{"id":"https://openalex.org/W3020045074","doi":"https://doi.org/10.1109/access.2020.2989469","title":"EnsemPseU: Identifying Pseudouridine Sites With an Ensemble Approach","display_name":"EnsemPseU: Identifying Pseudouridine Sites With an Ensemble Approach","publication_year":2020,"publication_date":"2020-01-01","ids":{"openalex":"https://openalex.org/W3020045074","doi":"https://doi.org/10.1109/access.2020.2989469","mag":"3020045074"},"language":"en","primary_location":{"id":"doi:10.1109/access.2020.2989469","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2020.2989469","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/8948470/09076050.pdf","source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://ieeexplore.ieee.org/ielx7/6287639/8948470/09076050.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5009378480","display_name":"Yue Bi","orcid":"https://orcid.org/0009-0001-6220-7475"},"institutions":[{"id":"https://openalex.org/I43313876","display_name":"Dalian Maritime University","ror":"https://ror.org/002b7nr53","country_code":"CN","type":"education","lineage":["https://openalex.org/I43313876"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yue Bi","raw_affiliation_strings":["School of Science, Dalian Maritime University, Dalian, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Science, Dalian Maritime University, Dalian, China","institution_ids":["https://openalex.org/I43313876"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069874950","display_name":"Jin Dong","orcid":"https://orcid.org/0000-0003-1131-6396"},"institutions":[{"id":"https://openalex.org/I43313876","display_name":"Dalian Maritime University","ror":"https://ror.org/002b7nr53","country_code":"CN","type":"education","lineage":["https://openalex.org/I43313876"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dong Jin","raw_affiliation_strings":["School of Science, Dalian Maritime University, Dalian, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Science, Dalian Maritime University, Dalian, China","institution_ids":["https://openalex.org/I43313876"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5066126756","display_name":"Cangzhi Jia","orcid":"https://orcid.org/0000-0002-4682-2881"},"institutions":[{"id":"https://openalex.org/I43313876","display_name":"Dalian Maritime University","ror":"https://ror.org/002b7nr53","country_code":"CN","type":"education","lineage":["https://openalex.org/I43313876"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Cangzhi Jia","raw_affiliation_strings":["School of Science, Dalian Maritime University, Dalian, China"],"raw_orcid":"https://orcid.org/0000-0002-4682-2881","affiliations":[{"raw_affiliation_string":"School of Science, Dalian Maritime University, Dalian, China","institution_ids":["https://openalex.org/I43313876"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I43313876"],"apc_list":{"value":1850,"currency":"USD","value_usd":1850},"apc_paid":{"value":1850,"currency":"USD","value_usd":1850},"fwci":1.4917,"has_fulltext":true,"cited_by_count":26,"citation_normalized_percentile":{"value":0.82048941,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"8","issue":null,"first_page":"79376","last_page":"79382"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9993000030517578,"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":0.9991999864578247,"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/pseudouridine","display_name":"Pseudouridine","score":0.8650328516960144},{"id":"https://openalex.org/keywords/feature-selection","display_name":"Feature selection","score":0.6722541451454163},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.641751766204834},{"id":"https://openalex.org/keywords/support-vector-machine","display_name":"Support vector machine","score":0.5900121331214905},{"id":"https://openalex.org/keywords/naive-bayes-classifier","display_name":"Naive Bayes classifier","score":0.5648213028907776},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5264528393745422},{"id":"https://openalex.org/keywords/random-forest","display_name":"Random forest","score":0.517240583896637},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.4681898355484009},{"id":"https://openalex.org/keywords/k-nearest-neighbors-algorithm","display_name":"k-nearest neighbors algorithm","score":0.46736857295036316},{"id":"https://openalex.org/keywords/ensemble-learning","display_name":"Ensemble learning","score":0.4311264157295227},{"id":"https://openalex.org/keywords/rna","display_name":"RNA","score":0.18948546051979065},{"id":"https://openalex.org/keywords/uridine","display_name":"Uridine","score":0.17038178443908691},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1531708538532257},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.14366933703422546},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.11957255005836487}],"concepts":[{"id":"https://openalex.org/C2779810333","wikidata":"https://www.wikidata.org/wiki/Q420445","display_name":"Pseudouridine","level":5,"score":0.8650328516960144},{"id":"https://openalex.org/C148483581","wikidata":"https://www.wikidata.org/wiki/Q446488","display_name":"Feature