{"id":"https://openalex.org/W2925284261","doi":"https://doi.org/10.3390/data4010045","title":"T4SS Effector Protein Prediction with Deep Learning","display_name":"T4SS Effector Protein Prediction with Deep Learning","publication_year":2019,"publication_date":"2019-03-25","ids":{"openalex":"https://openalex.org/W2925284261","doi":"https://doi.org/10.3390/data4010045","mag":"2925284261"},"language":"en","primary_location":{"id":"doi:10.3390/data4010045","is_oa":true,"landing_page_url":"https://doi.org/10.3390/data4010045","pdf_url":"https://www.mdpi.com/2306-5729/4/1/45/pdf?version=1553503204","source":{"id":"https://openalex.org/S4210226510","display_name":"Data","issn_l":"2306-5729","issn":["2306-5729"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Data","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.mdpi.com/2306-5729/4/1/45/pdf?version=1553503204","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5088721490","display_name":"Koray A\u00e7\u0131c\u0131","orcid":"https://orcid.org/0000-0002-3821-6419"},"institutions":[{"id":"https://openalex.org/I188740104","display_name":"Ba\u015fkent University","ror":"https://ror.org/02v9bqx10","country_code":"TR","type":"education","lineage":["https://openalex.org/I188740104"]},{"id":"https://openalex.org/I4210091745","display_name":"Eski\u015fehir City Hospital","ror":"https://ror.org/00czdkn85","country_code":"TR","type":"healthcare","lineage":["https://openalex.org/I1303077703","https://openalex.org/I4210091745"]}],"countries":["TR"],"is_corresponding":true,"raw_author_name":"Koray A\u00e7\u0131c\u0131","raw_affiliation_strings":["Department of Computer Engineering, Baskent University, Ba\u011fl\u0131ca Kamp\u00fcs\u00fc Fatih Sultan Mahallesi Eski\u015fehir Yolu 18.km, Ankara 06709, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Baskent University, Ba\u011fl\u0131ca Kamp\u00fcs\u00fc Fatih Sultan Mahallesi Eski\u015fehir Yolu 18.km, Ankara 06709, Turkey","institution_ids":["https://openalex.org/I188740104","https://openalex.org/I4210091745"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063767889","display_name":"Tun\u00e7 A\u015furo\u011flu","orcid":"https://orcid.org/0000-0003-4153-0764"},"institutions":[{"id":"https://openalex.org/I188740104","display_name":"Ba\u015fkent University","ror":"https://ror.org/02v9bqx10","country_code":"TR","type":"education","lineage":["https://openalex.org/I188740104"]},{"id":"https://openalex.org/I4210091745","display_name":"Eski\u015fehir City Hospital","ror":"https://ror.org/00czdkn85","country_code":"TR","type":"healthcare","lineage":["https://openalex.org/I1303077703","https://openalex.org/I4210091745"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Tun\u00e7 A\u015furo\u011flu","raw_affiliation_strings":["Department of Computer Engineering, Baskent University, Ba\u011fl\u0131ca Kamp\u00fcs\u00fc Fatih Sultan Mahallesi Eski\u015fehir Yolu 18.km, Ankara 06709, Turkey"],"raw_orcid":"https://orcid.org/0000-0003-4153-0764","affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Baskent University, Ba\u011fl\u0131ca Kamp\u00fcs\u00fc Fatih Sultan Mahallesi Eski\u015fehir Yolu 18.km, Ankara 06709, Turkey","institution_ids":["https://openalex.org/I188740104","https://openalex.org/I4210091745"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044196969","display_name":"\u00c7a\u011fatay Berke Erda\u015f","orcid":"https://orcid.org/0000-0003-3467-9923"},"institutions":[{"id":"https://openalex.org/I188740104","display_name":"Ba\u015fkent University","ror":"https://ror.org/02v9bqx10","country_code":"TR","type":"education","lineage":["https://openalex.org/I188740104"]},{"id":"https://openalex.org/I4210091745","display_name":"Eski\u015fehir City Hospital","ror":"https://ror.org/00czdkn85","country_code":"TR","type":"healthcare","lineage":["https://openalex.org/I1303077703","https://openalex.org/I4210091745"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"\u00c7a\u011fatay Berke Erda\u015f","raw_affiliation_strings":["Department of Computer Engineering, Baskent University, Ba\u011fl\u0131ca Kamp\u00fcs\u00fc Fatih Sultan Mahallesi Eski\u015fehir Yolu 18.km, Ankara 06709, Turkey"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Baskent University, Ba\u011fl\u0131ca Kamp\u00fcs\u00fc Fatih Sultan Mahallesi Eski\u015fehir Yolu 18.km, Ankara 06709, Turkey","institution_ids":["https://openalex.org/I188740104","https://openalex.org/I4210091745"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5086873572","display_name":"Hasan O\u011ful","orcid":"https://orcid.org/0000-0002-6043-1860"},"institutions":[{"id":"https://openalex.org/I188740104","display_name":"Ba\u015fkent University","ror":"https://ror.org/02v9bqx10","country_code":"TR","type":"education","lineage":["https://openalex.org/I188740104"]},{"id":"https://openalex.org/I19923696","display_name":"\u00d8stfold University College","ror":"https://ror.org/04gf7fp41","country_code":"NO","type":"education","lineage":["https://openalex.org/I19923696"]},{"id":"https://openalex.org/I4210091745","display_name":"Eski\u015fehir