{"id":"https://openalex.org/W4399563163","doi":"https://doi.org/10.1109/jbhi.2024.3413146","title":"Characterizing Secretion System Effector Proteins With Structure-Aware Graph Neural Networks and Pre-Trained Language Models","display_name":"Characterizing Secretion System Effector Proteins With Structure-Aware Graph Neural Networks and Pre-Trained Language Models","publication_year":2024,"publication_date":"2024-06-12","ids":{"openalex":"https://openalex.org/W4399563163","doi":"https://doi.org/10.1109/jbhi.2024.3413146","pmid":"https://pubmed.ncbi.nlm.nih.gov/38865232"},"language":"en","primary_location":{"id":"doi:10.1109/jbhi.2024.3413146","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2024.3413146","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Journal of Biomedical and Health Informatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5099099501","display_name":"Zixu Ran","orcid":null},"institutions":[{"id":"https://openalex.org/I11701301","display_name":"Griffith University","ror":"https://ror.org/02sc3r913","country_code":"AU","type":"education","lineage":["https://openalex.org/I11701301"]},{"id":"https://openalex.org/I4210132539","display_name":"Northwest Institute of Mechanical and Electrical Engineering","ror":"https://ror.org/03pz37k82","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210132539"]},{"id":"https://openalex.org/I4210140852","display_name":"Centre for Cancer Biology","ror":"https://ror.org/03yg7hz06","country_code":"AU","type":"facility","lineage":["https://openalex.org/I107656453","https://openalex.org/I4210140852"]},{"id":"https://openalex.org/I5681781","display_name":"The University of Adelaide","ror":"https://ror.org/00892tw58","country_code":"AU","type":"education","lineage":["https://openalex.org/I5681781"]},{"id":"https://openalex.org/I89652312","display_name":"Northwest A&F University","ror":"https://ror.org/0051rme32","country_code":"CN","type":"education","lineage":["https://openalex.org/I89652312"]}],"countries":["AU","CN"],"is_corresponding":false,"raw_author_name":"Zixu Ran","raw_affiliation_strings":["College of Information Engineering, Northwest A&amp;F University, Xianyang, China","School of Information and Communication Technology, Griffith University, QLD 4222, Australia","College of Information Engineering, Northwest A&F University, Shaanxi 712100, China. Heyun Sun","South Australian immunoGENomics Cancer Institute (SAiGENCI), University of Adelaide, SA 5000, Australia"],"raw_orcid":"https://orcid.org/0009-0005-5831-1607","affiliations":[{"raw_affiliation_string":"College of Information Engineering, Northwest A&amp;F University, Xianyang, China","institution_ids":["https://openalex.org/I4210132539"]},{"raw_affiliation_string":"School of Information and Communication Technology, Griffith University, QLD 4222, Australia","institution_ids":["https://openalex.org/I11701301"]},{"raw_affiliation_string":"College of Information Engineering, Northwest A&F University, Shaanxi 712100, China. Heyun Sun","institution_ids":["https://openalex.org/I89652312"]},{"raw_affiliation_string":"South Australian immunoGENomics Cancer Institute (SAiGENCI), University of Adelaide, SA 5000, Australia","institution_ids":["https://openalex.org/I4210140852","https://openalex.org/I5681781"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100390545","display_name":"Cong Wang","orcid":"https://orcid.org/0009-0004-3865-1033"},"institutions":[{"id":"https://openalex.org/I11701301","display_name":"Griffith University","ror":"https://ror.org/02sc3r913","country_code":"AU","type":"education","lineage":["https://openalex.org/I11701301"]},{"id":"https://openalex.org/I4210132539","display_name":"Northwest Institute of Mechanical and Electrical Engineering","ror":"https://ror.org/03pz37k82","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210132539"]},{"id":"https://openalex.org/I4210140852","display_name":"Centre for Cancer Biology","ror":"https://ror.org/03yg7hz06","country_code":"AU","type":"facility","lineage":["https://openalex.org/I107656453","https://openalex.org/I4210140852"]},{"id":"https://openalex.org/I5681781","display_name":"The University of Adelaide","ror":"https://ror.org/00892tw58","country_code":"AU","type":"education","lineage":["https://openalex.org/I5681781"]},{"id":"https://openalex.org/I89652312","display_name":"Northwest A&F University","ror":"https://ror.org/0051rme32","country_code":"CN","type":"education","lineage":["https://openalex.org/I89652312"]}],"countries":["AU","CN"],"is_corresponding":false,"raw_author_name":"Cong Wang","raw_affiliation_strings":["College of Information Engineering, Northwest A&amp;F University, Xianyang, China","School of Information and Communication Technology, Griffith University, QLD 4222, Australia","South Australian immunoGENomics Cancer Institute (SAiGENCI), University of Adelaide, SA 5000, Australia","College of Information Engineering, Northwest A&F University, Shaanxi 712100, China. Heyun Sun"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Information Engineering, Northwest A&amp;F