{"id":"https://openalex.org/W4390347983","doi":"https://doi.org/10.1093/bib/bbad472","title":"\u2018Bingo\u2019\u2014a large language model- and graph neural network-based workflow for the prediction of essential genes from protein data","display_name":"\u2018Bingo\u2019\u2014a large language model- and graph neural network-based workflow for the prediction of essential genes from protein data","publication_year":2023,"publication_date":"2023-11-22","ids":{"openalex":"https://openalex.org/W4390347983","doi":"https://doi.org/10.1093/bib/bbad472","pmid":"https://pubmed.ncbi.nlm.nih.gov/38152979"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad472","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad472","pdf_url":"https://academic.oup.com/bib/article-pdf/25/1/bbad472/54910122/bbad472.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bib/article-pdf/25/1/bbad472/54910122/bbad472.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103140066","display_name":"Jiani Ma","orcid":"https://orcid.org/0000-0002-8126-0431"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I25757504","display_name":"China University of Mining and Technology","ror":"https://ror.org/01xt2dr21","country_code":"CN","type":"education","lineage":["https://openalex.org/I25757504"]},{"id":"https://openalex.org/I4210149301","display_name":"AgriBio","ror":"https://ror.org/042kgb568","country_code":"AU","type":"facility","lineage":["https://openalex.org/I4210149301"]}],"countries":["AU","CN"],"is_corresponding":false,"raw_author_name":"Jiani Ma","raw_affiliation_strings":["Department of Veterinary Biosciences , Melbourne Veterinary School, , Parkville, Victoria 3010 , Australia","School of Information and Control Engineering, China University of Mining and Technology , Xuzhou 221116 , China","The University of Melbourne , Melbourne Veterinary School, , Parkville, Victoria 3010 , Australia","Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia","School of Information and Control Engineering, China University of Mining and Technology, Xuzhou 221116, China"],"raw_orcid":"https://orcid.org/0000-0002-8126-0431","affiliations":[{"raw_affiliation_string":"Department of Veterinary Biosciences , Melbourne Veterinary School, , Parkville, Victoria 3010 , Australia","institution_ids":["https://openalex.org/I165779595","https://openalex.org/I4210149301"]},{"raw_affiliation_string":"School of Information and Control Engineering, China University of Mining and Technology , Xuzhou 221116 , China","institution_ids":["https://openalex.org/I25757504"]},{"raw_affiliation_string":"The University of Melbourne , Melbourne Veterinary School, , Parkville, Victoria 3010 , Australia","institution_ids":["https://openalex.org/I165779595"]},{"raw_affiliation_string":"Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia","institution_ids":["https://openalex.org/I165779595"]},{"raw_affiliation_string":"School of Information and Control Engineering, China University of Mining and Technology, Xuzhou 221116, China","institution_ids":["https://openalex.org/I25757504"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012709797","display_name":"Jiangning Song","orcid":"https://orcid.org/0000-0001-8031-9086"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I4210149301","display_name":"AgriBio","ror":"https://ror.org/042kgb568","country_code":"AU","type":"facility","lineage":["https://openalex.org/I4210149301"]},{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Jiangning Song","raw_affiliation_strings":["Department of Veterinary Biosciences , Melbourne Veterinary School, , Parkville, Victoria 3010 , Australia","Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University , Melbourne, Victoria 3800 , Australia","The University of Melbourne , Melbourne Veterinary School, , Parkville, Victoria 3010 , Australia","Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia","Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia"],"raw_orcid":"https://orcid.org/0000-0001-8031-9086","affiliations":[{"raw_affiliation_string":"Department of Veterinary Biosciences , Melbourne Veterinary School, , Parkville, Victoria 3010 , Australia","institution_ids":["https://openalex.org/I165779595","https://openalex.org/I4210149301"]},{"raw_affiliation_string":"Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University , Melbourne, Victoria 3800 , Australia","institution_ids":["https://openalex.org/I56590836"]},{"raw_affiliation_string":"The University of Melbourne , Melbourne Veterinary School, , Parkville, Victoria 3010 , Australia","institution_ids":["https://openalex.org/I165779595"]},{"raw_affiliation_string":"Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia","institution_ids":["https://openalex.org/I165779595"]},{"raw_affiliation_string":"Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Melbourne, Victoria 