{"id":"https://openalex.org/W4402963971","doi":"https://doi.org/10.1093/bib/bbae484","title":"DeepPBI-KG: a deep learning method for the prediction of phage-bacteria interactions based on key genes","display_name":"DeepPBI-KG: a deep learning method for the prediction of phage-bacteria interactions based on key genes","publication_year":2024,"publication_date":"2024-09-23","ids":{"openalex":"https://openalex.org/W4402963971","doi":"https://doi.org/10.1093/bib/bbae484","pmid":"https://pubmed.ncbi.nlm.nih.gov/39344712"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae484","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae484","pdf_url":"https://academic.oup.com/bib/article-pdf/25/6/bbae484/59428529/bbae484.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/25/6/bbae484/59428529/bbae484.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5082924301","display_name":"Tongqing Wei","orcid":null},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I4391768242","display_name":"State Key Laboratory of Genetic Engineering","ror":"https://ror.org/01n3rg866","country_code":null,"type":"facility","lineage":["https://openalex.org/I24943067","https://openalex.org/I4391768242"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Tongqing Wei","raw_affiliation_strings":["Fudan University , School of Life Sciences, , No. 2005 Songhu Road, Shanghai, 200433,","State Key Laboratory of Genetic Engineering , School of Life Sciences, , No. 2005 Songhu Road, Shanghai, 200433,"],"affiliations":[{"raw_affiliation_string":"Fudan University , School of Life Sciences, , No. 2005 Songhu Road, Shanghai, 200433,","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"State Key Laboratory of Genetic Engineering , School of Life Sciences, , No. 2005 Songhu Road, Shanghai, 200433,","institution_ids":["https://openalex.org/I4391768242"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083326009","display_name":"Chenqi Lu","orcid":"https://orcid.org/0000-0003-2748-6031"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I4391768242","display_name":"State Key Laboratory of Genetic Engineering","ror":"https://ror.org/01n3rg866","country_code":null,"type":"facility","lineage":["https://openalex.org/I24943067","https://openalex.org/I4391768242"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chenqi Lu","raw_affiliation_strings":["Fudan University , School of Life Sciences, , No. 2005 Songhu Road, Shanghai, 200433,","State Key Laboratory of Genetic Engineering , School of Life Sciences, , No. 2005 Songhu Road, Shanghai, 200433,"],"affiliations":[{"raw_affiliation_string":"Fudan University , School of Life Sciences, , No. 2005 Songhu Road, Shanghai, 200433,","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"State Key Laboratory of Genetic Engineering , School of Life Sciences, , No. 2005 Songhu Road, Shanghai, 200433,","institution_ids":["https://openalex.org/I4391768242"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103787597","display_name":"Hanxiao Du","orcid":null},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I4391768242","display_name":"State Key Laboratory of Genetic Engineering","ror":"https://ror.org/01n3rg866","country_code":null,"type":"facility","lineage":["https://openalex.org/I24943067","https://openalex.org/I4391768242"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hanxiao Du","raw_affiliation_strings":["Fudan University , School of Life Sciences, , No. 2005 Songhu Road, Shanghai, 200433,","State Key Laboratory of Genetic Engineering , School of Life Sciences, , No. 2005 Songhu Road, Shanghai, 200433,"],"affiliations":[{"raw_affiliation_string":"Fudan University , School of Life Sciences, , No. 2005 Songhu Road, Shanghai, 200433,","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"State Key Laboratory of Genetic Engineering , School of Life Sciences, , No. 2005 Songhu Road, Shanghai, 200433,","institution_ids":["https://openalex.org/I4391768242"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073396030","display_name":"Qianru Yang","orcid":"https://orcid.org/0000-0003-4245-6631"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I4391768242","display_name":"State Key Laboratory of Genetic Engineering","ror":"https://ror.org/01n3rg866","country_code":null,"type":"facility","lineage":["https://openalex.org/I24943067","https://openalex.org/I4391768242"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qianru Yang","raw_affiliation_strings":["Fudan University , School of Life Sciences, , No. 2005 Songhu Road, Shanghai, 200433,","State Key Laboratory of Genetic Engineering , School of Life Sciences, , No. 2005 Songhu Road, Shanghai, 200433,"],"affiliations":[{"raw_affiliation_string":"Fudan University , School of Life Sciences, , No. 2005 Songhu Road, Shanghai, 200433,","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"State Key Laboratory of Genetic Engineering , School of Life Sciences, , No. 2005 Songhu Road, Shanghai, 200433,","institution_ids":["https://openalex.org/I4391768242"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100626344","display_name":"Xinru