalex.org/W2989608901","https://openalex.org/W2996361766","https://openalex.org/W3019023988","https://openalex.org/W3025468292","https://openalex.org/W3083304049","https://openalex.org/W3128968985","https://openalex.org/W4250359879","https://openalex.org/W6683686091","https://openalex.org/W6757615455","https://openalex.org/W6763742817","https://openalex.org/W6769617620","https://openalex.org/W6772460303","https://openalex.org/W6981678552"],"related_works":["https://openalex.org/W4300899577","https://openalex.org/W3194471551","https://openalex.org/W4375956809","https://openalex.org/W2130345139","https://openalex.org/W1581373162","https://openalex.org/W1988893860","https://openalex.org/W4393325717","https://openalex.org/W1973978937","https://openalex.org/W121594594","https://openalex.org/W2784911598"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,36],"computational":[2],"prediction":[3,135,189,243],"of":[4,15,73,105,129,136,149,157,166,172,203,215,221,228],"gene":[5],"function":[6,130,150,158,207,216],"is":[7,20,236],"a":[8,122,193],"key":[9],"step":[10],"in":[11,102,146,188],"making":[12,47,121],"full":[13],"use":[14,83],"newly":[16],"sequenced":[17],"genomes.":[18],"Function":[19],"generally":[21],"predicted":[22],"by":[23],"transferring":[24],"annotations":[25,85],"from":[26,86,92,232],"homologous":[27],"genes":[28,42],"or":[29,234],"proteins":[30],"for":[31,65,206,224],"which":[32],"experimental":[33,84],"evidence":[34,141],"exists.":[35],"'ortholog":[37],"conjecture'":[38],"proposes":[39],"that":[40,174,200],"orthologous":[41],"should":[43],"be":[44,176],"preferred":[45],"when":[46],"such":[48],"predictions,":[49],"as":[50,182,184,192],"they":[51],"evolve":[52],"functions":[53],"more":[54],"slowly":[55],"than":[56],"paralogous":[57],"genes.":[58],"Previous":[59],"research":[60],"has":[61],"provided":[62],"little":[63],"support":[64,197],"the":[66,70,74,79,99,127,134,143,147,155,170,185,198,201,213,219],"ortholog":[67,100,144],"conjecture,":[68],"though":[69,152],"incomplete":[71],"nature":[72],"data":[75,222,252],"cast":[76],"doubt":[77],"on":[78],"conclusions.":[80],"RESULTS:":[81],"We":[82],"over":[87,93],"40":[88],"000":[89,95],"proteins,":[90],"drawn":[91],"80":[94],"publications,":[96],"to":[97,161,212,239,241],"revisit":[98],"conjecture":[101,145],"two":[103],"pairs":[104,165],"species:":[106],"(i)":[107],"Homo":[108],"sapiens":[109],"and":[110,113,117],"Mus":[111],"musculus":[112],"(ii)":[114],"Saccharomyces":[115],"cerevisiae":[116],"Schizosaccharomyces":[118],"pombe.":[119],"By":[120],"distinction":[123],"between":[124],"questions":[125,132,153],"about":[126,133,154],"evolution":[128,156],"versus":[131],"function,":[137],"we":[138,168],"find":[139],"strong":[140],"against":[142],"context":[148],"prediction,":[151],"remain":[159],"difficult":[160],"address.":[162],"In":[163],"both":[164],"species,":[167],"quantify":[169],"amount":[171,220],"information":[173],"would":[175],"ignored":[177],"if":[178],"paralogs":[179],"are":[180,209,253],"discarded,":[181],"well":[183],"resulting":[186],"loss":[187],"accuracy.":[190,244],"Taken":[191],"whole,":[194],"our":[195],"results":[196],"view":[199],"types":[202],"homologs":[204],"used":[205,223],"transfer":[208],"largely":[210],"irrelevant":[211],"task":[214],"prediction.":[217],"Maximizing":[218],"this":[225],"task,":[226],"regardless":[227],"whether":[229],"it":[230],"comes":[231],"orthologs":[233],"paralogs,":[235],"most":[237],"likely":[238],"lead":[240],"higher":[242],"AVAILABILITY":[245],"AND":[246],"IMPLEMENTATION:":[247],"https://github.com/predragradivojac/oc.":[248],"SUPPLEMENTARY":[249],"INFORMATION:":[250],"Supplementary":[251],"available":[254],"at":[255],"Bioinformatics":[256],"online.":[257]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":11},{"year":2024,"cited_by_count":19},{"year":2023,"cited_by_count":12},{"year":2022,"cited_by_count":14},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