City Hospital","ror":"https://ror.org/00czdkn85","country_code":"TR","type":"healthcare","lineage":["https://openalex.org/I1303077703","https://openalex.org/I4210091745"]}],"countries":["NO","TR"],"is_corresponding":false,"raw_author_name":"Hasan O\u011ful","raw_affiliation_strings":["Department of Computer Engineering, Baskent University, Ba\u011fl\u0131ca Kamp\u00fcs\u00fc Fatih Sultan Mahallesi Eski\u015fehir Yolu 18.km, Ankara 06709, Turkey","Faculty of Computer Science, \u00d8stfold University College, P.O. Box 700, 1757 Halden, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Baskent University, Ba\u011fl\u0131ca Kamp\u00fcs\u00fc Fatih Sultan Mahallesi Eski\u015fehir Yolu 18.km, Ankara 06709, Turkey","institution_ids":["https://openalex.org/I188740104","https://openalex.org/I4210091745"]},{"raw_affiliation_string":"Faculty of Computer Science, \u00d8stfold University College, P.O. Box 700, 1757 Halden, Norway","institution_ids":["https://openalex.org/I19923696"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5088721490"],"corresponding_institution_ids":["https://openalex.org/I188740104","https://openalex.org/I4210091745"],"apc_list":{"value":1600,"currency":"CHF","value_usd":1732},"apc_paid":{"value":1600,"currency":"CHF","value_usd":1732},"fwci":0.7731,"has_fulltext":false,"cited_by_count":13,"citation_normalized_percentile":{"value":0.70585477,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"4","issue":"1","first_page":"45","last_page":"45"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13326","display_name":"Biochemical and Structural Characterization","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"}},"topics":[{"id":"https://openalex.org/T13326","display_name":"Biochemical and Structural Characterization","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"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9891999959945679,"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":0.977400004863739,"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/effector","display_name":"Effector","score":0.965256929397583},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.7435360550880432},{"id":"https://openalex.org/keywords/secretion","display_name":"Secretion","score":0.5989810228347778},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5120165944099426},{"id":"https://openalex.org/keywords/cytoplasm","display_name":"Cytoplasm","score":0.4618121385574341},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4535650908946991},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.4509597718715668},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.4445949196815491},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.43053919076919556},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.35375866293907166},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2798702120780945},{"id":"https://openalex.org/keywords/cell-biology","display_name":"Cell biology","score":0.19839778542518616},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.10100772976875305}],"concepts":[{"id":"https://openalex.org/C51785407","wikidata":"https://www.wikidata.org/wiki/Q2627568","display_name":"Effector","level":2,"score":0.965256929397583},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.7435360550880432},{"id":"https://openalex.org/C49039625","wikidata":"https://www.wikidata.org/wiki/Q84230","display_name":"Secretion","level":2,"score":0.5989810228347778},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5120165944099426},{"id":"https://openalex.org/C190062978","wikidata":"https://www.wikidata.org/wiki/Q79899","display_name":"Cytoplasm","level":2,"score":0.4618121385574341},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4535650908946991},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.4509597718715668},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.4445949196815491},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.43053919076919556},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.35375866293907166},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2798702120780945},{"id":"https://openalex.org/C95444343","wikidata":"https://www.wikidata.org/wiki/Q7141","display_name":"Cell biology","level":1,"score":0.19839778542518616},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.10100772976875305},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","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}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.3390/data4010045","is_oa":true,"landing_page_url":"https://doi.org/10.3390/data4010045","pdf_url":"https://www.mdpi.com/2306-5729/4/1/45/pdf?version=1553503204","source":{"id":"https://openalex.org/S4210226510","display_name":"Data","issn_l":"2306-5729","issn":["2306-5729"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Data","raw_type":"journal-article"},{"id":"pmh:oai:RePEc:gam:jdataj:v:4:y:2019:i:1:p:45-:d:216917","is_oa":false,"landing_page_url":"https://www.mdpi.com/2306-5729/4/1/45/","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:2196b55e73964e9ebe4efe8bbcc623d1","is_oa":true,"landing_page_url":"https://doaj.org/article/2196b55e73964e9ebe4efe8bbcc623d1","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Data, Vol 