3800, Australia","institution_ids":["https://openalex.org/I56590836"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040055695","display_name":"Neil D. Young","orcid":"https://orcid.org/0000-0001-8756-229X"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I4210149301","display_name":"AgriBio","ror":"https://ror.org/042kgb568","country_code":"AU","type":"facility","lineage":["https://openalex.org/I4210149301"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Neil D Young","raw_affiliation_strings":["Department of Veterinary Biosciences , Melbourne Veterinary School, , Parkville, Victoria 3010 , Australia","The University of Melbourne , Melbourne Veterinary School, , Parkville, Victoria 3010 , Australia","Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Veterinary Biosciences , Melbourne Veterinary School, , Parkville, Victoria 3010 , Australia","institution_ids":["https://openalex.org/I165779595","https://openalex.org/I4210149301"]},{"raw_affiliation_string":"The University of Melbourne , Melbourne Veterinary School, , Parkville, Victoria 3010 , Australia","institution_ids":["https://openalex.org/I165779595"]},{"raw_affiliation_string":"Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia","institution_ids":["https://openalex.org/I165779595"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009058834","display_name":"Bill C. H. Chang","orcid":"https://orcid.org/0000-0001-5313-4852"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I4210149301","display_name":"AgriBio","ror":"https://ror.org/042kgb568","country_code":"AU","type":"facility","lineage":["https://openalex.org/I4210149301"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Bill C H Chang","raw_affiliation_strings":["Department of Veterinary Biosciences , Melbourne Veterinary School, , Parkville, Victoria 3010 , Australia","The University of Melbourne , Melbourne Veterinary School, , Parkville, Victoria 3010 , Australia","Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Veterinary Biosciences , Melbourne Veterinary School, , Parkville, Victoria 3010 , Australia","institution_ids":["https://openalex.org/I165779595","https://openalex.org/I4210149301"]},{"raw_affiliation_string":"The University of Melbourne , Melbourne Veterinary School, , Parkville, Victoria 3010 , Australia","institution_ids":["https://openalex.org/I165779595"]},{"raw_affiliation_string":"Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia","institution_ids":["https://openalex.org/I165779595"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053972908","display_name":"Pasi K. Korhonen","orcid":"https://orcid.org/0000-0002-9957-4674"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I4210149301","display_name":"AgriBio","ror":"https://ror.org/042kgb568","country_code":"AU","type":"facility","lineage":["https://openalex.org/I4210149301"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Pasi K Korhonen","raw_affiliation_strings":["Department of Veterinary Biosciences , Melbourne Veterinary School, , Parkville, Victoria 3010 , Australia","The University of Melbourne , Melbourne Veterinary School, , Parkville, Victoria 3010 , Australia","Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Veterinary Biosciences , Melbourne Veterinary School, , Parkville, Victoria 3010 , Australia","institution_ids":["https://openalex.org/I165779595","https://openalex.org/I4210149301"]},{"raw_affiliation_string":"The University of Melbourne , Melbourne Veterinary School, , Parkville, Victoria 3010 , Australia","institution_ids":["https://openalex.org/I165779595"]},{"raw_affiliation_string":"Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia","institution_ids":["https://openalex.org/I165779595"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070209032","display_name":"T\u00falio de Lima Campos","orcid":"https://orcid.org/0000-0003-0446-848X"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I4210149301","display_name":"AgriBio","ror":"https://ror.org/042kgb568","country_code":"AU","type":"facility","lineage":["https://openalex.org/I4210149301"]},{"id":"https://openalex.org/I52325","display_name":"Funda\u00e7\u00e3o Oswaldo Cruz","ror":"https://ror.org/04jhswv08","country_code":"BR","type":"facility","lineage":["https://openalex.org/I52325"]}],"countries":["AU","BR"],"is_corresponding":false,"raw_author_name":"Tulio L Campos","raw_affiliation_strings":["Bioinformatics Core Facility, Instituto Aggeu Magalhaes, Funda\u00e7ao Oswaldo Cruz (IAM-Fiocruz), Recife , Pernambuco , Brazil","Department of Veterinary Biosciences , Melbourne Veterinary School, , Parkville, Victoria 3010 , Australia","The University of Melbourne , Melbourne Veterinary School, , Parkville, Victoria 3010 , Australia","Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Core Facility, Instituto Aggeu Magalhaes, Funda\u00e7ao Oswaldo Cruz (IAM-Fiocruz), Recife , Pernambuco , Brazil","institution_ids":["https://openalex.org/I52325"]},{"raw_affiliation_string":"Department of Veterinary Biosciences , Melbourne Veterinary School, , Parkville, Victoria 3010 , Australia","institution_ids":["https://openalex.org/I165779595","https://openalex.org/I4210149301"]},{"raw_affiliation_string":"The University of Melbourne , Melbourne Veterinary School, , Parkville, Victoria 3010 , Australia","institution_ids":["https://openalex.org/I165779595"]},{"raw_affiliation_string":"Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia","institution_ids":["https://openalex.org/I165779595"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086297899","display_name":"Hui Liu","orcid":"https://orcid.org/0000-0003-1980-5952"},"institutions":[{"id":"https://openalex.org/I25757504","display_name":"China University of Mining and Technology","ror":"https://ror.org/01xt2dr21","country_code":"CN","type":"education","lineage":["https://openalex.org/I25757504"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hui Liu","raw_affiliation_strings":["School of Information and Control Engineering, China University of Mining and Technology , Xuzhou 221116 , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information and Control Engineering, China University of Mining and Technology , Xuzhou 221116 , China","institution_ids":["https://openalex.org/I25757504"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085039675","display_name":"Robin B. Gasser","orcid":"https://orcid.org/0000-0002-4423-1690"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]},{"id":"https://openalex.org/I4210149301","display_name":"AgriBio","ror":"https://ror.org/042kgb568","country_code":"AU","type":"facility","lineage":["https://openalex.org/I4210149301"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Robin B Gasser","raw_affiliation_strings":["Department of Veterinary Biosciences , Melbourne Veterinary School, , Parkville, Victoria 3010 , Australia","The University of Melbourne , Melbourne Veterinary School, , Parkville, Victoria 3010 , Australia","Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Veterinary Biosciences , Melbourne Veterinary School, , Parkville, Victoria 3010 , Australia","institution_ids":["https://openalex.org/I165779595","https://openalex.org/I4210149301"]},{"raw_affiliation_string":"The University of Melbourne , Melbourne Veterinary School, , Parkville, Victoria 3010 , Australia","institution_ids":["https://openalex.org/I165779595"]},{"raw_affiliation_string":"Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia","institution_ids":["https://openalex.org/I165779595"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5085039675"],"corresponding_institution_ids":["https://openalex.org/I165779595","https://openalex.org/I4210149301"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":2.5842,"has_fulltext":true,"cited_by_count":28,"citation_normalized_percentile":{"value":0.91039903,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"25","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9972000122070312,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9972000122070312,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9952999949455261,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9922000169754028,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5966147184371948},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5398703217506409},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5328508019447327},{"id":"https://openalex.org/keywords/caenorhabditis-elegans","display_name":"Caenorhabditis elegans","score":0.48429980874061584},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.4832356870174408},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.4625363349914551},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4582068920135498},{"id":"https://openalex.org/keywords/model-organism","display_name":"Model organism","score":0.4530690014362335},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.4399445056915283},{"id":"https://openalex.org/keywords/homo-sapiens","display_name":"Homo sapiens","score":0.4101915955543518},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.2939344644546509}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5966147184371948},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5398703217506409},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5328508019447327},{"id":"https://openalex.org/C2778944004","wikidata":"https://www.wikidata.org/wiki/Q91703","display_name":"Caenorhabditis elegans","level":3,"score":0.48429980874061584},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.4832356870174408},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.4625363349914551},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4582068920135498},{"id":"https://openalex.org/C19843653","wikidata":"https://www.wikidata.org/wiki/Q213907","display_name":"Model