{"id":"https://openalex.org/W4283220517","doi":"https://doi.org/10.1093/bib/bbac239","title":"PCfun: a hybrid computational framework for systematic characterization of protein complex function","display_name":"PCfun: a hybrid computational framework for systematic characterization of protein complex function","publication_year":2022,"publication_date":"2022-06-20","ids":{"openalex":"https://openalex.org/W4283220517","doi":"https://doi.org/10.1093/bib/bbac239","pmid":"https://pubmed.ncbi.nlm.nih.gov/35724564"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbac239","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbac239","pdf_url":"https://academic.oup.com/bib/article-pdf/23/4/bbac239/45059183/bbac239.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"hybrid","oa_url":"https://academic.oup.com/bib/article-pdf/23/4/bbac239/45059183/bbac239.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5054740348","display_name":"Varun Sharma","orcid":"https://orcid.org/0000-0002-4531-640X"},"institutions":[{"id":"https://openalex.org/I138211613","display_name":"Austrian Academy of Sciences","ror":"https://ror.org/03anc3s24","country_code":"AT","type":"government","lineage":["https://openalex.org/I138211613"]},{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]},{"id":"https://openalex.org/I4210127611","display_name":"CeMM Research Center for Molecular Medicine","ror":"https://ror.org/02z2dfb58","country_code":"AT","type":"facility","lineage":["https://openalex.org/I138211613","https://openalex.org/I4210127611"]}],"countries":["AT","CH"],"is_corresponding":false,"raw_author_name":"Varun S Sharma","raw_affiliation_strings":["CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences , Vienna, Austria","Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, Switzerland"],"affiliations":[{"raw_affiliation_string":"CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences , Vienna, Austria","institution_ids":["https://openalex.org/I4210127611","https://openalex.org/I138211613"]},{"raw_affiliation_string":"Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011766022","display_name":"Andrea Fossati","orcid":"https://orcid.org/0000-0001-5170-4903"},"institutions":[{"id":"https://openalex.org/I1321430492","display_name":"Gladstone Institutes","ror":"https://ror.org/038321296","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1321430492"]},{"id":"https://openalex.org/I180670191","display_name":"University of California, San Francisco","ror":"https://ror.org/043mz5j54","country_code":"US","type":"education","lineage":["https://openalex.org/I180670191"]},{"id":"https://openalex.org/I4210098931","display_name":"Quantitative BioSciences","ror":"https://ror.org/010brsj79","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210098931"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Andrea Fossati","raw_affiliation_strings":["J. David Gladstone Institutes , San Francisco, CA 94158, USA","Quantitative Biosciences Institute (QBI) and Department of Cellular and Molecular Pharmacology, University of California , San Francisco, CA 94158, USA"],"affiliations":[{"raw_affiliation_string":"J. David Gladstone Institutes , San Francisco, CA 94158, USA","institution_ids":["https://openalex.org/I1321430492"]},{"raw_affiliation_string":"Quantitative Biosciences Institute (QBI) and Department of Cellular and Molecular Pharmacology, University of California , San Francisco, CA 94158, USA","institution_ids":["https://openalex.org/I4210098931","https://openalex.org/I180670191"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076106368","display_name":"Rodolfo Ciuffa","orcid":"https://orcid.org/0000-0002-7611-7665"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Rodolfo Ciuffa","raw_affiliation_strings":["Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, Switzerland"],"affiliations":[{"raw_affiliation_string":"Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031825621","display_name":"Marija Buljan","orcid":"https://orcid.org/0000-0003-3615-6691"},"institutions":[{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"nonprofit","lineage":["https://openalex.org/I12708293"]},{"id":"https://openalex.org/I71824836","display_name":"Swiss Federal Laboratories for Materials Science and Technology","ror":"https://ror.org/02x681a42","country_code":"CH","type":"facility","lineage":["https://openalex.org/I2799323385","https://openalex.org/I71824836"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Marija Buljan","raw_affiliation_strings":["Empa - Swiss Federal Laboratories for Materials Science and Technology , St. Gallen, Switzerland","Swiss Institute of Bioinformatics (SIB) , Lausanne, Switzerland"],"affiliations":[{"raw_affiliation_string":"Empa - Swiss Federal Laboratories for Materials Science and Technology , St. Gallen, Switzerland","institution_ids":["https://openalex.org/I71824836"]},{"raw_affiliation_string":"Swiss Institute of Bioinformatics (SIB) , Lausanne, Switzerland","institution_ids":["https://openalex.org/I12708293"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089781009","display_name":"Evan G. Williams","orcid":"https://orcid.org/0000-0002-9746-376X"},"institutions":[{"id":"https://openalex.org/I186903577","display_name":"University of Luxembourg","ror":"https://ror.org/036x5ad56","country_code":"LU","type":"education","lineage":["https://openalex.org/I186903577"]}],"countries":["LU"],"is_corresponding":false,"raw_author_name":"Evan G Williams","raw_affiliation_strings":["Luxembourg Centre for Systems Biomedicine, University of Luxembourg , Esch-sur-Alzette Luxembourg"],"affiliations":[{"raw_affiliation_string":"Luxembourg Centre for Systems Biomedicine, University of Luxembourg , Esch-sur-Alzette Luxembourg","institution_ids":["https://openalex.org/I186903577"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013433350","display_name":"Zhen Chen","orcid":"https://orcid.org/0000-0002-9412-9774"},"institutions":[{"id":"https://openalex.org/I4750791","display_name":"Henan Agricultural University","ror":"https://ror.org/04eq83d71","country_code":"CN","type":"education","lineage":["https://openalex.org/I4750791"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhen Chen","raw_affiliation_strings":["Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University , Zhengzhou 450046, China"],"affiliations":[{"raw_affiliation_string":"Collaborative Innovation Center of Henan Grain Crops, Henan Agricultural University , Zhengzhou 450046, China","institution_ids":["https://openalex.org/I4750791"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049672690","display_name":"Wenguang Shao","orcid":"https://orcid.org/0000-0003-0905-0728"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Wenguang Shao","raw_affiliation_strings":["Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, Switzerland"],"affiliations":[{"raw_affiliation_string":"Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008430398","display_name":"Patrick G. A. Pedrioli","orcid":"https://orcid.org/0000-0001-6719-9139"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Patrick G A Pedrioli","raw_affiliation_strings":["Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, Switzerland"],"affiliations":[{"raw_affiliation_string":"Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5087347737","display_name":"Anthony W. Purcell","orcid":"https://orcid.org/0000-0003-0532-8331"},"institutions":[{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Anthony W Purcell","raw_affiliation_strings":["Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University , Melbourne, VIC 3800, Australia"],"affiliations":[{"raw_affiliation_string":"Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University , Melbourne, VIC 3800, Australia","institution_ids":["https://openalex.org/I56590836"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016524881","display_name":"Mar\u00eda Rodr\u00edguez Mart\u00ednez","orcid":"https://orcid.org/0000-0003-3766-4233"},"institutions":[{"id":"https://openalex.org/I4210126328","display_name":"IBM Research - Zurich","ror":"https://ror.org/02js37d36","country_code":"CH","type":"facility","lineage":["https://openalex.org/I1341412227","https://openalex.org/I4210114115","https://openalex.org/I4210126328"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Mar\u00eda Rodr\u00edguez Mart\u00ednez","raw_affiliation_strings":["IBM Research Europe , Zurich, Switzerland"],"affiliations":[{"raw_affiliation_string":"IBM Research Europe , Zurich, Switzerland","institution_ids":["https://openalex.org/I4210126328"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012709797","display_name":"Jiangning Song","orcid":"https://orcid.org/0000-0001-8031-9086"},"institutions":[{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Jiangning Song","raw_affiliation_strings":["Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University , Melbourne, VIC 3800, Australia","Monash Data Futures Institute, Monash University , Melbourne, VIC 3800, Australia"],"affiliations":[{"raw_affiliation_string":"Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University , Melbourne, VIC 3800, Australia","institution_ids":["https://openalex.org/I56590836"]},{"raw_affiliation_string":"Monash Data Futures Institute, Monash University , Melbourne, VIC 3800, Australia","institution_ids":["https://openalex.org/I56590836"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005561269","display_name":"Matteo