{"id":"https://openalex.org/W4210920677","doi":"https://doi.org/10.1093/bioinformatics/btac087","title":"Effectidor: an automated machine-learning-based web server for the prediction of type-III secretion system effectors","display_name":"Effectidor: an automated machine-learning-based web server for the prediction of type-III secretion system effectors","publication_year":2022,"publication_date":"2022-02-08","ids":{"openalex":"https://openalex.org/W4210920677","doi":"https://doi.org/10.1093/bioinformatics/btac087","pmid":"https://pubmed.ncbi.nlm.nih.gov/35157036"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac087","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac087","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/A5077105151","display_name":"Naama Wagner","orcid":"https://orcid.org/0000-0001-7759-3009"},"institutions":[{"id":"https://openalex.org/I16391192","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49","country_code":"IL","type":"education","lineage":["https://openalex.org/I16391192"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Naama Wagner","raw_affiliation_strings":["The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University , Tel Aviv 69978, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University , Tel Aviv 69978, Israel","institution_ids":["https://openalex.org/I16391192"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086925096","display_name":"Oren Avram","orcid":"https://orcid.org/0000-0003-1984-2139"},"institutions":[{"id":"https://openalex.org/I16391192","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49","country_code":"IL","type":"education","lineage":["https://openalex.org/I16391192"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Oren Avram","raw_affiliation_strings":["The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University , Tel Aviv 69978, Israel"],"raw_orcid":"https://orcid.org/0000-0003-1984-2139","affiliations":[{"raw_affiliation_string":"The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University , Tel Aviv 69978, Israel","institution_ids":["https://openalex.org/I16391192"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053803583","display_name":"Dafna Gold-Binshtok","orcid":null},"institutions":[{"id":"https://openalex.org/I16391192","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49","country_code":"IL","type":"education","lineage":["https://openalex.org/I16391192"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Dafna Gold-Binshtok","raw_affiliation_strings":["The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University , Tel Aviv 69978, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University , Tel Aviv 69978, Israel","institution_ids":["https://openalex.org/I16391192"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080600431","display_name":"Ben Zerah","orcid":null},"institutions":[{"id":"https://openalex.org/I16391192","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49","country_code":"IL","type":"education","lineage":["https://openalex.org/I16391192"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Ben Zerah","raw_affiliation_strings":["The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University , Tel Aviv 69978, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University , Tel Aviv 69978, Israel","institution_ids":["https://openalex.org/I16391192"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055880726","display_name":"Doron Teper","orcid":"https://orcid.org/0000-0002-5608-1917"},"institutions":[{"id":"https://openalex.org/I376102","display_name":"Agricultural Research Organization","ror":"https://ror.org/05hbrxp80","country_code":"IL","type":"government","lineage":["https://openalex.org/I376102"]}],"countries":["IL"],"is_corresponding":false,"raw_author_name":"Doron Teper","raw_affiliation_strings":["Department of Plant Pathology and Weed Research, Institute of Plant Protection Agricultural Research Organization (ARO), Volcani Center , Rishon LeZion 7505101, Israel"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Plant Pathology and Weed Research, Institute of Plant Protection Agricultural Research Organization (ARO), Volcani Center , Rishon LeZion 7505101, Israel","institution_ids":["https://openalex.org/I376102"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5070736617","display_name":"Tal Pupko","orcid":"https://orcid.org/0000-0001-9463-2575"},"institutions":[{"id":"https://openalex.org/I16391192","display_name":"Tel Aviv University","ror":"https://ror.org/04mhzgx49","country_code":"IL","type":"education","lineage":["https://openalex.org/I16391192"]}],"countries":["IL"],"is_corresponding":true,"raw_author_name":"Tal Pupko","raw_affiliation_strings":["The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University , Tel Aviv 69978, Israel"],"raw_orcid":"https://orcid.org/0000-0001-9463-2575","affiliations":[{"raw_affiliation_string":"The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University , Tel Aviv 69978, Israel","institution_ids":["https://openalex.org/I16391192"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5070736617"],"corresponding_institution_ids":["https://openalex.org/I16391192"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.4343,"has_fulltext":false,"cited_by_count":35,"citation_normalized_percentile":{"value":0.89795244,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":100},"biblio":{"volume":"38","issue":"8","first_page":"2341","last_page":"2343"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.7013999819755554,"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":0.7013999819755554,"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/T10943","display_name":"Escherichia coli research studies","score":0.04879999905824661,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.04170000180602074,"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":0.6996443271636963},{"id":"https://openalex.org/keywords/effector","display_name":"Effector","score":0.5981902480125427},{"id":"https://openalex.org/keywords/secretion","display_name":"Secretion","score":0.5525305271148682},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.48424217104911804},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.46556639671325684},{"id":"https://openalex.org/keywords/type","display_name":"Type (biology)","score":0.4590619206428528},{"id":"https://openalex.org/keywords/web-application","display_name":"Web