{"id":"https://openalex.org/W2994430460","doi":"https://doi.org/10.1007/s40484-019-0184-7","title":"WEDeepT3: predicting type III secreted effectors based on word embedding and deep learning","display_name":"WEDeepT3: predicting type III secreted effectors based on word embedding and deep learning","publication_year":2019,"publication_date":"2019-12-01","ids":{"openalex":"https://openalex.org/W2994430460","doi":"https://doi.org/10.1007/s40484-019-0184-7","mag":"2994430460"},"language":"en","primary_location":{"id":"doi:10.1007/s40484-019-0184-7","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s40484-019-0184-7","pdf_url":"https://link.springer.com/content/pdf/10.1007/s40484-019-0184-7.pdf","source":{"id":"https://openalex.org/S4210172333","display_name":"Quantitative Biology","issn_l":"2095-4689","issn":["2095-4689","2095-4697"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Quantitative Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://link.springer.com/content/pdf/10.1007/s40484-019-0184-7.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101048670","display_name":"Xiaofeng Fu","orcid":null},"institutions":[{"id":"https://openalex.org/I4210165726","display_name":"Shanghai Municipal Education Commission","ror":"https://ror.org/05tewj457","country_code":"CN","type":"funder","lineage":["https://openalex.org/I4210165456","https://openalex.org/I4210165726"]},{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xiaofeng Fu","raw_affiliation_strings":["Department of Computer Science and Engineering Shanghai Jiao Tong University, and Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering Shanghai 200240 China","Department of Computer Science and Engineering, Shanghai Jiao Tong University, and Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering, Shanghai 200240, China"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering Shanghai Jiao Tong University, and Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering Shanghai 200240 China","institution_ids":["https://openalex.org/I4210165726"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, Shanghai Jiao Tong University, and Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering, Shanghai 200240, China","institution_ids":["https://openalex.org/I4210165726","https://openalex.org/I183067930"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100397381","display_name":"Yang Yang","orcid":"https://orcid.org/0000-0001-5720-773X"},"institutions":[{"id":"https://openalex.org/I4210165726","display_name":"Shanghai Municipal Education Commission","ror":"https://ror.org/05tewj457","country_code":"CN","type":"funder","lineage":["https://openalex.org/I4210165456","https://openalex.org/I4210165726"]},{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yang Yang","raw_affiliation_strings":["Department of Computer Science and Engineering Shanghai Jiao Tong University, and Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering Shanghai 200240 China","Department of Computer Science and Engineering, Shanghai Jiao Tong University, and Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering, Shanghai 200240, China"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Engineering Shanghai Jiao Tong University, and Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering Shanghai 200240 China","institution_ids":["https://openalex.org/I4210165726"]},{"raw_affiliation_string":"Department of Computer Science and Engineering, Shanghai Jiao Tong University, and Key Laboratory of Shanghai Education Commission for Intelligent Interaction and Cognitive Engineering, Shanghai 200240, China","institution_ids":["https://openalex.org/I4210165726","https://openalex.org/I183067930"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5101048670"],"corresponding_institution_ids":["https://openalex.org/I183067930","https://openalex.org/I4210165726"],"apc_list":null,"apc_paid":null,"fwci":0.5153,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.65725302,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":97},"biblio":{"volume":"7","issue":"4","first_page":"293","last_page":"301"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9994000196456909,"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":0.9994000196456909,"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":0.9966999888420105,"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":0.991100013256073,"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/word-embedding","display_name":"Word