Manica","orcid":"https://orcid.org/0000-0002-8872-0269"},"institutions":[{"id":"https://openalex.org/I4210126328","display_name":"IBM Research - Zurich","ror":"https://ror.org/02js37d36","country_code":"CH","type":"facility","lineage":["https://openalex.org/I1341412227","https://openalex.org/I4210114115","https://openalex.org/I4210126328"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Matteo Manica","raw_affiliation_strings":["IBM Research Europe , Zurich, Switzerland"],"affiliations":[{"raw_affiliation_string":"IBM Research Europe , Zurich, Switzerland","institution_ids":["https://openalex.org/I4210126328"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053361384","display_name":"Ruedi Aebersold","orcid":"https://orcid.org/0000-0002-9576-3267"},"institutions":[{"id":"https://openalex.org/I202697423","display_name":"University of Zurich","ror":"https://ror.org/02crff812","country_code":"CH","type":"education","lineage":["https://openalex.org/I202697423"]},{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Ruedi Aebersold","raw_affiliation_strings":["Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, Switzerland","Faculty of Science, University of Zurich , Switzerland"],"affiliations":[{"raw_affiliation_string":"Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"Faculty of Science, University of Zurich , Switzerland","institution_ids":["https://openalex.org/I202697423"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100369818","display_name":"Chen Li","orcid":"https://orcid.org/0000-0002-1847-754X"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]},{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU","CH"],"is_corresponding":true,"raw_author_name":"Chen Li","raw_affiliation_strings":["Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, Switzerland","Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University , Melbourne, VIC 3800, Australia"],"affiliations":[{"raw_affiliation_string":"Department of Biology, Institute of Molecular Systems Biology , ETH Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University , Melbourne, VIC 3800, Australia","institution_ids":["https://openalex.org/I56590836"]}]}],"institutions":[],"countries_distinct_count":6,"institutions_distinct_count":14,"corresponding_author_ids":["https://openalex.org/A5005561269","https://openalex.org/A5012709797","https://openalex.org/A5053361384","https://openalex.org/A5100369818"],"corresponding_institution_ids":["https://openalex.org/I202697423","https://openalex.org/I35440088","https://openalex.org/I4210126328","https://openalex.org/I56590836"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":0.1736,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.47396497,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":95},"biblio":{"volume":"23","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9991999864578247,"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":0.9991999864578247,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9959999918937683,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9951000213623047,"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/computer-science","display_name":"Computer science","score":0.7525928020477295},{"id":"https://openalex.org/keywords/protein-function-prediction","display_name":"Protein function prediction","score":0.618799090385437},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.5744287967681885},{"id":"https://openalex.org/keywords/gene-ontology","display_name":"Gene ontology","score":0.45480650663375854},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.4288906455039978},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.42763176560401917},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3426179587841034},{"id":"https://openalex.org/keywords/protein-function","display_name":"Protein function","score":0.2831253409385681},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1619863510131836},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11626732349395752}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7525928020477295},{"id":"https://openalex.org/C207060522","wikidata":"https://www.wikidata.org/wiki/Q7251473","display_name":"Protein function prediction","level":4,"score":0.618799090385437},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.5744287967681885},{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.45480650663375854},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.4288906455039978},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.42763176560401917},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3426179587841034},{"id":"https://openalex.org/C2986374874","wikidata":"https://www.wikidata.org/wiki/Q8054","display_name":"Protein