organism","level":3,"score":0.4530690014362335},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.4399445056915283},{"id":"https://openalex.org/C2777938546","wikidata":"https://www.wikidata.org/wiki/Q5","display_name":"Homo sapiens","level":2,"score":0.4101915955543518},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.2939344644546509},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C19165224","wikidata":"https://www.wikidata.org/wiki/Q23404","display_name":"Anthropology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004331","descriptor_name":"Drosophila melanogaster","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008840","descriptor_name":"Microfilament Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008840","descriptor_name":"Microfilament Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008840","descriptor_name":"Microfilament Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008840","descriptor_name":"Microfilament Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008840","descriptor_name":"Microfilament Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020043","descriptor_name":"Genes, Essential","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020043","descriptor_name":"Genes, Essential","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020043","descriptor_name":"Genes, Essential","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020043","descriptor_name":"Genes, Essential","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020043","descriptor_name":"Genes, Essential","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D029721","descriptor_name":"Drosophila Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D029721","descriptor_name":"Drosophila Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D029721","descriptor_name":"Drosophila Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D029721","descriptor_name":"Drosophila Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D029721","descriptor_name":"Drosophila Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1093/bib/bbad472","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad472","pdf_url":"https://academic.oup.com/bib/article-pdf/25/1/bbad472/54910122/bbad472.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38152979","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38152979","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:10753293","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10753293","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10753293/pdf/bbad472.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:jupiter.its.unimelb.edu.au:11343/344347","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad472.","pdf_url":null,"source":{"id":"https://openalex.org/S4377196259","display_name":"Minerva Access (University of Melbourne)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I165779595","host_organization_name":"The University of Melbourne","host_organization_lineage":["https://openalex.org/I165779595"],"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":null,"raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1093/bib/bbad472","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad472","pdf_url":"https://academic.oup.com/bib/article-pdf/25/1/bbad472/54910122/bbad472.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2071191990","display_name":"Illuminating genomic dark matter to develop new interventions for parasites","funder_award_id":"LP180101085","funder_id":"https://openalex.org/F4320334704","funder_display_name":"Australian Research Council"},{"id":"https://openalex.org/G5286074384","display_name":"Artificial intelligence to explore and combat eukaryotic pathogens","funder_award_id":"LP220200614","funder_id":"https://openalex.org/F4320334704","funder_display_name":"Australian Research Council"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"},{"id":"https://openalex.org/F4320322725","display_name":"China Scholarship Council","ror":"https://ror.org/04atp4p48"},{"id":"https://openalex.org/F4320334704","display_name":"Australian Research Council","ror":"https://ror.org/05mmh0f86"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4390347983.pdf"},"referenced_works_count":61,"referenced_works":["https://openalex.org/W1635615463","https://openalex.org/W1700829084","https://openalex.org/W1815358876","https://openalex.org/W1832693441","https://openalex.org/W1974383394","https://openalex.org/W2006185455","https://openalex.org/W2008083733","https://openalex.org/W2042586732","https://openalex.org/W2059223767","https://openalex.org/W2085142868","https://openalex.org/W2099468911","https://openalex.org/W2102424043","https://openalex.org/W2107835138","https://openalex.org/W2131481416","https://openalex.org/W2132629607","https://openalex.org/W2143965359","https://openalex.org/W2155190953","https://openalex.org/W2159595936","https://openalex.org/