{"id":"https://openalex.org/W2986268970","doi":"https://doi.org/10.1093/bib/bbz120","title":"Convolutional neural network-based annotation of bacterial type IV secretion system effectors with enhanced accuracy and reduced false discovery","display_name":"Convolutional neural network-based annotation of bacterial type IV secretion system effectors with enhanced accuracy and reduced false discovery","publication_year":2019,"publication_date":"2019-08-22","ids":{"openalex":"https://openalex.org/W2986268970","doi":"https://doi.org/10.1093/bib/bbz120","mag":"2986268970","pmid":"https://pubmed.ncbi.nlm.nih.gov/31860715"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbz120","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbz120","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":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":null,"license_id":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5002772126","display_name":"Jiajun Hong","orcid":"https://orcid.org/0000-0002-2713-3917"},"institutions":[{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jiajun Hong","raw_affiliation_strings":["College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China","institution_ids":["https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085405957","display_name":"Yongchao Luo","orcid":"https://orcid.org/0000-0002-4140-5392"},"institutions":[{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yongchao Luo","raw_affiliation_strings":["College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China","institution_ids":["https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047043274","display_name":"Minjie Mou","orcid":"https://orcid.org/0000-0001-7619-2975"},"institutions":[{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Minjie Mou","raw_affiliation_strings":["College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China","institution_ids":["https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005927452","display_name":"Jianbo Fu","orcid":"https://orcid.org/0000-0003-3358-8106"},"institutions":[{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jianbo Fu","raw_affiliation_strings":["College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China","institution_ids":["https://openalex.org/I76130692"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100354659","display_name":"Yang Zhang","orcid":"https://orcid.org/0000-0002-2739-1916"},"institutions":[{"id":"https://openalex.org/I158842170","display_name":"Chongqing University","ror":"https://ror.org/023rhb549","country_code":"CN","type":"education","lineage":["https://openalex.org/I158842170"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yang Zhang","raw_affiliation_strings":["School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China","institution_ids":["https://openalex.org/I158842170"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027345342","display_name":"Weiwei Xue","orcid":"https://orcid.org/0000-0002-3285-0574"},"institutions":[{"id":"https://openalex.org/I158842170","display_name":"Chongqing University","ror":"https://ror.org/023rhb549","country_code":"CN","type":"education","lineage":["https://openalex.org/I158842170"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Weiwei Xue","raw_affiliation_strings":["School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Pharmaceutical Sciences, Chongqing University, Chongqing 401331, China","institution_ids":["https://openalex.org/I158842170"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080045714","display_name":"Tian Xie","orcid":"https://orcid.org/0000-0001-9893-2778"},"institutions":[{"id":"https://openalex.org/I163151501","display_name":"Hangzhou Normal University","ror":"https://ror.org/014v1mr15","country_code":"CN","type":"education","lineage":["https://openalex.org/I163151501"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tian Xie","raw_affiliation_strings":["Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province, School of Medicine, Hangzhou Normal University, Hangzhou 310036, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province, School of Medicine, Hangzhou Normal University, Hangzhou 310036, China","institution_ids":["https://openalex.org/I163151501"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5061697130","display_name":"Lin Tao","orcid":"https://orcid.org/0000-0001-7494-4758"},"institutions":[{"id":"https://openalex.org/I163151501","display_name":"Hangzhou Normal University","ror":"https://ror.org/014v1mr15","country_code":"CN","type":"education","lineage":["https://openalex.org/I163151501"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lin Tao","raw_affiliation_strings":["Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province, School of Medicine, Hangzhou Normal University, Hangzhou 310036, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Elemene Class Anti-Cancer Chinese Medicine of Zhejiang Province, School of Medicine, Hangzhou Normal University, Hangzhou 310036, China","institution_ids":["https://openalex.org/I163151501"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020010918","display_name":"Yan Lou","orcid":"https://orcid.org/0000-0002-9126-476X"},"institutions":[{"id":"https://openalex.org/I4210166576","display_name":"First Affiliated Hospital Zhejiang University","ror":"https://ror.org/05m1p5x56","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210166576"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yan Lou","raw_affiliation_strings":["Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, Zhejiang University, Hangzhou 310000, Zhejiang, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Zhejiang