application","score":0.45498529076576233},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.39739999175071716},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.36014723777770996},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.34550347924232483},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.3357023000717163},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.17873811721801758},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.07619962096214294},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.06379470229148865}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6996443271636963},{"id":"https://openalex.org/C51785407","wikidata":"https://www.wikidata.org/wiki/Q2627568","display_name":"Effector","level":2,"score":0.5981902480125427},{"id":"https://openalex.org/C49039625","wikidata":"https://www.wikidata.org/wiki/Q84230","display_name":"Secretion","level":2,"score":0.5525305271148682},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.48424217104911804},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.46556639671325684},{"id":"https://openalex.org/C2777299769","wikidata":"https://www.wikidata.org/wiki/Q3707858","display_name":"Type (biology)","level":2,"score":0.4590619206428528},{"id":"https://openalex.org/C118643609","wikidata":"https://www.wikidata.org/wiki/Q189210","display_name":"Web application","level":2,"score":0.45498529076576233},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.39739999175071716},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.36014723777770996},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.34550347924232483},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.3357023000717163},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.17873811721801758},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.07619962096214294},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.06379470229148865},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069296","descriptor_name":"Type III Secretion Systems","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D000069296","descriptor_name":"Type III Secretion Systems","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D000069296","descriptor_name":"Type III Secretion Systems","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D001426","descriptor_name":"Bacterial Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D006090","descriptor_name":"Gram-Negative Bacteria","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006090","descriptor_name":"Gram-Negative Bacteria","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D006090","descriptor_name":"Gram-Negative Bacteria","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btac087","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac087","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:35157036","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35157036","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":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":28,"referenced_works":["https://openalex.org/W1783180009","https://openalex.org/W1976930511","https://openalex.org/W1977152450","https://openalex.org/W2003336381","https://openalex.org/W2007747684","https://openalex.org/W2048063734","https://openalex.org/W2055043387","https://openalex.org/W2068532894","https://openalex.org/W2094201044","https://openalex.org/W2096730875","https://openalex.org/W2101234009","https://openalex.org/W2101783575","https://openalex.org/W2117534309","https://openalex.org/W2120190359","https://openalex.org/W2126478370","https://openalex.org/W2144788546","https://openalex.org/W2180617533","https://openalex.org/W2562690213","https://openalex.org/W2565256176","https://openalex.org/W2788167885","https://openalex.org/W2885179684","https://openalex.org/W2899105530","https://openalex.org/W2952444689","https://openalex.org/W2981645939","https://openalex.org/W3005919599","https://openalex.org/W3047430701","https://openalex.org/W3134336635","https://openalex.org/W6675354045"],"related_works":["https://openalex.org/W4230283440","https://openalex.org/W2148674193","https://openalex.org/W3213423095","https://openalex.org/W3184145232","https://openalex.org/W2158295903","https://openalex.org/W2582563843","https://openalex.org/W1899329792","https://openalex.org/W2808185338","https://openalex.org/W3175155005","https://openalex.org/W2018093685"],"abstract_inverted_index":{"MOTIVATION:":[0],"Type-III":[1],"secretion":[2],"systems":[3],"are":[4,149],"utilized":[5],"by":[6],"many":[7],"Gram-negative":[8],"bacteria":[9,28],"to":[10,15,65,86,98],"inject":[11],"type-3":[12],"effectors":[13,19],"(T3Es)":[14],"eukaryotic":[16],"cells.":[17],"These":[18],"manipulate":[20],"host":[21],"processes":[22],"for":[23,102],"the":[24,27,51,70,94,103,121,138],"benefit":[25],"of":[26,58,62,96,116],"and":[29,137],"thus":[30],"promote":[31],"disease.":[32],"They":[33],"can":[34],"also":[35],"function":[36],"as":[37,43],"host-specificity":[38],"determinants":[39],"through":[40],"their":[41],"recognition":[42],"avirulence":[44],"proteins":[45],"that":[46,81],"elicit":[47],"immune":[48],"response.":[49],"Identifying":[50],"full":[52],"effector":[53],"repertoire":[54],"within":[55,89],"a":[56,77],"set":[57],"bacterial":[59,90],"genomes":[60],"is":[61,133,141],"great":[63],"importance":[64],"develop":[66],"appropriate":[67],"treatments":[68],"against":[69],"associated":[71],"pathogens.":[72],"RESULTS:":[73],"We":[74,92],"present":[75],"Effectidor,":[76],"user-friendly":[78],"web":[79],"server":[80],"harnesses":[82],"several":[83],"machine-learning":[84],"techniques":[85],"predict":[87],"T3Es":[88],"genomes.":[91],"compared":[93],"performance":[95],"Effectidor":[97,110,132],"other":[99],"available":[100,134,142,150],"tools":[101,113],"same":[104],"task":[105],"on":[106],"three":[107],"pathogenic":[108],"bacteria.":[109],"outperformed":[111],"these":[112],"in":[114,126],"terms":[115],"classification":[117],"accuracy":[118],"(area":[119],"under":[120],"precision-recall":[122],"curve":[123],"above":[124],"0.98":[125],"all":[127],"cases).":[128],"AVAILABILITY":[129],"AND":[130],"IMPLEMENTATION:":[131],"at:":[135,143],"https://effectidor.tau.ac.il,":[136],"source":[139],"code":[140],"https://github.com/naamawagner/Effectidor.":[144],"SUPPLEMENTARY":[145],"INFORMATION:":[146],"Supplementary":[147],"data":[148],"at":[151],"Bioinformatics":[152],"online.":[153]},"counts_by_year":[{"year":2026,"cited_by_count":6},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":16},{"year":2022,"cited_by_count":4}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