University, Xianyang, China","institution_ids":["https://openalex.org/I4210132539"]},{"raw_affiliation_string":"School of Information and Communication Technology, Griffith University, QLD 4222, Australia","institution_ids":["https://openalex.org/I11701301"]},{"raw_affiliation_string":"South Australian immunoGENomics Cancer Institute (SAiGENCI), University of Adelaide, SA 5000, Australia","institution_ids":["https://openalex.org/I4210140852","https://openalex.org/I5681781"]},{"raw_affiliation_string":"College of Information Engineering, Northwest A&F University, Shaanxi 712100, China. Heyun Sun","institution_ids":["https://openalex.org/I89652312"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112567358","display_name":"Heyun Sun","orcid":null},"institutions":[{"id":"https://openalex.org/I11701301","display_name":"Griffith University","ror":"https://ror.org/02sc3r913","country_code":"AU","type":"education","lineage":["https://openalex.org/I11701301"]},{"id":"https://openalex.org/I4210140852","display_name":"Centre for Cancer Biology","ror":"https://ror.org/03yg7hz06","country_code":"AU","type":"facility","lineage":["https://openalex.org/I107656453","https://openalex.org/I4210140852"]},{"id":"https://openalex.org/I5681781","display_name":"The University of Adelaide","ror":"https://ror.org/00892tw58","country_code":"AU","type":"education","lineage":["https://openalex.org/I5681781"]},{"id":"https://openalex.org/I89652312","display_name":"Northwest A&F University","ror":"https://ror.org/0051rme32","country_code":"CN","type":"education","lineage":["https://openalex.org/I89652312"]}],"countries":["AU","CN"],"is_corresponding":false,"raw_author_name":"Heyun Sun","raw_affiliation_strings":["South Australian immunoGENomics Cancer Institute (SAiGENCI), University of Adelaide, Adelaide, SA, Australia","College of Information Engineering, Northwest A&F University, Shaanxi 712100, China. Heyun Sun","School of Information and Communication Technology, Griffith University, QLD 4222, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"South Australian immunoGENomics Cancer Institute (SAiGENCI), University of Adelaide, Adelaide, SA, Australia","institution_ids":["https://openalex.org/I4210140852","https://openalex.org/I5681781"]},{"raw_affiliation_string":"College of Information Engineering, Northwest A&F University, Shaanxi 712100, China. Heyun Sun","institution_ids":["https://openalex.org/I89652312"]},{"raw_affiliation_string":"School of Information and Communication Technology, Griffith University, QLD 4222, Australia","institution_ids":["https://openalex.org/I11701301"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008056593","display_name":"Shirui Pan","orcid":"https://orcid.org/0000-0003-0794-527X"},"institutions":[{"id":"https://openalex.org/I11701301","display_name":"Griffith University","ror":"https://ror.org/02sc3r913","country_code":"AU","type":"education","lineage":["https://openalex.org/I11701301"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Shirui Pan","raw_affiliation_strings":["School of Information and Communication Technology, Griffith University, Brisbane, QLD, Australia"],"raw_orcid":"https://orcid.org/0000-0003-0794-527X","affiliations":[{"raw_affiliation_string":"School of Information and Communication Technology, Griffith University, Brisbane, QLD, Australia","institution_ids":["https://openalex.org/I11701301"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5063409460","display_name":"Fuyi Li","orcid":"https://orcid.org/0000-0001-5216-3213"},"institutions":[{"id":"https://openalex.org/I11701301","display_name":"Griffith University","ror":"https://ror.org/02sc3r913","country_code":"AU","type":"education","lineage":["https://openalex.org/I11701301"]},{"id":"https://openalex.org/I4210132539","display_name":"Northwest Institute of Mechanical and Electrical Engineering","ror":"https://ror.org/03pz37k82","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210132539"]},{"id":"https://openalex.org/I4210140852","display_name":"Centre for Cancer Biology","ror":"https://ror.org/03yg7hz06","country_code":"AU","type":"facility","lineage":["https://openalex.org/I107656453","https://openalex.org/I4210140852"]},{"id":"https://openalex.org/I5681781","display_name":"The University of Adelaide","ror":"https://ror.org/00892tw58","country_code":"AU","type":"education","lineage":["https://openalex.org/I5681781"]},{"id":"https://openalex.org/I89652312","display_name":"Northwest A&F University","ror":"https://ror.org/0051rme32","country_code":"CN","type":"education","lineage":["https://openalex.org/I89652312"]}],"countries":["AU","CN"],"is_corresponding":true,"raw_author_name":"Fuyi Li","raw_affiliation_strings":["College of Information Engineering, Northwest A&amp;F University, Xianyang, China","College of Information Engineering, Northwest A&F University, Shaanxi 712100, China. Heyun Sun","School of Information and Communication Technology, Griffith University, QLD 4222, Australia","South Australian immunoGENomics Cancer Institute (SAiGENCI), University of Adelaide, SA 