{"id":"https://openalex.org/W4406735181","doi":"https://doi.org/10.1093/bib/bbaf014","title":"GOPhage: protein function annotation for bacteriophages by integrating the genomic context","display_name":"GOPhage: protein function annotation for bacteriophages by integrating the genomic context","publication_year":2024,"publication_date":"2024-11-22","ids":{"openalex":"https://openalex.org/W4406735181","doi":"https://doi.org/10.1093/bib/bbaf014","pmid":"https://pubmed.ncbi.nlm.nih.gov/39838963"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf014","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf014","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"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":"gold","oa_url":"https://doi.org/10.1093/bib/bbaf014","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5057508867","display_name":"Jiaojiao Guan","orcid":"https://orcid.org/0009-0005-9200-4862"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Jiaojiao Guan","raw_affiliation_strings":["Department of Electrical Engineering, City University of Hong Kong , 83 Tat Chee Ave, Kowloon Tong, Hong Kong (SAR),"],"raw_orcid":"https://orcid.org/0009-0005-9200-4862","affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering, City University of Hong Kong , 83 Tat Chee Ave, Kowloon Tong, Hong Kong (SAR),","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Yongxin Ji","orcid":"https://orcid.org/0000-0001-5974-4985"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Yongxin Ji","raw_affiliation_strings":["Department of Electrical Engineering, City University of Hong Kong , 83 Tat Chee Ave, Kowloon Tong, Hong Kong (SAR),"],"raw_orcid":"https://orcid.org/0000-0001-5974-4985","affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering, City University of Hong Kong , 83 Tat Chee Ave, Kowloon Tong, Hong Kong (SAR),","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100346437","display_name":"Cheng Peng","orcid":"https://orcid.org/0000-0002-8566-0707"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Cheng Peng","raw_affiliation_strings":["Department of Electrical Engineering, City University of Hong Kong , 83 Tat Chee Ave, Kowloon Tong, Hong Kong (SAR),"],"raw_orcid":"https://orcid.org/0000-0002-8566-0707","affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering, City University of Hong Kong , 83 Tat Chee Ave, Kowloon Tong, Hong Kong (SAR),","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101795361","display_name":"Wei Zou","orcid":"https://orcid.org/0000-0003-2559-2519"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Wei Zou","raw_affiliation_strings":["Department of Electrical Engineering, City University of Hong Kong , 83 Tat Chee Ave, Kowloon Tong, Hong Kong (SAR),"],"raw_orcid":"https://orcid.org/0000-0003-2559-2519","affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering, City University of Hong Kong , 83 Tat Chee Ave, Kowloon Tong, Hong Kong (SAR),","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076779212","display_name":"Xubo Tang","orcid":"https://orcid.org/0000-0003-1304-6983"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Xubo Tang","raw_affiliation_strings":["Department of Electrical Engineering, City University of Hong Kong , 83 Tat Chee Ave, Kowloon Tong, Hong Kong (SAR),"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering, City University of Hong Kong , 83 Tat Chee Ave, Kowloon Tong, Hong Kong (SAR),","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083607843","display_name":"Jiayu Shang","orcid":"https://orcid.org/0000-0001-5974-4985"},"institutions":[{"id":"https://openalex.org/I177725633","display_name":"Chinese University of Hong Kong","ror":"https://ror.org/00t33hh48","country_code":"HK","type":"education","lineage":["https://openalex.org/I177725633"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Jiayu Shang","raw_affiliation_strings":["Department of Information Engineering, Chinese University of Hong Kong , Shatin, New Territories, Hong Kong (SAR),"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Information Engineering, Chinese University of Hong Kong , Shatin, New Territories, Hong Kong (SAR),","institution_ids":["https://openalex.org/I177725633"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5081855118","display_name":"Yanni Sun","orcid":"https://orcid.org/0000-0003-1373-8023"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Yanni Sun","raw_affiliation_strings":["Department of Electrical Engineering, City University of Hong Kong , 83 Tat Chee Ave, Kowloon Tong, Hong Kong (SAR),"],"raw_orcid":"https://orcid.org/0000-0003-1373-8023","affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering, City University of Hong Kong , 83 Tat Chee Ave, Kowloon Tong, Hong Kong (SAR),","institution_ids":["https://openalex.org/I168719708"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":2.708,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.90119537,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"26","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11048","display_name":"Bacteriophages