Qi","orcid":"https://orcid.org/0000-0001-5697-9789"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Xin Qi","raw_affiliation_strings":["Shanghai Sci-Tech Inno Center for Infection & Immunity , No. 1688 Guoquan Bei Road, Shanghai,"],"affiliations":[{"raw_affiliation_string":"Shanghai Sci-Tech Inno Center for Infection & Immunity , No. 1688 Guoquan Bei Road, Shanghai,","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051592914","display_name":"Yankun Liu","orcid":"https://orcid.org/0000-0002-7239-0832"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yankun Liu","raw_affiliation_strings":["Shanghai Sci-Tech Inno Center for Infection & Immunity , No. 1688 Guoquan Bei Road, Shanghai,"],"affiliations":[{"raw_affiliation_string":"Shanghai Sci-Tech Inno Center for Infection & Immunity , No. 1688 Guoquan Bei Road, Shanghai,","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100388227","display_name":"Yi Zhang","orcid":"https://orcid.org/0000-0002-8228-2560"},"institutions":[{"id":"https://openalex.org/I4210159575","display_name":"Huashan Hospital","ror":"https://ror.org/05201qm87","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210159575"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yi Zhang","raw_affiliation_strings":["Department of Infectious Diseases, Huashan Hospital , Shanghai Medical College, Fudan Univerisy, No. 12 Wulumuqi Zhong Road, Shanghai,"],"affiliations":[{"raw_affiliation_string":"Department of Infectious Diseases, Huashan Hospital , Shanghai Medical College, Fudan Univerisy, No. 12 Wulumuqi Zhong Road, Shanghai,","institution_ids":["https://openalex.org/I4210159575"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100418370","display_name":"Chen Chen","orcid":"https://orcid.org/0000-0001-7587-3314"},"institutions":[{"id":"https://openalex.org/I4210159575","display_name":"Huashan Hospital","ror":"https://ror.org/05201qm87","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210159575"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chen Chen","raw_affiliation_strings":["Department of Infectious Diseases, Huashan Hospital , Shanghai Medical College, Fudan Univerisy, No. 12 Wulumuqi Zhong Road, Shanghai,"],"affiliations":[{"raw_affiliation_string":"Department of Infectious Diseases, Huashan Hospital , Shanghai Medical College, Fudan Univerisy, No. 12 Wulumuqi Zhong Road, Shanghai,","institution_ids":["https://openalex.org/I4210159575"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100349721","display_name":"Yutong Li","orcid":"https://orcid.org/0000-0001-8653-6698"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I4391768242","display_name":"State Key Laboratory of Genetic Engineering","ror":"https://ror.org/01n3rg866","country_code":null,"type":"facility","lineage":["https://openalex.org/I24943067","https://openalex.org/I4391768242"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yutong Li","raw_affiliation_strings":["Fudan University , School of Life Sciences, , No. 2005 Songhu Road, Shanghai, 200433,","State Key Laboratory of Genetic Engineering , School of Life Sciences, , No. 2005 Songhu Road, Shanghai, 200433,"],"affiliations":[{"raw_affiliation_string":"Fudan University , School of Life Sciences, , No. 2005 Songhu Road, Shanghai, 200433,","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"State Key Laboratory of Genetic Engineering , School of Life Sciences, , No. 2005 Songhu Road, Shanghai, 200433,","institution_ids":["https://openalex.org/I4391768242"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5110592719","display_name":"Yuanhao Tang","orcid":null},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I4391768242","display_name":"State Key Laboratory of Genetic Engineering","ror":"https://ror.org/01n3rg866","country_code":null,"type":"facility","lineage":["https://openalex.org/I24943067","https://openalex.org/I4391768242"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuanhao Tang","raw_affiliation_strings":["Fudan University , School of Life Sciences, , No. 2005 Songhu Road, Shanghai, 200433,","State Key Laboratory of Genetic Engineering , School of Life Sciences, , No. 2005 Songhu Road, Shanghai, 200433,"],"affiliations":[{"raw_affiliation_string":"Fudan University , School of Life Sciences, , No. 2005 Songhu Road, Shanghai, 200433,","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"State Key Laboratory of Genetic Engineering , School of Life Sciences, , No. 2005 Songhu Road, Shanghai, 200433,","institution_ids":["https://openalex.org/I4391768242"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101891248","display_name":"Wenhong Zhang","orcid":"https://orcid.org/0000-0002-1246-0747"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I4210159575","display_name":"Huashan Hospital","ror":"https://ror.org/05201qm87","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210159575"]},{"id":"https://openalex.org/I4391768242","display_name":"State Key Laboratory of Genetic Engineering","ror":"https://ror.org/01n3rg866","country_code":null,"type":"facility","lineage":["https://openalex.org/I24943067","https://openalex.org/I4391768242"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wen-Hong