5000, Australia"],"raw_orcid":"https://orcid.org/0000-0001-5216-3213","affiliations":[{"raw_affiliation_string":"College of Information Engineering, Northwest A&amp;F University, Xianyang, China","institution_ids":["https://openalex.org/I4210132539"]},{"raw_affiliation_string":"College of Information Engineering, Northwest A&F University, Shaanxi 712100, China. Heyun Sun","institution_ids":["https://openalex.org/I89652312"]},{"raw_affiliation_string":"School of Information and Communication Technology, Griffith University, QLD 4222, Australia","institution_ids":["https://openalex.org/I11701301"]},{"raw_affiliation_string":"South Australian immunoGENomics Cancer Institute (SAiGENCI), University of Adelaide, SA 5000, Australia","institution_ids":["https://openalex.org/I4210140852","https://openalex.org/I5681781"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5063409460"],"corresponding_institution_ids":["https://openalex.org/I11701301","https://openalex.org/I4210132539","https://openalex.org/I4210140852","https://openalex.org/I5681781","https://openalex.org/I89652312"],"apc_list":null,"apc_paid":null,"fwci":1.1133,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.76595895,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"28","issue":"9","first_page":"5649","last_page":"5657"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","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/T12254","display_name":"Machine Learning in Bioinformatics","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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9848999977111816,"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":0.982699990272522,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7316538095474243},{"id":"https://openalex.org/keywords/effector","display_name":"Effector","score":0.6753722429275513},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.47365865111351013},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.47268134355545044},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.45249128341674805},{"id":"https://openalex.org/keywords/secretion","display_name":"Secretion","score":0.4268282651901245},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3452266454696655},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3293081223964691},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.1591794788837433},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13099679350852966},{"id":"https://openalex.org/keywords/immunology","display_name":"Immunology","score":0.11756959557533264},{"id":"https://openalex.org/keywords/internal-medicine","display_name":"Internal medicine","score":0.07727327942848206}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7316538095474243},{"id":"https://openalex.org/C51785407","wikidata":"https://www.wikidata.org/wiki/Q2627568","display_name":"Effector","level":2,"score":0.6753722429275513},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.47365865111351013},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.47268134355545044},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.45249128341674805},{"id":"https://openalex.org/C49039625","wikidata":"https://www.wikidata.org/wiki/Q84230","display_name":"Secretion","level":2,"score":0.4268282651901245},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3452266454696655},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3293081223964691},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.1591794788837433},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13099679350852966},{"id":"https://openalex.org/C203014093","wikidata":"https://www.wikidata.org/wiki/Q101929","display_name":"Immunology","level":1,"score":0.11756959557533264},{"id":"https://openalex.org/C126322002","wikidata":"https://www.wikidata.org/wiki/Q11180","display_name":"Internal medicine","level":1,"score":0.07727327942848206}],"mesh":[{"descriptor_ui":"D000069296","descriptor_name":"Type III Secretion Systems","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D000069296","descriptor_name":"Type III Secretion Systems","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D000069296","descriptor_name":"Type III Secretion Systems","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D000069296","descriptor_name":"Type III Secretion Systems","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":true},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"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":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:10.1109/jbhi.2024.3413146","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2024.3413146","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Journal of Biomedical and Health Informatics","raw_type":"journal-article"},{"id":"pmid:38865232","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38865232","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":"IEEE journal of biomedical and health