Provincial Key Laboratory for Drug Clinical Research and Evaluation, The First Affiliated Hospital, Zhejiang University, Hangzhou 310000, Zhejiang, China","institution_ids":["https://openalex.org/I4210166576"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100755257","display_name":"Feng Zhu","orcid":"https://orcid.org/0000-0001-8069-0053"},"institutions":[{"id":"https://openalex.org/I76130692","display_name":"Zhejiang University","ror":"https://ror.org/00a2xv884","country_code":"CN","type":"education","lineage":["https://openalex.org/I76130692"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Feng Zhu","raw_affiliation_strings":["College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China"],"raw_orcid":"https://orcid.org/0000-0001-8069-0053","affiliations":[{"raw_affiliation_string":"College of Pharmaceutical Sciences, Zhejiang University, Hangzhou 310058, China","institution_ids":["https://openalex.org/I76130692"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5002772126"],"corresponding_institution_ids":["https://openalex.org/I76130692"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":6.3227,"has_fulltext":false,"cited_by_count":119,"citation_normalized_percentile":{"value":0.9752641,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"21","issue":"5","first_page":"1825","last_page":"1836"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9984999895095825,"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":0.9984999895095825,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9944000244140625,"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/T11684","display_name":"Vibrio bacteria research studies","score":0.993399977684021,"subfield":{"id":"https://openalex.org/subfields/1310","display_name":"Endocrinology"},"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/convolutional-neural-network","display_name":"Convolutional neural network","score":0.8308824300765991},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7940822839736938},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.7834618091583252},{"id":"https://openalex.org/keywords/encoding","display_name":"Encoding (memory)","score":0.6083227396011353},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5303792357444763},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.5048707127571106},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.4216429889202118},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4133356213569641},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.32667744159698486},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10133200883865356}],"concepts":[{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.8308824300765991},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7940822839736938},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.7834618091583252},{"id":"https://openalex.org/C125411270","wikidata":"https://www.wikidata.org/wiki/Q18653","display_name":"Encoding (memory)","level":2,"score":0.6083227396011353},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5303792357444763},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.5048707127571106},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.4216429889202118},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4133356213569641},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.32667744159698486},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10133200883865356},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000069319","descriptor_name":"Type IV Secretion Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069319","descriptor_name":"Type IV Secretion Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069319","descriptor_name":"Type IV Secretion Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D056510","descriptor_name":"Position-Specific Scoring Matrices","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056510","descriptor_name":"Position-Specific Scoring Matrices","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056510","descriptor_name":"Position-Specific Scoring Matrices","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbz120","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbz120","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:31860715","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31860715","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}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1340903678","display_name":null,"funder_award_id":"81872935","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G1724776241","display_name":null,"funder_award_id":"2018YFC0910500","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G2446395889","display_name":null,"funder_award_id":"81872798","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5067993379","display_name":null,"funder_award_id":"81730108","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8051173748","display_name":null,"funder_award_id":"81573502","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":70,"referenced_works":["https://openalex.org/W1457602677","https://openalex.org/W1520303385","https://openalex.org/W1783180009","https://openalex.org/W1988272131","https://openalex.org/W2072735345","https://openalex.org/W2085102470","https://openalex.org/W2097694646","https://openalex.org/W2114024619","https://openalex.org/W2115434912","https://openalex.org/W2130599662","https://openalex.org/W2131474431","https://openalex.org/W2134233898","https://openalex.org/W2136769496","https://openalex.org/W2154139219","https://openalex.org/W2162980545","https://openalex.org/