W2187089797","https://openalex.org/W2317303533","https://openalex.org/W2334956771","https://openalex.org/W2344533005","https://openalex.org/W2428003863","https://openalex.org/W2561201681","https://openalex.org/W2592549418","https://openalex.org/W2747329762","https://openalex.org/W2766955181","https://openalex.org/W2800834635","https://openalex.org/W2898311987","https://openalex.org/W2910705748","https://openalex.org/W2912802963","https://openalex.org/W2913448170","https://openalex.org/W2915554882","https://openalex.org/W2916803445","https://openalex.org/W2951756882","https://openalex.org/W2970119293","https://openalex.org/W2971136217","https://openalex.org/W2991321419","https://openalex.org/W3012055802","https://openalex.org/W3024367627","https://openalex.org/W3042748728","https://openalex.org/W3044758851","https://openalex.org/W3094351441","https://openalex.org/W3152564577","https://openalex.org/W3160750023","https://openalex.org/W3198485382","https://openalex.org/W3210734461","https://openalex.org/W3212259269","https://openalex.org/W3216419673","https://openalex.org/W4206816857","https://openalex.org/W4221139076","https://openalex.org/W4296774313","https://openalex.org/W4310594072","https://openalex.org/W4321003857","https://openalex.org/W4327550249","https://openalex.org/W6702949759","https://openalex.org/W6704500078","https://openalex.org/W6754929296","https://openalex.org/W6758516871","https://openalex.org/W6758830137","https://openalex.org/W6780542308"],"related_works":["https://openalex.org/W2971505853","https://openalex.org/W2465065470","https://openalex.org/W4297906920","https://openalex.org/W3041017960","https://openalex.org/W4206310443","https://openalex.org/W2013960851","https://openalex.org/W2518550345","https://openalex.org/W1556437567","https://openalex.org/W2086868805","https://openalex.org/W1971840302"],"abstract_inverted_index":{"The":[0],"identification":[1],"and":[2,20,34,105,119,125,145,154,164,190,201,210,240],"characterization":[3],"of":[4,12,27,44,46,56,84,109,187,224,233,238],"essential":[5,85,110,135,171,231],"genes":[6,45,86,111,137,172,232],"are":[7],"central":[8],"to":[9,53,73,87,101,133,182,205,216,227],"our":[10],"understanding":[11],"the":[13,25,37,42,50,54,79,107,139,198,207,222,230],"core":[14],"biological":[15,90,243],"functions":[16,43],"in":[17,40,49,57,75,94,138,151],"eukaryotic":[18],"organisms,":[19],"has":[21,69],"important":[22],"implications":[23],"for":[24,31,64,78,184,193,245],"treatment":[26],"diseases":[28],"caused":[29],"by,":[30],"example,":[32],"cancers":[33],"pathogens.":[35],"Given":[36],"major":[38],"constraints":[39],"testing":[41],"many":[47],"organisms":[48,142,237],"laboratory,":[51],"due":[52],"absence":[55],"vitro":[58],"cultures":[59],"and/or":[60],"gene":[61,246],"perturbation":[62],"assays":[63],"most":[65,214],"metazoan":[66,140],"species,":[67],"there":[68],"been":[70],"a":[71,113,121,185,242],"need":[72],"develop":[74],"silico":[76],"tools":[77],"accurate":[80],"prediction":[81],"or":[82,235],"inference":[83],"underpin":[88],"systems":[89],"investigations.":[91],"Major":[92],"advances":[93],"machine":[95],"learning":[96],"approaches":[97],"provide":[98],"unprecedented":[99],"opportunities":[100],"overcome":[102],"these":[103],"limitations":[104],"accelerate":[106],"discovery":[108],"on":[112],"genome-wide":[114],"scale.":[115],"Here,":[116],"we":[117],"developed":[118],"evaluated":[120],"large":[122],"language":[123],"model-":[124],"graph":[126],"neural":[127],"network":[128],"(LLM-GNN)-based":[129],"approach,":[130],"called":[131],"'Bingo',":[132],"predict":[134],"protein-coding":[136],"model":[141],"Caenorhabditis":[143],"elegans":[144],"Drosophila":[146],"melanogaster":[147],"as":[148,150],"well":[149],"Mus":[152],"musculus":[153],"Homo":[155],"sapiens":[156],"(a":[157],"HepG2":[158],"cell":[159],"line)":[160],"by":[161],"integrating":[162],"LLM":[163],"GNNs":[165],"with":[166,177,213],"adversarial":[167],"training.":[168],"Bingo":[169,220],"predicts":[170],"under":[173],"two":[174],"'zero-shot'":[175],"scenarios":[176],"transfer":[178],"learning,":[179],"showing":[180],"promise":[181],"compensate":[183],"lack":[186],"high-quality":[188],"genomic":[189],"proteomic":[191],"data":[192],"non-model":[194],"organisms.":[195],"In":[196,218],"addition,":[197],"attention":[199],"mechanisms":[200],"GNNExplainer":[202],"were":[203],"employed":[204],"manifest":[206],"functional":[208],"sites":[209],"structural":[211],"domain":[212],"contribution":[215],"essentiality.":[217,247],"conclusion,":[219],"provides":[221,241],"prospect":[223],"being":[225],"able":[226],"accurately":[228],"infer":[229],"little-":[234],"under-studied":[236],"interest,":[239],"explanation":[244]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":18},{"year":2024,"cited_by_count":4}],"updated_date":"2026-08-08T01:25:22.217667","created_date":"2025-10-10T00:00:00"}