{"id":"https://openalex.org/W4414064795","doi":"https://doi.org/10.1093/bib/bbaf461","title":"Graph neural network integrated with pretrained protein language model for predicting human\u2013virus protein\u2013protein interactions","display_name":"Graph neural network integrated with pretrained protein language model for predicting human\u2013virus protein\u2013protein interactions","publication_year":2025,"publication_date":"2025-08-31","ids":{"openalex":"https://openalex.org/W4414064795","doi":"https://doi.org/10.1093/bib/bbaf461","pmid":"https://pubmed.ncbi.nlm.nih.gov/40919914"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf461","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf461","pdf_url":"https://academic.oup.com/bib/article-pdf/26/5/bbaf461/64220323/bbaf461.pdf","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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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://academic.oup.com/bib/article-pdf/26/5/bbaf461/64220323/bbaf461.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5042087675","display_name":"Linyang Jiang","orcid":null},"institutions":[{"id":"https://openalex.org/I52158045","display_name":"China Agricultural University","ror":"https://ror.org/04v3ywz14","country_code":"CN","type":"education","lineage":["https://openalex.org/I52158045"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Linyang Jiang","raw_affiliation_strings":["State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University , No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193 ,","State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China"],"raw_orcid":"https://orcid.org/0009-0007-2253-5005","affiliations":[{"raw_affiliation_string":"State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University , No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193 ,","institution_ids":["https://openalex.org/I52158045"]},{"raw_affiliation_string":"State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China","institution_ids":["https://openalex.org/I52158045"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101479635","display_name":"Xiaodi Yang","orcid":"https://orcid.org/0000-0002-3229-5865"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]},{"id":"https://openalex.org/I4210130930","display_name":"Peking University First Hospital","ror":"https://ror.org/02z1vqm45","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210130930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaodi Yang","raw_affiliation_strings":["Department of Hematology, Peking University First Hospital , No. 8 Xishiku Street, Xicheng District, Beijing 100034 ,","Department of Hematology, Peking University First Hospital, No. 8 Xishiku Street, Xicheng District, Beijing 100034, China"],"raw_orcid":"https://orcid.org/0000-0002-3229-5865","affiliations":[{"raw_affiliation_string":"Department of Hematology, Peking University First Hospital , No. 8 Xishiku Street, Xicheng District, Beijing 100034 ,","institution_ids":["https://openalex.org/I20231570","https://openalex.org/I4210130930"]},{"raw_affiliation_string":"Department of Hematology, Peking University First Hospital, No. 8 Xishiku Street, Xicheng District, Beijing 100034, China","institution_ids":["https://openalex.org/I20231570","https://openalex.org/I4210130930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047571981","display_name":"Xiaokun Guo","orcid":"https://orcid.org/0000-0001-6471-3155"},"institutions":[{"id":"https://openalex.org/I52158045","display_name":"China Agricultural University","ror":"https://ror.org/04v3ywz14","country_code":"CN","type":"education","lineage":["https://openalex.org/I52158045"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaokun Guo","raw_affiliation_strings":["State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University , No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193 ,","State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University , No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193 ,","institution_ids":["https://openalex.org/I52158045"]},{"raw_affiliation_string":"State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China","institution_ids":["https://openalex.org/I52158045"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012359122","display_name":"Dianke Li","orcid":"https://orcid.org/0000-0001-9580-3292"},"institutions":[{"id":"https://openalex.org/I52158045","display_name":"China Agricultural University","ror":"https://ror.org/04v3ywz14","country_code":"CN","type":"education","lineage":["https://openalex.org/I52158045"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dianke Li","raw_affiliation_strings":["State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University , No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193 ,","State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China"],"raw_orcid":"https://orcid.org/0000-0001-9580-3292","affiliations":[{"raw_affiliation_string":"State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University , No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193 ,","institution_ids":["https://openalex.org/I52158045"]},{"raw_affiliation_string":"State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China","institution_ids":["https://openalex.org/I52158045"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100352048","display_name":"Jiajun Li","orcid":"https://orcid.org/0000-0003-4848-1715"},"institutions":[{"id":"https://openalex.org/I52158045","display_name":"China Agricultural University","ror":"https://ror.org/04v3ywz14","country_code":"CN","type":"education","lineage":["https://openalex.org/I52158045"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiajun Li","raw_affiliation_strings":["State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University , No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193 ,","State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University , No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193 ,","institution_ids":["https://openalex.org/I52158045"]},{"raw_affiliation_string":"State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China","institution_ids":["https://openalex.org/I52158045"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076755077","display_name":"Stefan Wuchty","orcid":"https://orcid.org/0000-0001-8916-6522"},"institutions":[{"id":"https://openalex.org/I145608581","display_name":"University of Miami","ror":"https://ror.org/02dgjyy92","country_code":"US","type":"education","lineage":["https://openalex.org/I145608581"]},{"id":"https://openalex.org/I4210157065","display_name":"Sylvester Comprehensive Cancer Center","ror":"https://ror.org/0552r4b12","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I145608581","https://openalex.org/I4210101935","https://openalex.org/I4210157065"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Stefan Wuchty","raw_affiliation_strings":["Department of Biology, University of Miami , 215 Cox Science Center, 1301 Memorial Drive, Coral Gables, FL 33124-0421 ,","Department of Computer Science, University of Miami , 310A Ungar Building, 1365 Memorial Drive, Coral Gables, FL 33146-4245 ,","Sylvester Comprehensive Cancer Center, University of Miami ,","Sylvester Comprehensive Cancer Center, University of Miami, 1475 NW 12th Ave, Miami, FL 33136, USA"],"raw_orcid":"https://orcid.org/0000-0001-8916-6522","affiliations":[{"raw_affiliation_string":"Department of Biology, University of Miami , 215 Cox Science Center, 1301 Memorial Drive, Coral Gables, FL 33124-0421 ,","institution_ids":["https://openalex.org/I145608581"]},{"raw_affiliation_string":"Department of Computer Science, University of Miami , 310A Ungar Building, 1365 Memorial Drive, Coral Gables, FL 33146-4245 ,","institution_ids":["https://openalex.org/I145608581"]},{"raw_affiliation_string":"Sylvester Comprehensive Cancer Center, University of Miami ,","institution_ids":["https://openalex.org/I4210157065"]},{"raw_affiliation_string":"Sylvester Comprehensive Cancer Center, University of Miami, 1475 NW 12th Ave, Miami, FL 33136, USA","institution_ids":["https://openalex.org/I145608581","https://openalex.org/I4210157065"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085232801","display_name":"Wenyu Shi","orcid":"https://orcid.org/0000-0001-7036-8917"},"institutions":[{"id":"https://openalex.org/I52158045","display_name":"China Agricultural University","ror":"https://ror.org/04v3ywz14","country_code":"CN","type":"education","lineage":["https://openalex.org/I52158045"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wenyu Shi","raw_affiliation_strings":["State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University , No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193 ,","State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University , No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193 ,","institution_ids":["https://openalex.org/I52158045"]},{"raw_affiliation_string":"State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China","institution_ids":["https://openalex.org/I52158045"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5031348514","display_name":"Ziding Zhang","orcid":"https://orcid.org/0000-0002-9296-571X"},"institutions":[{"id":"https://openalex.org/I52158045","display_name":"China Agricultural University","ror":"https://ror.org/04v3ywz14","country_code":"CN","type":"education","lineage":["https://openalex.org/I52158045"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ziding Zhang","raw_affiliation_strings":["State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University , No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193 ,","State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China"],"raw_orcid":"https://orcid.org/0000-0002-9296-571X","affiliations":[{"raw_affiliation_string":"State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University , No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193 ,","institution_ids":["https://openalex.org/I52158045"]},{"raw_affiliation_string":"State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing 100193, China","institution_ids":["https://openalex.org/I52158045"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"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":3.3907,"has_fulltext":true,"cited_by_count":8,"citation_normalized_percentile":{"value":0.93119433,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":91,"max":100},"biblio":{"volume":"26","issue":"5","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":0.9987999796867371,"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":0.9987999796867371,"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":0.9983999729156494,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9977999925613403,"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/robustness","display_name":"Robustness (evolution)","score":0.61080002784729},{"id":"https://openalex.org/keywords/generalization","display_name":"Generalization","score":0.5702999830245972},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5174999833106995},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.47130000591278076},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4603999853134155},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.3822000026702881},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.33559998869895935}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7700999975204468},{"id":"https://openalex.org/C63479239","wikidata":"https://www.wikidata.org/wiki/Q7353546","display_name":"Robustness (evolution)","level":3,"score":0.61080002784729},{"id":"https://openalex.org/C177148314","wikidata":"https://www.wikidata.org/wiki/Q170084","display_name":"Generalization","level":2,"score":0.5702999830245972},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5181999802589417},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5174999833106995},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.47130000591278076},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4603999853134155},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.45010000467300415},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.3822000026702881},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.33559998869895935},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.3294000029563904},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.3244999945163727},{"id":"https://openalex.org/C137293760","wikidata":"https://www.wikidata.org/wiki/Q3621696","display_name":"Language model","level":2,"score":0.313400000333786},{"id":"https://openalex.org/C2984842247","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep neural networks","level":3,"score":0.296099990606308},{"id":"https://openalex.org/C55105296","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interaction network","level":3,"score":0.2930000126361847},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.29010000824928284},{"id":"https://openalex.org/C126831891","wikidata":"https://www.wikidata.org/wiki/Q221673","display_name":"Host (biology)","level":2,"score":0.27559998631477356},{"id":"https://openalex.org/C51632099","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Training set","level":2,"score":0.26330000162124634}],"mesh":[{"descriptor_ui":"D000098422","descriptor_name":"Graph Neural Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098422","descriptor_name":"Graph Neural Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098422","descriptor_name":"Graph Neural Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098422","descriptor_name":"Graph Neural Networks","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":"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":"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":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D054884","descriptor_name":"Host-Pathogen Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054884","descriptor_name":"Host-Pathogen Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054884","descriptor_name":"Host-Pathogen Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054884","descriptor_name":"Host-Pathogen Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbaf461","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf461","pdf_url":"https://academic.oup.com/bib/article-pdf/26/5/bbaf461/64220323/bbaf461.pdf","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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40919914","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40919914","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:12415850","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12415850/","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbaf461","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf461","pdf_url":"https://academic.oup.com/bib/article-pdf/26/5/bbaf461/64220323/bbaf461.pdf","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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G8922444948","display_name":null,"funder_award_id":"32270703","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321131","display_name":"China