informatics","raw_type":null},{"id":"pmh:oai:research-repository.griffith.edu.au:10072/432312","is_oa":false,"landing_page_url":"https://hdl.handle.net/10072/432312","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4194776581","display_name":null,"funder_award_id":"2022YFF1000100","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G7070826438","display_name":null,"funder_award_id":"62202388","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7777819896","display_name":null,"funder_award_id":"-2022","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program 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/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":54,"referenced_works":["https://openalex.org/W1522301498","https://openalex.org/W1783180009","https://openalex.org/W1994902865","https://openalex.org/W2021071631","https://openalex.org/W2037490797","https://openalex.org/W2050745211","https://openalex.org/W2055509168","https://openalex.org/W2066073349","https://openalex.org/W2081413516","https://openalex.org/W2085806556","https://openalex.org/W2095705004","https://openalex.org/W2097606916","https://openalex.org/W2110026675","https://openalex.org/W2125948219","https://openalex.org/W2132645859","https://openalex.org/W2144878722","https://openalex.org/W2147209844","https://openalex.org/W2158352115","https://openalex.org/W2158787690","https://openalex.org/W2159086320","https://openalex.org/W2163670463","https://openalex.org/W2528774686","https://openalex.org/W2582563843","https://openalex.org/W2788167885","https://openalex.org/W2794120121","https://openalex.org/W2899105530","https://openalex.org/W2948035163","https://openalex.org/W2952444689","https://openalex.org/W2956769933","https://openalex.org/W2964321699","https://openalex.org/W2985331920","https://openalex.org/W3024086681","https://openalex.org/W3111450368","https://openalex.org/W3112376646","https://openalex.org/W3144701084","https://openalex.org/W4200554941","https://openalex.org/W4205773061","https://openalex.org/W4213228186","https://openalex.org/W4245184283","https://openalex.org/W4254751698","https://openalex.org/W4297733535","https://openalex.org/W4308370554","https://openalex.org/W4327550249","https://openalex.org/W4381487128","https://openalex.org/W4385245566","https://openalex.org/W4387912681","https://openalex.org/W4389558882","https://openalex.org/W4390591106","https://openalex.org/W4401510771","https://openalex.org/W6631190155","https://openalex.org/W6674330103","https://openalex.org/W6726873649","https://openalex.org/W6755207826","https://openalex.org/W6767288045"],"related_works":["https://openalex.org/W4230283440","https://openalex.org/W2148674193","https://openalex.org/W4392860616","https://openalex.org/W3184145232","https://openalex.org/W3213423095","https://openalex.org/W2158295903","https://openalex.org/W2582563843","https://openalex.org/W1899329792","https://openalex.org/W2808185338","https://openalex.org/W3175155005"],"abstract_inverted_index":{"The":[0],"Type":[1],"III":[2,19],"Secretion":[3],"Systems":[4],"(T3SSs)":[5],"play":[6],"a":[7,64,75,91,138],"pivotal":[8],"role":[9],"in":[10,47,124],"host-pathogen":[11,164],"interactions":[12,35],"by":[13,154],"mediating":[14],"the":[15,96,102,132,152],"secretion":[16,20],"of":[17,106,163],"type":[18],"system":[21],"effectors":[22],"(T3SEs)":[23],"into":[24],"host":[25,30],"cells.":[26,59],"These":[27],"T3SEs":[28,44],"mimic":[29],"cell":[31],"protein":[32,86],"functions,":[33],"influencing":[34],"between":[36],"Gram-negative":[37],"bacterial":[38,52],"pathogens":[39],"and":[40,54,90,114],"their":[41],"hosts.":[42],"Identifying":[43],"is":[45,141],"essential":[46],"biomedical":[48],"research":[49],"for":[50,69],"comprehending":[51],"pathogenesis":[53],"its":[55],"implications":[56],"on":[57,95],"human":[58],"This":[60],"study":[61],"presents":[62],"EDIFIER,":[63],"novel":[65],"multi-channel":[66],"model":[67,99],"designed":[68],"accurate":[70],"T3SE":[71,125,157],"prediction.":[72,126],"It":[73],"incorporates":[74],"graph":[76,80],"structural":[77,88],"channel,":[78],"utilizing":[79],"convolutional":[81],"networks":[82],"(GCN)":[83],"to":[84,100,131,151],"capture":[85],"3D":[87],"features":[89,105],"sequence":[92,103],"channel":[93],"based":[94],"ProteinBERT":[97],"pre-trained":[98],"extract":[101],"context":[104],"T3SEs.":[107],"Rigorous":[108],"benchmarking":[109],"tests,":[110],"including":[111],"ablation":[112],"studies":[113],"comparative":[115],"analysis,":[116],"validate":[117],"that":[118,140],"EDIFIER":[119,148],"outperforms":[120],"current":[121],"state-of-the-art":[122],"tools":[123],"To":[127],"enhance":[128],"EDIFIER's":[129],"accessibility":[130],"broader":[133],"scientific":[134],"community,":[135],"we":[136],"developed":[137],"webserver":[139],"publicly":[142],"accessible":[143],"at":[144],"http://edifier.unimelb-biotools.cloud.edu.au/.":[145],"We":[146],"anticipate":[147],"will":[149],"contribute":[150],"field":[153],"providing":[155],"reliable":[156],"predictions,":[158],"thereby":[159],"advancing":[160],"our":[161],"understanding":[162],"dynamics.":[165]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":1}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