Zhang","raw_affiliation_strings":["Department of Infectious Diseases, Huashan Hospital , Shanghai Medical College, Fudan Univerisy, No. 12 Wulumuqi Zhong Road, Shanghai,","Fudan University , School of Life Sciences, , No. 2005 Songhu Road, Shanghai, 200433,","Shanghai Sci-Tech Inno Center for Infection & Immunity , No. 1688 Guoquan Bei Road, Shanghai,","State Key Laboratory of Genetic Engineering , School of Life Sciences, , No. 2005 Songhu Road, Shanghai, 200433,"],"affiliations":[{"raw_affiliation_string":"Department of Infectious Diseases, Huashan Hospital , Shanghai Medical College, Fudan Univerisy, No. 12 Wulumuqi Zhong Road, Shanghai,","institution_ids":["https://openalex.org/I4210159575"]},{"raw_affiliation_string":"Fudan University , School of Life Sciences, , No. 2005 Songhu Road, Shanghai, 200433,","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"Shanghai Sci-Tech Inno Center for Infection & Immunity , No. 1688 Guoquan Bei Road, Shanghai,","institution_ids":[]},{"raw_affiliation_string":"State Key Laboratory of Genetic Engineering , School of Life Sciences, , No. 2005 Songhu Road, Shanghai, 200433,","institution_ids":["https://openalex.org/I4391768242"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056541282","display_name":"Tao Xu","orcid":"https://orcid.org/0000-0001-8738-5799"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I4210159575","display_name":"Huashan Hospital","ror":"https://ror.org/05201qm87","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210159575"]},{"id":"https://openalex.org/I4391768242","display_name":"State Key Laboratory of Genetic Engineering","ror":"https://ror.org/01n3rg866","country_code":null,"type":"facility","lineage":["https://openalex.org/I24943067","https://openalex.org/I4391768242"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xu Tao","raw_affiliation_strings":["Department of Infectious Diseases, Huashan Hospital , Shanghai Medical College, Fudan Univerisy, No. 12 Wulumuqi Zhong Road, Shanghai,","Fudan University , School of Life Sciences, , No. 2005 Songhu Road, Shanghai, 200433,","Shanghai Sci-Tech Inno Center for Infection & Immunity , No. 1688 Guoquan Bei Road, Shanghai,","State Key Laboratory of Genetic Engineering , School of Life Sciences, , No. 2005 Songhu Road, Shanghai, 200433,"],"affiliations":[{"raw_affiliation_string":"Department of Infectious Diseases, Huashan Hospital , Shanghai Medical College, Fudan Univerisy, No. 12 Wulumuqi Zhong Road, Shanghai,","institution_ids":["https://openalex.org/I4210159575"]},{"raw_affiliation_string":"Fudan University , School of Life Sciences, , No. 2005 Songhu Road, Shanghai, 200433,","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"Shanghai Sci-Tech Inno Center for Infection & Immunity , No. 1688 Guoquan Bei Road, Shanghai,","institution_ids":[]},{"raw_affiliation_string":"State Key Laboratory of Genetic Engineering , School of Life Sciences, , No. 2005 Songhu Road, Shanghai, 200433,","institution_ids":["https://openalex.org/I4391768242"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5090920261","display_name":"Ning Jiang","orcid":null},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]},{"id":"https://openalex.org/I4210159575","display_name":"Huashan Hospital","ror":"https://ror.org/05201qm87","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210159575"]},{"id":"https://openalex.org/I4391768242","display_name":"State Key Laboratory of Genetic Engineering","ror":"https://ror.org/01n3rg866","country_code":null,"type":"facility","lineage":["https://openalex.org/I24943067","https://openalex.org/I4391768242"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ning Jiang","raw_affiliation_strings":["Department of Infectious Diseases, Huashan Hospital , Shanghai Medical College, Fudan Univerisy, No. 12 Wulumuqi Zhong Road, Shanghai,","Fudan University , School of Life Sciences, , No. 2005 Songhu Road, Shanghai, 200433,","Shanghai Sci-Tech Inno Center for Infection & Immunity , No. 1688 Guoquan Bei Road, Shanghai,","State Key Laboratory of Genetic Engineering , School of Life Sciences, , No. 2005 Songhu Road, Shanghai, 200433,"],"affiliations":[{"raw_affiliation_string":"Department of Infectious Diseases, Huashan Hospital , Shanghai Medical College, Fudan Univerisy, No. 12 Wulumuqi Zhong Road, Shanghai,","institution_ids":["https://openalex.org/I4210159575"]},{"raw_affiliation_string":"Fudan University , School of Life Sciences, , No. 2005 Songhu Road, Shanghai, 200433,","institution_ids":["https://openalex.org/I24943067"]},{"raw_affiliation_string":"Shanghai Sci-Tech Inno Center for Infection & Immunity , No. 1688 Guoquan Bei Road, Shanghai,","institution_ids":[]},{"raw_affiliation_string":"State Key Laboratory of Genetic Engineering , School of Life Sciences, , No. 2005 Songhu Road, Shanghai, 