and microbial interactions","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/2303","display_name":"Ecology"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9990000128746033,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9860000014305115,"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/computational-biology","display_name":"Computational biology","score":0.692500650882721},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6795960068702698},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.6727744340896606},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6386882662773132},{"id":"https://openalex.org/keywords/bacteriophage","display_name":"Bacteriophage","score":0.5699833035469055},{"id":"https://openalex.org/keywords/metagenomics","display_name":"Metagenomics","score":0.46497225761413574},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.4319494366645813},{"id":"https://openalex.org/keywords/genome-project","display_name":"Genome project","score":0.4247903823852539},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.420918732881546},{"id":"https://openalex.org/keywords/phage-display","display_name":"Phage display","score":0.4200184643268585},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.4133090376853943},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.34378135204315186},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2588944733142853},{"id":"https://openalex.org/keywords/escherichia-coli","display_name":"Escherichia coli","score":0.08498632907867432}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.692500650882721},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6795960068702698},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.6727744340896606},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6386882662773132},{"id":"https://openalex.org/C2776441376","wikidata":"https://www.wikidata.org/wiki/Q165028","display_name":"Bacteriophage","level":4,"score":0.5699833035469055},{"id":"https://openalex.org/C15151743","wikidata":"https://www.wikidata.org/wiki/Q903778","display_name":"Metagenomics","level":3,"score":0.46497225761413574},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4319494366645813},{"id":"https://openalex.org/C89566754","wikidata":"https://www.wikidata.org/wiki/Q2273828","display_name":"Genome project","level":4,"score":0.4247903823852539},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.420918732881546},{"id":"https://openalex.org/C186268636","wikidata":"https://www.wikidata.org/wiki/Q896217","display_name":"Phage display","level":3,"score":0.4200184643268585},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.4133090376853943},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.34378135204315186},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2588944733142853},{"id":"https://openalex.org/C547475151","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli","level":3,"score":0.08498632907867432},{"id":"https://openalex.org/C159654299","wikidata":"https://www.wikidata.org/wiki/Q79460","display_name":"Antibody","level":2,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D001435","descriptor_name":"Bacteriophages","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001435","descriptor_name":"Bacteriophages","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001435","descriptor_name":"Bacteriophages","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001435","descriptor_name":"Bacteriophages","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D001435","descriptor_name":"Bacteriophages","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D014764","descriptor_name":"Viral Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016679","descriptor_name":"Genome, Viral","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":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":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bib/bbaf014","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf014","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"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:39838963","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39838963","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:oai:pubmedcentral.nih.gov:11751364","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11751364","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11751364/pdf/bbaf014.pdf","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":"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"},{"id":"pmh:oai:pure.atira.dk:publications/82d5f3e8-1dd6-49a4-94f4-79447d953ea0","is_oa":true,"landing_page_url":"https://hdl.handle.net/2031/82d5f3e8-1dd6-49a4-94f4-79447d953ea0","pdf_url":null,"source":{"id":"https://openalex.org/S7407055387","display_name":"CityU