function","level":3,"score":0.2831253409385681},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1619863510131836},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11626732349395752},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"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":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009323","descriptor_name":"Natural Language Processing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"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":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":7,"locations":[{"id":"doi:10.1093/bib/bbac239","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbac239","pdf_url":"https://academic.oup.com/bib/article-pdf/23/4/bbac239/45059183/bbac239.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:35724564","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35724564","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":null},{"id":"pmh:ark:/13030/qt7cx5k9rx","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null},{"id":"pmh:oai:dora:empa_31172","is_oa":false,"landing_page_url":"https://www.dora.lib4ri.ch/empa/islandora/object/empa%3A31172","pdf_url":null,"source":{"id":"https://openalex.org/S4306401298","display_name":"DORA Empa (Swiss Federal Laboratories for Materials Science and Technology (Empa))","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I71824836","host_organization_name":"Swiss Federal Laboratories for Materials Science and Technology","host_organization_lineage":["https://openalex.org/I71824836"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"},{"id":"pmh:oai:escholarship.org:ark:/13030/qt7cx5k9rx","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/7cx5k9rx","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Briefings in Bioinformatics, vol 23, iss 4","raw_type":"article"},{"id":"pmh:oai:orbilu.uni.lu:10993/53479","is_oa":true,"landing_page_url":"http://orbilu.uni.lu/handle/10993/53479","pdf_url":null,"source":{"id":"https://openalex.org/S4306401815","display_name":"Open Repository and Bibliography (University of Luxembourg)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I186903577","host_organization_name":"University of Luxembourg","host_organization_lineage":["https://openalex.org/I186903577"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-sa","license_id":"https://openalex.org/licenses/cc-by-nc-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Briefings in Bioinformatics, 23 (4), bbac239 (2022-07-23)","raw_type":"peer reviewed"},{"id":"pmh:oai:pubmedcentral.nih.gov:9310514","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9310514","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbac239","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbac239","pdf_url":"https://academic.oup.com/bib/article-pdf/23/4/bbac239/45059183/bbac239.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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.5,"id":"https://metadata.un.org/sdg/8","display_name":"Decent work and economic growth"}],"awards":[{"id":"https://openalex.org/G1408620370","display_name":null,"funder_award_id":"ERC-20140AdG 670821","funder_id":"https://openalex.org/F4320334678","funder_display_name":"European Research Council"},{"id":"https://openalex.org/G3025194821","display_name":null,"funder_award_id":"31003A_166435","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"}],"funders":[{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"},{"id":"https://openalex.org/F4320334678","display_name":"European Research Council","ror":"https://ror.org/0472cxd90"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4283220517.pdf","grobid_xml":"https://content.openalex.org/works/W4283220517.grobid-xml"},"referenced_works_count":68,"referenced_works":["https://openalex.org/W141966795","https://openalex.org/W1551743743","https://openalex.org/W1593505700","https://openalex.org/W1644749979","https://openalex.org/W1780426348","https://openalex.org/W1980506662","https://openalex.org/W1987363726","https://openalex.org/W2012750155","https://openalex.org/W2024668293","https://openalex.org/W2043764521","https://openalex.org/W2044475989","https://openalex.org/W2044987829","https://openalex.org/W2048839385","https://openalex.org/W2053039860","https://openalex.org/W2054199688","https://openalex.org/W2056601446","https://openalex.org/W2095605427","https://openalex.org/W2098407161","https://openalex.org/W2106393550","https://openalex.org/W2110845720","https://openalex.org/W2121893605","https://openalex.org/W2122146830","https://openalex.org/W2122964432","https://openalex.org/W2123766055","https://openalex.org/W2124821604","https://openalex.org/W2128049108","https