200433,","institution_ids":["https://openalex.org/I4391768242"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":13,"corresponding_author_ids":["https://openalex.org/A5082924301"],"corresponding_institution_ids":["https://openalex.org/I24943067","https://openalex.org/I4391768242"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":3.1448,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.91350809,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"25","issue":"6","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":1.0,"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":1.0,"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":0.9976999759674072,"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/T10494","display_name":"Plant Virus Research Studies","score":0.9889000058174133,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.6223337650299072},{"id":"https://openalex.org/keywords/intraspecific-competition","display_name":"Intraspecific competition","score":0.5679481029510498},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5412535071372986},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5377251505851746},{"id":"https://openalex.org/keywords/feature-selection","display_name":"Feature selection","score":0.5079572796821594},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.504165530204773},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.49288034439086914},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.48196813464164734},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.43469518423080444},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.4170437753200531},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4137979745864868},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.34508460760116577},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32346880435943604},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.19221383333206177},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.08265519142150879}],"concepts":[{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.6223337650299072},{"id":"https://openalex.org/C131892835","wikidata":"https://www.wikidata.org/wiki/Q770985","display_name":"Intraspecific competition","level":2,"score":0.5679481029510498},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5412535071372986},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5377251505851746},{"id":"https://openalex.org/C148483581","wikidata":"https://www.wikidata.org/wiki/Q446488","display_name":"Feature selection","level":2,"score":0.5079572796821594},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.504165530204773},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.49288034439086914},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.48196813464164734},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.43469518423080444},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.4170437753200531},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4137979745864868},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.34508460760116577},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32346880435943604},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.19221383333206177},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.08265519142150879},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"descriptor_ui":"D001419","descriptor_name":"Bacteria","qualifier_ui":"Q000821","qualifier_name":"virology","is_major_topic":false},{"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":"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}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbae484","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae484","pdf_url":"https://academic.oup.com/bib/article-pdf/25/6/bbae484/59428529/bbae484.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:39344712","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39344712","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:11440089","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11440089","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11440089/pdf/bbae484.pdf","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-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbae484","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae484","pdf_url":"https://academic.oup.com/bib/article-pdf/25/6/bbae484/59428529/bbae484.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":[{"score":0.5400000214576721,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[{"id":"https://openalex.org/G2495752485","display_name":null,"funder_award_id":"2022YFA","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G6624196571","display_name":null,"funder_award_id":"2021YFC","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G7736677968","display_name":null,"funder_award_id":"2021YFC2501800","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G8947960417","display_name":null,"funder_award_id":"2022YFA0806200","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"}],"funders":[{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4402963971.pdf","grobid_xml":"https://content.openalex.org/works/W4402963971.grobid-xml"},"referenced_works_count":46,"referenced_works":["https://openalex.org/W114564532","https://openalex.org/W1989686186","https://openalex.org/W2019197162","https://openalex.org/W2028869026","https://openalex.org/W2056