{"id":"https://openalex.org/W2900062265","doi":"https://doi.org/10.1093/bioinformatics/bty931","title":"DeepT3: deep convolutional neural networks accurately identify Gram-negative bacterial type III secreted effectors using the N-terminal sequence","display_name":"DeepT3: deep convolutional neural networks accurately identify Gram-negative bacterial type III secreted effectors using the N-terminal sequence","publication_year":2018,"publication_date":"2018-11-07","ids":{"openalex":"https://openalex.org/W2900062265","doi":"https://doi.org/10.1093/bioinformatics/bty931","mag":"2900062265","pmid":"https://pubmed.ncbi.nlm.nih.gov/30407530"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty931","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty931","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"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/A5100372201","display_name":"Xue Li","orcid":"https://orcid.org/0000-0002-4515-6792"},"institutions":[{"id":"https://openalex.org/I3017480383","display_name":"Southwest Medical University","ror":"https://ror.org/00g2rqs52","country_code":"CN","type":"funder","lineage":["https://openalex.org/I3017480383"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Li Xue","raw_affiliation_strings":["School of Public Health, Southwest Medical University, Luzhou, Sichuan, PR, China"],"affiliations":[{"raw_affiliation_string":"School of Public Health, Southwest Medical University, Luzhou, Sichuan, PR, China","institution_ids":["https://openalex.org/I3017480383"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101402777","display_name":"Bin Tang","orcid":"https://orcid.org/0000-0002-4251-1867"},"institutions":[{"id":"https://openalex.org/I3017480383","display_name":"Southwest Medical University","ror":"https://ror.org/00g2rqs52","country_code":"CN","type":"funder","lineage":["https://openalex.org/I3017480383"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bin Tang","raw_affiliation_strings":["Basic Medical College of Southwest Medical University, Luzhou, Sichuan, PR, China"],"affiliations":[{"raw_affiliation_string":"Basic Medical College of Southwest Medical University, Luzhou, Sichuan, PR, China","institution_ids":["https://openalex.org/I3017480383"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100344463","display_name":"Wei Chen","orcid":"https://orcid.org/0000-0002-6857-7696"},"institutions":[{"id":"https://openalex.org/I1301076528","display_name":"City Of Hope National Medical Center","ror":"https://ror.org/00w6g5w60","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1301076528"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Wei Chen","raw_affiliation_strings":["Integrative Genomics Core, City of Hope National Medical Center, Duarte, CA, USA"],"affiliations":[{"raw_affiliation_string":"Integrative Genomics Core, City of Hope National Medical Center, Duarte, CA, USA","institution_ids":["https://openalex.org/I1301076528"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5061944036","display_name":"Jiesi Luo","orcid":"https://orcid.org/0000-0002-1199-7024"},"institutions":[{"id":"https://openalex.org/I3017480383","display_name":"Southwest Medical University","ror":"https://ror.org/00g2rqs52","country_code":"CN","type":"funder","lineage":["https://openalex.org/I3017480383"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jiesi Luo","raw_affiliation_strings":["Key Laboratory for Aging and Regenerative Medicine, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China"],"affiliations":[{"raw_affiliation_string":"Key Laboratory for Aging and Regenerative Medicine, Department of Pharmacology, School of Pharmacy, Southwest Medical University, Luzhou, Sichuan, China","institution_ids":["https://openalex.org/I3017480383"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5061944036"],"corresponding_institution_ids":["https://openalex.org/I3017480383"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.3271,"has_fulltext":false,"cited_by_count":49,"citation_normalized_percentile":{"value":0.89506117,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"35","issue":"12","first_page":"2051","last_page":"2057"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9983999729156494,"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":0.9983999729156494,"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":0.9711999893188477,"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"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9693999886512756,"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/terminal","display_name":"Terminal (telecommunication)","score":0.7152379155158997},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.6595388054847717},{"id":"https://openalex.org/keywords/effector","display_name":"Effector","score":0.6203022599220276},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.6134340167045593},{"id":"https://openalex.org/keywords/gram","display_name":"Gram","score":0.608128011226654},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5376777052879333},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5070810317993164},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.4741615355014801},{"id":"https://openalex.org/keywords/gram-negative-bacteria","display_name":"Gram-negative bacteria","score":0.44879499077796936},{"id":"https://openalex.org/keywords/type","display_name":"Type (biology)","score":0.4407830834388733},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3729172348976135},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.33730438351631165},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.26273638010025024},{"id":"https://openalex.org/keywords/bacteria","display_name":"Bacteria","score":0.24374139308929443},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.18308785557746887},{"id":"https://openalex.org/keywords/escherichia-coli","display_name":"Escherichia