Scholars","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Guan, J, Ji, Y, Peng, C, Zou, W, Tang, X, Shang, J & Sun, Y 2025, 'GOPhage : protein function annotation for bacteriophages by integrating the genomic context', Briefings in Bioinformatics, vol. 26, no. 1, bbaf014. https://doi.org/10.1093/bib/bbaf014","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf014","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf014","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"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":0.7400000095367432,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[{"id":"https://openalex.org/G3705880144","display_name":null,"funder_award_id":"11209823","funder_id":"https://openalex.org/F4320309893","funder_display_name":"City University of Hong Kong"}],"funders":[{"id":"https://openalex.org/F4320309893","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":34,"referenced_works":["https://openalex.org/W2002850151","https://openalex.org/W2007435893","https://openalex.org/W2045204781","https://openalex.org/W2070906511","https://openalex.org/W2102245393","https://openalex.org/W2117486996","https://openalex.org/W2125910575","https://openalex.org/W2158714788","https://openalex.org/W2256397674","https://openalex.org/W2320294474","https://openalex.org/W2443992611","https://openalex.org/W2791956910","https://openalex.org/W2803838774","https://openalex.org/W2950595506","https://openalex.org/W2972411752","https://openalex.org/W2973579020","https://openalex.org/W3013140229","https://openalex.org/W3137270128","https://openalex.org/W3165795318","https://openalex.org/W3177828909","https://openalex.org/W3189053267","https://openalex.org/W4210584212","https://openalex.org/W4236358448","https://openalex.org/W4280526308","https://openalex.org/W4309506674","https://openalex.org/W4312097792","https://openalex.org/W4320933419","https://openalex.org/W4327550249","https://openalex.org/W4366163632","https://openalex.org/W4388594088","https://openalex.org/W4391821988","https://openalex.org/W4392095606","https://openalex.org/W4392297989","https://openalex.org/W4396871936"],"related_works":["https://openalex.org/W1533264849","https://openalex.org/W2162782320","https://openalex.org/W2059565715","https://openalex.org/W3111061871","https://openalex.org/W2009940763","https://openalex.org/W2114034054","https://openalex.org/W4232413416","https://openalex.org/W45826765","https://openalex.org/W1585937270","https://openalex.org/W2537312848"],"abstract_inverted_index":{"Bacteriophages":[0],"are":[1,15],"viruses":[2],"that":[3],"target":[4],"bacteria,":[5],"playing":[6],"a":[7,29,89],"crucial":[8],"role":[9],"in":[10,17,80,123,130,174],"microbial":[11],"ecology.":[12],"Phage":[13],"proteins":[14,54,122,133,135,148],"important":[16],"understanding":[18,194],"phage":[19,53,104,124,161],"biology,":[20],"such":[21],"as":[22],"virus":[23],"infection,":[24],"replication,":[25],"and":[26,62,115,134,141],"evolution.":[27],"Although":[28],"large":[30],"number":[31],"of":[32,42,52,65,78,103,167,189,195],"new":[33,90],"phages":[34,79,96],"have":[35,44,70],"been":[36],"identified":[37],"via":[38],"metagenomic":[39],"sequencing,":[40],"many":[41],"them":[43],"limited":[45],"protein":[46,82,91,112],"function":[47,50,92],"annotation.":[48],"Accurate":[49],"annotation":[51,93],"presents":[55],"several":[56],"challenges,":[57],"including":[58],"their":[59],"inherent":[60],"diversity":[61],"the":[63,75,99,110,158,165,187],"scarcity":[64],"annotated":[66],"ones.":[67],"Existing":[68],"tools":[69],"yet":[71],"to":[72,117,191],"fully":[73],"leverage":[74],"unique":[76],"properties":[77],"annotating":[81,131],"functions.":[83],"In":[84],"this":[85],"work,":[86],"we":[87],"propose":[88],"tool":[94],"for":[95,156],"by":[97,139,169],"leveraging":[98],"modular":[100],"genomic":[101],"structure":[102],"genomes.":[105,162],"By":[106],"employing":[107],"embeddings":[108],"from":[109],"latest":[111],"foundation":[113],"models":[114],"Transformer":[116],"capture":[118],"contextual":[119],"information":[120],"between":[121],"genomes,":[125],"GOPhage":[126,145,168,190],"surpasses":[127],"state-of-the-art":[128],"methods":[129],"diverged":[132],"with":[136,181],"uncommon":[137],"functions":[138],"6.78%":[140],"13.05%":[142],"improvement,":[143],"respectively.":[144],"can":[146],"annotate":[147],"lacking":[149],"homology":[150],"search":[151],"results,":[152],"which":[153,176],"is":[154],"critical":[155],"characterizing":[157],"rapidly":[159],"accumulating":[160],"We":[163],"demonstrate":[164],"utility":[166],"identifying":[170],"688":[171],"potential":[172,188],"holins":[173],"phages,":[175],"exhibit":[177],"high":[178],"structural":[179],"conservation":[180],"known":[182],"holins.":[183],"The":[184],"results":[185],"show":[186],"extend":[192],"our":[193],"newly":[196],"discovered":[197],"phages.":[198]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":4}],"updated_date":"2026-07-21T08:15:58.654021","created_date":"2025-10-10T00:00:00"}