Agricultural University","ror":"https://ror.org/04v3ywz14"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4414064795.pdf","grobid_xml":"https://content.openalex.org/works/W4414064795.grobid-xml"},"referenced_works_count":54,"referenced_works":["https://openalex.org/W1774721170","https://openalex.org/W1966478716","https://openalex.org/W1966958204","https://openalex.org/W2010889823","https://openalex.org/W2022403117","https://openalex.org/W2027877546","https://openalex.org/W2043764521","https://openalex.org/W2062725722","https://openalex.org/W2095867585","https://openalex.org/W2115048111","https://openalex.org/W2124249167","https://openalex.org/W2124463526","https://openalex.org/W2142436238","https://openalex.org/W2154019529","https://openalex.org/W2159126118","https://openalex.org/W2163485494","https://openalex.org/W2164813401","https://openalex.org/W2168637722","https://openalex.org/W2170564629","https://openalex.org/W2272509401","https://openalex.org/W2345139079","https://openalex.org/W2465613542","https://openalex.org/W2743857398","https://openalex.org/W2904824676","https://openalex.org/W2951433247","https://openalex.org/W2952615074","https://openalex.org/W2970119293","https://openalex.org/W2971227267","https://openalex.org/W2972317931","https://openalex.org/W2997591727","https://openalex.org/W2998220730","https://openalex.org/W3022285953","https://openalex.org/W3134084134","https://openalex.org/W3146944767","https://openalex.org/W3164046276","https://openalex.org/W3177500196","https://openalex.org/W3177828909","https://openalex.org/W3185942550","https://openalex.org/W3194795934","https://openalex.org/W3200728736","https://openalex.org/W3211403530","https://openalex.org/W3217806496","https://openalex.org/W4205773061","https://openalex.org/W4288419263","https://openalex.org/W4297733535","https://openalex.org/W4303520619","https://openalex.org/W4317703013","https://openalex.org/W4327550249","https://openalex.org/W4387303685","https://openalex.org/W4388464011","https://openalex.org/W4390521376","https://openalex.org/W4396721167","https://openalex.org/W4405388956","https://openalex.org/W4407356649"],"related_works":["https://openalex.org/W3162204513","https://openalex.org/W2371138613","https://openalex.org/W2048963458","https://openalex.org/W43109613","https://openalex.org/W2359952343","https://openalex.org/W2239445980","https://openalex.org/W2080152487","https://openalex.org/W3083152911","https://openalex.org/W3022347918","https://openalex.org/W2770593030"],"abstract_inverted_index":{"The":[0,165],"systematic":[1],"identification":[2],"of":[3,17,24,117,126,145,168],"human-virus":[4,62],"protein-protein":[5],"interactions":[6],"(PPIs)":[7],"is":[8,173],"a":[9,44,149],"critical":[10,158],"step":[11],"toward":[12],"elucidating":[13],"the":[14,22,83,142,162],"underlying":[15],"mechanisms":[16],"viral":[18,31,79],"infection,":[19],"directly":[20],"informing":[21],"development":[23],"targeted":[25],"interventions":[26],"against":[27],"existing":[28],"and":[29,55,105,128,170],"emerging":[30,94],"threats.":[32],"In":[33,64],"this":[34],"work,":[35],"we":[36,113,147],"presented":[37],"DeepGNHV,":[38,146],"an":[39],"end-to-end":[40],"framework":[41],"that":[42,133,156],"integrated":[43],"pretrained":[45],"protein":[46],"language":[47],"model":[48],"with":[49,136],"structural":[50],"features":[51],"derived":[52],"from":[53,82],"AlphaFold2":[54],"leveraged":[56],"graph":[57],"attention":[58],"networks":[59],"to":[60,66,78,152],"predict":[61],"PPIs.":[63,96,164],"comparison":[65],"other":[67],"state-of-the-art":[68],"approaches,":[69],"DeepGNHV":[70,169],"exhibited":[71],"superior":[72],"predictive":[73],"performance,":[74],"especially":[75],"when":[76],"applied":[77],"proteins":[80],"absent":[81],"training":[84],"process,":[85],"indicating":[86],"its":[87,106],"strong":[88],"generalization":[89],"capability":[90],"for":[91],"detecting":[92],"newly":[93],"virus-related":[95],"We":[97],"further":[98,140],"demonstrated":[99],"DeepGNHV's":[100],"robustness":[101],"across":[102],"diverse":[103],"perturbations":[104],"practical":[107],"application":[108],"under":[109],"high-confidence":[110],"thresholds.":[111],"Additionally,":[112],"conducted":[114],"extensive":[115],"predictions":[116],"human-HPV":[118],"PPIs,":[119],"which":[120],"were":[121],"supported":[122],"by":[123],"multiple":[124],"lines":[125],"evidence":[127],"identified":[129],"several":[130],"host":[131],"factors":[132],"specifically":[134],"interact":[135],"high-risk":[137],"HPV.":[138],"To":[139],"explore":[141],"biological":[143],"significance":[144],"provided":[148],"case":[150],"study":[151],"pinpoint":[153],"specific":[154],"residues":[155],"play":[157],"roles":[159],"in":[160],"facilitating":[161],"corresponding":[163],"source":[166],"code":[167],"related":[171],"data":[172],"publicly":[174],"available":[175],"on":[176],"GitHub":[177],"(https://github.com/bioboy0415/DeepGNHV).":[178]},"counts_by_year":[{"year":2026,"cited_by_count":7},{"year":2025,"cited_by_count":1}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