W2171753456","https://openalex.org/W2173073884","https://openalex.org/W2176660792","https://openalex.org/W2255352529","https://openalex.org/W2261652338","https://openalex.org/W2291003704","https://openalex.org/W2293515080","https://openalex.org/W2311607323","https://openalex.org/W2342838938","https://openalex.org/W2489984778","https://openalex.org/W2518034873","https://openalex.org/W2532873024","https://openalex.org/W2612935389","https://openalex.org/W2614935527","https://openalex.org/W2716141585","https://openalex.org/W2726111596","https://openalex.org/W2737918457","https://openalex.org/W2750692136","https://openalex.org/W2765926865","https://openalex.org/W2765950793","https://openalex.org/W2766300642","https://openalex.org/W2767233548","https://openalex.org/W2768723560","https://openalex.org/W2769518858","https://openalex.org/W2769755511","https://openalex.org/W2770194301","https://openalex.org/W2772043080","https://openalex.org/W2780777007","https://openalex.org/W2782769512","https://openalex.org/W2787339353","https://openalex.org/W2790792696","https://openalex.org/W2792806930","https://openalex.org/W2797793416","https://openalex.org/W2799307902","https://openalex.org/W2804672687","https://openalex.org/W2807818025","https://openalex.org/W2809363952","https://openalex.org/W2888358121","https://openalex.org/W2889815395","https://openalex.org/W2891463586","https://openalex.org/W2893880892","https://openalex.org/W2898454434","https://openalex.org/W2900557017","https://openalex.org/W2900694973","https://openalex.org/W2910644930","https://openalex.org/W2920338801","https://openalex.org/W2941555836","https://openalex.org/W2951748044","https://openalex.org/W2952218450","https://openalex.org/W4233120011","https://openalex.org/W6698064614","https://openalex.org/W6726657909","https://openalex.org/W6728760601","https://openalex.org/W6747735691","https://openalex.org/W6749184843"],"related_works":["https://openalex.org/W2361861616","https://openalex.org/W2263699433","https://openalex.org/W2377979023","https://openalex.org/W2218034408","https://openalex.org/W2392921965","https://openalex.org/W2378211422","https://openalex.org/W4226493464","https://openalex.org/W3133861977","https://openalex.org/W2951211570","https://openalex.org/W3103566983"],"abstract_inverted_index":{"The":[0],"type":[1,26],"IV":[2,27],"bacterial":[3],"secretion":[4],"system":[5],"(SS)":[6],"is":[7],"reported":[8,65],"to":[9,57,78,91,218],"be":[10,79],"one":[11],"of":[12,47,104,117,131,142,234,237,249,257],"the":[13,32,44,70,101,118,140,151,160,163,200,232,247,255],"most":[14],"ubiquitous":[15],"SSs":[16],"in":[17,223,251],"nature":[18],"and":[19,50,73,113,148,179,206,210,253],"can":[20],"induce":[21],"serious":[22],"conditions":[23],"by":[24,94,137],"secreting":[25],"SS":[28],"effectors":[29],"(T4SEs)":[30],"into":[31],"host":[33],"cells.":[34],"Recent":[35],"studies":[36],"mainly":[37],"focus":[38],"on":[39,69,124,159,231],"annotating":[40],"new":[41,212],"T4SE":[42,59,120,220],"from":[43],"huge":[45],"amount":[46],"sequencing":[48],"data,":[49],"various":[51,132],"computational":[52],"tools":[53,63,122],"are":[54,64],"therefore":[55],"developed":[56],"accelerate":[58],"annotation.":[60,221],"However,":[61],"these":[62],"as":[66,187],"heavily":[67],"dependent":[68],"selected":[71],"methods":[72],"their":[74],"annotation":[75,102,121],"performance":[76,233],"need":[77],"further":[80],"enhanced.":[81],"Herein,":[82],"a":[83,194,211,228,235],"convolution":[84],"neural":[85],"network":[86],"(CNN)":[87],"technique":[88],"was":[89,208,216],"used":[90],"annotate":[92],"T4SEs":[93],"integrating":[95],"multiple":[96],"protein":[97,172],"encoding":[98,106,164,182,238],"strategies.":[99],"First,":[100],"accuracies":[103],"nine":[105],"strategies":[107,239],"integrated":[108,190,241],"with":[109,115,191,242],"CNN":[110],"were":[111,134,185],"assessed":[112],"compared":[114],"that":[116,197],"popular":[119],"based":[123],"independent":[125],"benchmark.":[126],"Second,":[127],"false":[128],"discovery":[129],"rates":[130],"models":[133,203],"systematically":[135],"evaluated":[136],"(1)":[138],"scanning":[139],"genome":[141],"Legionella":[143],"pneumophila":[144],"subsp.":[145],"ATCC":[146],"33152":[147],"(2)":[149],"predicting":[150],"real-world":[152],"non-T4SEs":[153],"validated":[154],"using":[155],"published":[156],"experiments.":[157],"Based":[158],"above":[161],"analyses,":[162],"strategies,":[165],"(a)":[166],"position-specific":[167],"scoring":[168],"matrix":[169],"(PSSM),":[170],"(b)":[171],"secondary":[173],"structure":[174],"&":[175],"solvent":[176],"accessibility":[177],"(PSSSA)":[178],"(c)":[180],"one-hot":[181],"scheme":[183],"(Onehot),":[184],"identified":[186],"well-performing":[188,202],"when":[189,240],"CNN.":[192],"Finally,":[193],"novel":[195],"strategy":[196],"collectively":[198],"considers":[199],"three":[201],"(CNN-PSSM,":[204],"CNN-PSSSA":[205],"CNN-Onehot)":[207],"proposed,":[209],"tool":[213],"(CNN-T4SE,":[214],"https://idrblab.org/cnnt4se/)":[215],"constructed":[217],"facilitate":[219,246],"All":[222],"all,":[224],"this":[225],"study":[226],"conducted":[227],"comprehensive":[229],"analysis":[230],"collection":[236],"CNN,":[243],"which":[244],"could":[245],"suppression":[248],"T4SS":[250],"infection":[252],"limit":[254],"spread":[256],"antimicrobial":[258],"resistance.":[259]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":9},{"year":2024,"cited_by_count":17},{"year":2023,"cited_by_count":15},{"year":2022,"cited_by_count":38},{"year":2021,"cited_by_count":20},{"year":2020,"cited_by_count":16}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}