embedding","score":0.6868817806243896},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.670211672782898},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.65291428565979},{"id":"https://openalex.org/keywords/construct","display_name":"Construct (python library)","score":0.6500727534294128},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6450618505477905},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.6405868530273438},{"id":"https://openalex.org/keywords/embedding","display_name":"Embedding","score":0.6117018461227417},{"id":"https://openalex.org/keywords/effector","display_name":"Effector","score":0.5954252481460571},{"id":"https://openalex.org/keywords/word","display_name":"Word (group theory)","score":0.5568493604660034},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.4908342957496643},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.4685676395893097},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.4542369246482849},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3556750416755676},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3514788746833801},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2682201564311981},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.11730316281318665}],"concepts":[{"id":"https://openalex.org/C2777462759","wikidata":"https://www.wikidata.org/wiki/Q18395344","display_name":"Word embedding","level":3,"score":0.6868817806243896},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.670211672782898},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.65291428565979},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.6500727534294128},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6450618505477905},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.6405868530273438},{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.6117018461227417},{"id":"https://openalex.org/C51785407","wikidata":"https://www.wikidata.org/wiki/Q2627568","display_name":"Effector","level":2,"score":0.5954252481460571},{"id":"https://openalex.org/C90805587","wikidata":"https://www.wikidata.org/wiki/Q10944557","display_name":"Word (group theory)","level":2,"score":0.5568493604660034},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.4908342957496643},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.4685676395893097},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.4542369246482849},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3556750416755676},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3514788746833801},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2682201564311981},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.11730316281318665},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1007/s40484-019-0184-7","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s40484-019-0184-7","pdf_url":"https://link.springer.com/content/pdf/10.1007/s40484-019-0184-7.pdf","source":{"id":"https://openalex.org/S4210172333","display_name":"Quantitative Biology","issn_l":"2095-4689","issn":["2095-4689","2095-4697"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Quantitative Biology","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.1007/s40484-019-0184-7","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s40484-019-0184-7","pdf_url":"https://link.springer.com/content/pdf/10.1007/s40484-019-0184-7.pdf","source":{"id":"https://openalex.org/S4210172333","display_name":"Quantitative Biology","issn_l":"2095-4689","issn":["2095-4689","2095-4697"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Quantitative Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2087396116","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3317480652","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3365264765","display_name":null,"funder_award_id":"61972251","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5994120800","display_name":null,"funder_award_id":"Natural","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"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2994430460.pdf","grobid_xml":"https://content.openalex.org/works/W2994430460.grobid-xml"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W74870555","https://openalex.org/W1501531009","https://openalex.org/W1973409583","https://openalex.org/W1981306857","https://openalex.org/W1994902865","https://openalex.org/W2018271515","https://openalex.org/W2021071631","https://openalex.org/W2021312899","https://openalex.org/W2025767948","https://openalex.org/W2029525597","https://openalex.org/W2066073349","https://openalex.org/W2068532894","https://openalex.org/W2075934337","https://openalex.org/W2082538292","https://openalex.org/W2126478370","https