coli","score":0.17495614290237427},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.1251031458377838},{"id":"https://openalex.org/keywords/computer-network","display_name":"Computer network","score":0.11846315860748291},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.10108068585395813}],"concepts":[{"id":"https://openalex.org/C2779664074","wikidata":"https://www.wikidata.org/wiki/Q3518405","display_name":"Terminal (telecommunication)","level":2,"score":0.7152379155158997},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.6595388054847717},{"id":"https://openalex.org/C51785407","wikidata":"https://www.wikidata.org/wiki/Q2627568","display_name":"Effector","level":2,"score":0.6203022599220276},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.6134340167045593},{"id":"https://openalex.org/C161369605","wikidata":"https://www.wikidata.org/wiki/Q41803","display_name":"Gram","level":3,"score":0.608128011226654},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5376777052879333},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5070810317993164},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.4741615355014801},{"id":"https://openalex.org/C2776051709","wikidata":"https://www.wikidata.org/wiki/Q632006","display_name":"Gram-negative bacteria","level":4,"score":0.44879499077796936},{"id":"https://openalex.org/C2777299769","wikidata":"https://www.wikidata.org/wiki/Q3707858","display_name":"Type (biology)","level":2,"score":0.4407830834388733},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3729172348976135},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.33730438351631165},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.26273638010025024},{"id":"https://openalex.org/C523546767","wikidata":"https://www.wikidata.org/wiki/Q10876","display_name":"Bacteria","level":2,"score":0.24374139308929443},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.18308785557746887},{"id":"https://openalex.org/C547475151","wikidata":"https://www.wikidata.org/wiki/Q25419","display_name":"Escherichia coli","level":3,"score":0.17495614290237427},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.1251031458377838},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.11846315860748291},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.10108068585395813},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0}],"mesh":[{"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":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006090","descriptor_name":"Gram-Negative Bacteria","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006090","descriptor_name":"Gram-Negative Bacteria","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006090","descriptor_name":"Gram-Negative Bacteria","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","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":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016680","descriptor_name":"Genome, Bacterial","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bty931","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty931","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30407530","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30407530","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G920474130","display_name":null,"funder_award_id":"21803045","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":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":54,"referenced_works":["https://openalex.org/W1019830208","https://openalex.org/W1506060468","https://openalex.org/W1529552501","https://openalex.org/W1557850387","https://openalex.org/W1976930511","https://openalex.org/W1980767305","https://openalex.org/W1994902865","https://openalex.org/W2003961381","https://openalex.org/W2009961953","https://openalex.org/W2018271515","https://openalex.org/W2043545998","https://openalex.org/W2050745211","https://openalex.org/W2062688070","https://openalex.org/W2063030367","https://openalex.org/W2066073349","https://openalex.org/W2068532894","https://openalex.org/W2069070108","https://openalex.org/W2075391884","https://openalex.org/W2081413516","https://openalex.org/W2090470862","https://openalex.org/W2097606916","https://openalex.org/W2099421377","https://openalex.org/W2101234009","https://openalex.org/W2103777723","https://openalex.org/W2104267395","https://openalex.org/W2115933717","https://openalex.org/W2126478370","https://openalex.org/W2132809955","https://openalex.org/W2141818629","https://openalex.org/W2144251138","https://openalex.org/W2144375173","https://openalex.org/W2155997698","https://openalex.org/W2161062388","https://openalex.org/W2163670463","https://openalex.org/W2170482677","https://openalex.org/W2170644493","https://openalex.org/W2311607323","https://openalex.org/W2345512687","https://openalex.org/W2479945688","https://openalex.org/W2502949459","https://openalex.org/W2510934692","https://openalex.org/W2606791689","https://openalex.org/W2607268717","https://openalex.org/W2610332124","https://openalex.org/W2730472814","https://openalex.org/W2749122933","https://openalex.org/W2765651856","https://openalex.org/W2791848964","https://openalex.org/W2793278779","https://openalex.org/W2795735651","https://openalex.org/W4211208250","https://openalex.org/W6675354045","https://openalex.org/W6698064614","https://openalex.org/W6736817290"],"related_works":["https://openalex.org/W2062803132","https://openalex.org/W2046512825","https://openalex.org/W4242417780","https://openalex.org/W2944073656","https://openalex.org/W2413474316","https://openalex.org/W1991977026","https://openalex.org/W3207468706","https://openalex.org/W2059139108","https://openalex.org/W1605926837","https://openalex.org/W2741043342"],"abstract_inverted_index":{"Supplementary":[0],"data":[1],"are":[2],"available":[3],"at":[4],"Bioinformatics":[5],"online.":[6]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":10},{"year":2021,"cited_by_count":10},{"year":2020,"cited_by_count":10},{"year":2019,"cited_by_count":5}],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2025-10-10T00:00:00"}