://openalex.org/W2146243727","https://openalex.org/W2148043260","https://openalex.org/W2150650678","https://openalex.org/W2155440340","https://openalex.org/W2168316093","https://openalex.org/W2168930979","https://openalex.org/W2187478032","https://openalex.org/W2217908275","https://openalex.org/W2519691041","https://openalex.org/W2765241646","https://openalex.org/W2770135693","https://openalex.org/W2783536957","https://openalex.org/W2786738307","https://openalex.org/W2800980602","https://openalex.org/W2884165257","https://openalex.org/W2889722506","https://openalex.org/W2898458979","https://openalex.org/W2904339731","https://openalex.org/W2911964244","https://openalex.org/W2914171828","https://openalex.org/W2922210059","https://openalex.org/W2949311246","https://openalex.org/W2951603212","https://openalex.org/W2952523648","https://openalex.org/W2959238762","https://openalex.org/W2964255204","https://openalex.org/W2988426147","https://openalex.org/W3004538692","https://openalex.org/W3009246021","https://openalex.org/W3009760307","https://openalex.org/W3014935338","https://openalex.org/W3037489518","https://openalex.org/W3042241962","https://openalex.org/W3059956750","https://openalex.org/W3104744878","https://openalex.org/W3112963616","https://openalex.org/W3156930754","https://openalex.org/W3164046276","https://openalex.org/W3176329976","https://openalex.org/W3209094369","https://openalex.org/W3210198252","https://openalex.org/W4243979784"],"related_works":["https://openalex.org/W3132344302","https://openalex.org/W2082380079","https://openalex.org/W2061838210","https://openalex.org/W2033366093","https://openalex.org/W2039416962","https://openalex.org/W3104092632","https://openalex.org/W2060079687","https://openalex.org/W2411047100","https://openalex.org/W2143801201","https://openalex.org/W2426363820"],"abstract_inverted_index":{"In":[0],"molecular":[1],"biology,":[2],"it":[3],"is":[4,92],"a":[5,95,139,146,178,221],"general":[6],"assumption":[7],"that":[8,128,216],"the":[9,32,74,79,130,158,167,184,190,194,199,207,228],"ensemble":[10],"of":[11,82,161,193,206,231],"expressed":[12],"molecules,":[13],"their":[14,47,59],"activities":[15],"and":[16,23,37,46,55,63,144,204,224],"interactions":[17],"determine":[18],"biological":[19,40],"function,":[20,122],"cellular":[21],"states":[22],"phenotypes.":[24],"Stable":[25],"protein":[26,44,83,120,140,162,169,232],"complexes-or":[27],"macromolecular":[28],"machines-are,":[29],"in":[30,166],"turn,":[31],"key":[33],"functional":[34],"entities":[35],"mediating":[36],"modulating":[38],"most":[39],"processes.":[41],"Although":[42],"identifying":[43,119],"complexes":[45],"subunit":[48],"composition":[49],"can":[50],"now":[51],"be":[52],"done":[53],"inexpensively":[54],"at":[56,212],"scale,":[57],"determining":[58],"function":[60],"remains":[61],"challenging":[62],"labor":[64],"intensive.":[65],"This":[66],"study":[67],"describes":[68],"Protein":[69],"Complex":[70],"Function":[71],"predictor":[72],"(PCfun),":[73],"first":[75],"computational":[76],"framework":[77],"for":[78,117,138,156,227],"systematic":[80],"annotation":[81],"complex":[84,121,141,163,170,233],"functions":[85],"using":[86,98,149],"Gene":[87],"Ontology":[88],"(GO)":[89],"terms.":[90],"PCfun":[91,113,172,208,217],"built":[93],"upon":[94],"word":[96,136],"embedding":[97],"natural":[99],"language":[100],"processing":[101],"techniques":[102],"based":[103],"on":[104],"1":[105],"million":[106],"open":[107],"access":[108],"PubMed":[109],"Central":[110],"articles.":[111],"Specifically,":[112],"leverages":[114],"two":[115],"approaches":[116,175],"accurately":[118],"including:":[123],"(i)":[124],"an":[125],"unsupervised":[126],"approach":[127,148],"obtains":[129],"nearest":[131],"neighbor":[132],"(NN)":[133],"GO":[134,159,187,195],"term":[135],"vectors":[137],"query":[142],"vector":[143],"(ii)":[145],"supervised":[147],"Random":[150],"Forest":[151],"(RF)":[152],"models":[153],"trained":[154],"specifically":[155],"recovering":[157],"terms":[160,188,192,196],"queries":[164],"described":[165],"CORUM":[168],"database.":[171],"consolidates":[173],"both":[174],"by":[176,198],"performing":[177],"hypergeometric":[179],"statistical":[180],"test":[181],"to":[182],"enrich":[183],"top":[185],"NN":[186],"within":[189],"child":[191],"predicted":[197],"RF":[200],"models.":[201],"The":[202],"documentation":[203],"implementation":[205],"package":[209],"are":[210],"available":[211],"https://github.com/sharmavaruns/PCfun.":[213],"We":[214],"anticipate":[215],"will":[218],"serve":[219],"as":[220],"useful":[222],"tool":[223],"novel":[225],"paradigm":[226],"large-scale":[229],"characterization":[230],"function.":[234]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