731969","https://openalex.org/W2096093282","https://openalex.org/W2107903949","https://openalex.org/W2111538183","https://openalex.org/W2118417130","https://openalex.org/W2136723682","https://openalex.org/W2145640762","https://openalex.org/W2159808296","https://openalex.org/W2235238101","https://openalex.org/W2245444176","https://openalex.org/W2329901740","https://openalex.org/W2405903593","https://openalex.org/W2496221212","https://openalex.org/W2559100382","https://openalex.org/W2734399491","https://openalex.org/W2769959144","https://openalex.org/W2793168264","https://openalex.org/W2905291356","https://openalex.org/W2969999319","https://openalex.org/W2990458240","https://openalex.org/W3051688178","https://openalex.org/W3103398320","https://openalex.org/W3112043731","https://openalex.org/W3118981004","https://openalex.org/W3122809531","https://openalex.org/W3132890345","https://openalex.org/W3171187312","https://openalex.org/W3175812678","https://openalex.org/W3200765011","https://openalex.org/W4211100962","https://openalex.org/W4220770541","https://openalex.org/W4230932396","https://openalex.org/W4239690181","https://openalex.org/W4293456291","https://openalex.org/W4313560729","https://openalex.org/W4320732021","https://openalex.org/W4379743275","https://openalex.org/W4389142474","https://openalex.org/W4391766310","https://openalex.org/W6657736081","https://openalex.org/W6787428992","https://openalex.org/W6821734526"],"related_works":["https://openalex.org/W1525303497","https://openalex.org/W2811459610","https://openalex.org/W4245136235","https://openalex.org/W2004764425","https://openalex.org/W4393861002","https://openalex.org/W2164605607","https://openalex.org/W2912837731","https://openalex.org/W50819732","https://openalex.org/W4386564352","https://openalex.org/W2952668426"],"abstract_inverted_index":{"Phages,":[0],"the":[1,47,74,118,151,155,165,171,180,211,215,218,231,241,255],"natural":[2],"predators":[3],"of":[4,120,190,217,234,259],"bacteria,":[5],"were":[6],"discovered":[7],"more":[8,25],"than":[9,29,188],"100":[10],"years":[11],"ago.":[12],"However,":[13],"increasing":[14],"antimicrobial":[15],"resistance":[16],"rates":[17],"have":[18],"revitalized":[19],"phage":[20,275],"research.":[21],"Methods":[22,59],"that":[23,49,150,202],"are":[24,32,52,63,186],"time-consuming":[26],"and":[27,57,76,115,142,164,168,176,197,205,209,244,257,266,271],"efficient":[28],"wet-laboratory":[30],"experiments":[31,224],"needed":[33],"to":[34,97,123],"help":[35],"screen":[36],"phages":[37],"quickly":[38],"for":[39,60,93,105,128,157,161,236,273,277],"therapeutic":[40],"use.":[41],"Traditional":[42],"computational":[43],"methods":[44,69],"usually":[45],"ignore":[46],"fact":[48],"phage-bacteria":[50],"interactions":[51,72],"achieved":[53],"by":[54,108],"key":[55,113,203,206],"genes":[56,114,204],"proteins.":[58],"intraspecific":[61,222,237],"prediction":[62,107,136,158,193,223,246],"rare":[64],"since":[65],"almost":[66],"all":[67],"existing":[68,83,192],"consider":[70],"only":[71,86],"at":[73],"species":[75,94],"genus":[77],"levels.":[78],"Moreover,":[79],"most":[80],"strains":[81],"in":[82,249],"databases":[84],"contain":[85],"partial":[87],"genome":[88],"information":[89,92],"because":[90],"whole-genome":[91],"is":[95],"difficult":[96],"obtain.":[98],"Here,":[99],"we":[100,131],"propose":[101],"a":[102,134,143],"new":[103,110,269],"approach":[104],"interaction":[106,245,260],"constructing":[109],"features":[111],"from":[112],"proteins":[116,207],"via":[117],"application":[119],"K-means":[121],"sampling":[122],"select":[124],"high-quality":[125],"negative":[126],"samples":[127],"prediction.":[129,238],"Finally,":[130],"develop":[132],"DeepPBI-KG,":[133],"corresponding":[135],"tool":[137],"based":[138,225],"on":[139,179,226],"feature":[140,242],"selection":[141],"deep":[144],"neural":[145],"network.":[146],"The":[147,195],"results":[148,200],"show":[149],"average":[152],"area":[153,169],"under":[154,170],"curve":[156,173],"reached":[159,174],"0.93":[160],"each":[162],"strain,":[163],"overall":[166],"AUC":[167],"precision-recall":[172],"0.89":[175],"0.92,":[177],"respectively,":[178],"independent":[181],"test":[182],"set;":[183],"these":[184],"values":[185],"greater":[187],"those":[189],"other":[191],"tools.":[194],"forward":[196],"reverse":[198],"validation":[199],"indicate":[201],"regulate":[208],"influence":[210],"interaction,":[212],"which":[213],"supports":[214],"reliability":[216],"model.":[219],"In":[220,239],"addition,":[221],"Klebsiella":[227],"pneumoniae":[228],"data":[229],"demonstrate":[230],"potential":[232],"applicability":[233],"DeepPBI-KG":[235],"summary,":[240],"engineering":[243],"approaches":[247],"proposed":[248],"this":[250],"study":[251],"can":[252,262],"effectively":[253],"improve":[254],"robustness":[256],"stability":[258],"prediction,":[261],"achieve":[263],"high":[264],"generalizability,":[265],"may":[267],"provide":[268],"directions":[270],"insights":[272],"rapid":[274],"screening":[276],"therapy.":[278]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":5}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}