://openalex.org/W2144251138","https://openalex.org/W2145957695","https://openalex.org/W2147580225","https://openalex.org/W2148184404","https://openalex.org/W2155997698","https://openalex.org/W2156125289","https://openalex.org/W2159775055","https://openalex.org/W2170482677","https://openalex.org/W2171526970","https://openalex.org/W2187089797","https://openalex.org/W2250539671","https://openalex.org/W2606365851","https://openalex.org/W2881688145","https://openalex.org/W2884561390","https://openalex.org/W2899105530","https://openalex.org/W2900062265","https://openalex.org/W2952444689","https://openalex.org/W4302440596","https://openalex.org/W6742348326"],"related_works":["https://openalex.org/W4288407670","https://openalex.org/W2950396480","https://openalex.org/W947140380","https://openalex.org/W2911655849","https://openalex.org/W4286432911","https://openalex.org/W4230884544","https://openalex.org/W4245453790","https://openalex.org/W3194985222","https://openalex.org/W3216571906","https://openalex.org/W4214830338"],"abstract_inverted_index":{"Background":[0],"The":[1,50,225],"type":[2,31,107,220],"III":[3,32,108,221],"secreted":[4,33,222],"effectors":[5],"(T3SEs)":[6],"are":[7],"one":[8],"of":[9,18,25,53,59,74,101,106,166,219,228,231,257,267,276,283],"the":[10,14,23,30,43,57,71,75,95,99,104,130,135,189,217,244,251,255,258,263],"indispensable":[11],"proteins":[12],"in":[13,85,119,179,216],"growth":[15],"and":[16,35,56,68,103,141,235,262,280,291],"reproduction":[17],"Gram\u2010negative":[19,26],"bacteria.":[20],"In":[21,147],"particular,":[22],"pathogenesis":[24],"bacteria":[27],"depends":[28],"on":[29,156],"effectors,":[34],"by":[36],"injecting":[37],"T3SEs":[38,102,290],"into":[39],"a":[40,82,152,180,203,211],"host":[41,44],"cell,":[42],"cell\u2019s":[45],"immunity":[46],"can":[47,115],"be":[48],"destroyed.":[49],"high":[51],"diversity":[52],"T3SE":[54,80],"sequences":[55,178,285],"lack":[58],"defined":[60],"secretion":[61,109],"signals":[62],"make":[63],"it":[64],"difficult":[65],"to":[66,93,201,250,286],"identify":[67],"predict.":[69],"Moreover,":[70],"related":[72],"study":[73],"pathological":[76],"system":[77],"associated":[78],"with":[79,192,240],"remains":[81],"hot":[83],"topic":[84],"bioinformatics.":[86],"Some":[87],"computational":[88],"tools":[89,114],"have":[90],"been":[91],"developed":[92],"meet":[94],"growing":[96],"demand":[97],"for":[98,126,129,176],"recognition":[100],"studies":[105],"systems":[110],"(T3SS).":[111],"Although":[112],"these":[113],"help":[116],"biological":[117],"experiments":[118],"certain":[120],"procedures,":[121],"there":[122],"is":[123,294],"still":[124],"room":[125],"improvement,":[127],"even":[128],"current":[131],"best":[132],"model,":[133],"as":[134],"existing":[136],"methods":[137],"adopt":[138],"hand\u2010designed":[139],"feature":[140,206,226,260],"traditional":[142,193],"machine":[143],"learning":[144,158,265],"methods.":[145],"Methods":[146],"this":[148],"study,":[149],"we":[150,171,187,209],"propose":[151],"powerful":[153,264],"predictor":[154],"based":[155],"deep":[157,212,268],"methods,":[159,253],"called":[160],"WEDeepT3.":[161],"Our":[162],"work":[163],"consists":[164,230],"mainly":[165],"three":[167],"key":[168],"steps.":[169],"First,":[170],"train":[172],"word":[173,190,233],"embedding":[174,234],"vectors":[175,191],"protein":[177,197,284],"large\u2010scale":[181],"amino":[182],"acid":[183],"sequence":[184],"database.":[185],"Second,":[186],"combine":[188],"features":[194],"extracted":[195],"from":[196],"sequences,":[198],"like":[199],"PSSM,":[200],"construct":[202,210],"more":[204],"comprehensive":[205],"representation.":[207],"Finally,":[208],"neural":[213,242],"network":[214],"model":[215,246],"prediction":[218],"effectors.":[223],"Results":[224],"representation":[227,261],"WEDeepT3":[229,271,293],"both":[232,273],"position\u2010specific":[236],"features.":[237],"Working":[238],"together":[239],"convolutional":[241],"networks,":[243],"new":[245,259],"achieves":[247],"superior":[248],"performance":[249],"state\u2010of\u2010the\u2010art":[252],"demonstrating":[254],"effectiveness":[256],"ability":[266],"models.":[269],"Conclusion":[270],"exploits":[272],"semantic":[274],"information":[275,282],"k":[277],"\u2010mer":[278],"fragments":[279],"evolutional":[281],"accurately":[287],"differentiate":[288],"between":[289],"non\u2010T3SEs.":[292],"available":[295],"at":[296],"bcmi.sjtu.edu.cn/~yangyang/WEDeepT3.html":[297],".":[298]},"counts_by_year":[{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":2}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