4, Iss 1, p 45 (2019)","raw_type":"article"},{"id":"pmh:oai:hiof.brage.unit.no:11250/2634005","is_oa":true,"landing_page_url":"http://hdl.handle.net/11250/2634005","pdf_url":null,"source":{"id":"https://openalex.org/S4306401716","display_name":"Duo Research Archive (University of Oslo)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I184942183","host_organization_name":"University of Oslo","host_organization_lineage":["https://openalex.org/I184942183"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"4","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:mdpi.com:/2306-5729/4/1/45/","is_oa":true,"landing_page_url":"http://dx.doi.org/10.3390/data4010045","pdf_url":null,"source":{"id":"https://openalex.org/S4306400947","display_name":"MDPI (MDPI AG)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210097602","host_organization_name":"Multidisciplinary Digital Publishing Institute (Switzerland)","host_organization_lineage":["https://openalex.org/I4210097602"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Data","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3390/data4010045","is_oa":true,"landing_page_url":"https://doi.org/10.3390/data4010045","pdf_url":"https://www.mdpi.com/2306-5729/4/1/45/pdf?version=1553503204","source":{"id":"https://openalex.org/S4210226510","display_name":"Data","issn_l":"2306-5729","issn":["2306-5729"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Data","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2925284261.pdf","grobid_xml":"https://content.openalex.org/works/W2925284261.grobid-xml"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W1988272131","https://openalex.org/W2003781176","https://openalex.org/W2016510254","https://openalex.org/W2032773353","https://openalex.org/W2056145674","https://openalex.org/W2085102470","https://openalex.org/W2089594628","https://openalex.org/W2097165693","https://openalex.org/W2104933073","https://openalex.org/W2107921573","https://openalex.org/W2115434912","https://openalex.org/W2128250684","https://openalex.org/W2135771899","https://openalex.org/W2141125852","https://openalex.org/W2144814664","https://openalex.org/W2148143831","https://openalex.org/W2152092848","https://openalex.org/W2162969038","https://openalex.org/W2308145610","https://openalex.org/W2469483744","https://openalex.org/W2565912230","https://openalex.org/W2623533525","https://openalex.org/W2768723560","https://openalex.org/W2884058584","https://openalex.org/W2888570268","https://openalex.org/W6671890461","https://openalex.org/W6753321026"],"related_works":["https://openalex.org/W4230283440","https://openalex.org/W2148674193","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/W2913564413","https://openalex.org/W2075276277"],"abstract_inverted_index":{"Extensive":[0],"research":[1],"has":[2],"been":[3],"carried":[4],"out":[5],"on":[6,50],"bacterial":[7],"secretion":[8],"systems,":[9],"as":[10,90,99],"they":[11,37],"can":[12],"pass":[13],"effector":[14,137],"proteins":[15,106],"directly":[16],"into":[17],"the":[18,97,114,130,145],"cytoplasm":[19],"of":[20,26,133],"host":[21],"cells.":[22],"The":[23],"correct":[24],"prediction":[25,138],"type":[27],"IV":[28],"protein":[29,89],"effectors":[30,53,126,146],"secreted":[31],"by":[32],"T4SS":[33,52],"is":[34],"important,":[35],"since":[36],"are":[38],"known":[39],"to":[40,74,86,112,143],"play":[41],"a":[42,64,69],"noteworthy":[43],"role":[44],"in":[45,101,147],"various":[46],"human":[47],"pathogens.":[48],"Studies":[49],"predicting":[51],"involve":[54],"traditional":[55],"machine":[56],"learning":[57,66],"algorithms.":[58],"In":[59,128],"this":[60],"work":[61],"we":[62],"included":[63],"deep":[65],"architecture,":[67],"i.e.,":[68],"Convolutional":[70],"Neural":[71],"Network":[72],"(CNN),":[73],"predict":[75],"IVA":[76,125],"and":[77,93],"IVB":[78,136],"effectors.":[79],"Three":[80],"feature":[81],"extraction":[82],"methods":[83],"were":[84,107],"utilized":[85],"represent":[87],"each":[88],"an":[91],"image":[92],"these":[94],"images":[95],"fed":[96],"CNN":[98],"inputs":[100],"our":[102,121,140],"proposed":[103],"framework.":[104],"Pseudo":[105],"generated":[108],"using":[109],"ADASYN":[110],"algorithm":[111],"overcome":[113],"imbalanced":[115],"dataset":[116],"problem.":[117],"We":[118],"demonstrated":[119],"that":[120],"framework":[122],"predicted":[123],"all":[124],"correctly.":[127],"addition,":[129],"sensitivity":[131],"performance":[132],"94.2%":[134],"for":[135],"exhibited":[139],"framework\u2019s":[141],"ability":[142],"discern":[144],"unidentified":[148],"proteins.":[149]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":4}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