selection","level":2,"score":0.6722541451454163},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.641751766204834},{"id":"https://openalex.org/C12267149","wikidata":"https://www.wikidata.org/wiki/Q282453","display_name":"Support vector machine","level":2,"score":0.5900121331214905},{"id":"https://openalex.org/C52001869","wikidata":"https://www.wikidata.org/wiki/Q812530","display_name":"Naive Bayes classifier","level":3,"score":0.5648213028907776},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5264528393745422},{"id":"https://openalex.org/C169258074","wikidata":"https://www.wikidata.org/wiki/Q245748","display_name":"Random forest","level":2,"score":0.517240583896637},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.4681898355484009},{"id":"https://openalex.org/C113238511","wikidata":"https://www.wikidata.org/wiki/Q1071612","display_name":"k-nearest neighbors algorithm","level":2,"score":0.46736857295036316},{"id":"https://openalex.org/C45942800","wikidata":"https://www.wikidata.org/wiki/Q245652","display_name":"Ensemble learning","level":2,"score":0.4311264157295227},{"id":"https://openalex.org/C67705224","wikidata":"https://www.wikidata.org/wiki/Q11053","display_name":"RNA","level":3,"score":0.18948546051979065},{"id":"https://openalex.org/C2781259782","wikidata":"https://www.wikidata.org/wiki/Q422573","display_name":"Uridine","level":4,"score":0.17038178443908691},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1531708538532257},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.14366933703422546},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.11957255005836487}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/access.2020.2989469","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2020.2989469","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/8948470/09076050.pdf","source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:b2eae27ccb2e43789aa4b6233f3d6596","is_oa":true,"landing_page_url":"https://doaj.org/article/b2eae27ccb2e43789aa4b6233f3d6596","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"IEEE Access, Vol 8, Pp 79376-79382 (2020)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1109/access.2020.2989469","is_oa":true,"landing_page_url":"https://doi.org/10.1109/access.2020.2989469","pdf_url":"https://ieeexplore.ieee.org/ielx7/6287639/8948470/09076050.pdf","source":{"id":"https://openalex.org/S2485537415","display_name":"IEEE Access","issn_l":"2169-3536","issn":["2169-3536"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Access","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/15","display_name":"Life in Land","score":0.7400000095367432}],"awards":[{"id":"https://openalex.org/G2907842502","display_name":null,"funder_award_id":"20180550307","funder_id":"https://openalex.org/F4320323086","funder_display_name":"Natural Science Foundation of Liaoning Province"},{"id":"https://openalex.org/G3775048211","display_name":null,"funder_award_id":"3132019323","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G4131916014","display_name":null,"funder_award_id":"20180550307","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4140531804","display_name":null,"funder_award_id":"3132020170","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G7194626318","display_name":null,"funder_award_id":"20170540092","funder_id":"https://openalex.org/F4320323086","funder_display_name":"Natural Science Foundation of Liaoning Province"},{"id":"https://openalex.org/G7296354644","display_name":null,"funder_award_id":"61803065","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/F4320323086","display_name":"Natural Science Foundation of Liaoning Province","ror":null},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3020045074.pdf","grobid_xml":"https://content.openalex.org/works/W3020045074.grobid-xml"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W1612034467","https://openalex.org/W1947267113","https://openalex.org/W1988581590","https://openalex.org/W2026666393","https://openalex.org/W2053502852","https://openalex.org/W2080915318","https://openalex.org/W2085928743","https://openalex.org/W2094113855","https://openalex.org/W2139691165","https://openalex.org/W2141259072","https://openalex.org/W2149298154","https://openalex.org/W2151180344","https://openalex.org/W2156909104","https://openalex.org/W2177612949","https://openalex.org/W2295598076","https://openalex.org/W2326324325","https://openalex.org/W2435251607","https://openalex.org/W2467082561","https://openalex.org/W2472513547","https://openalex.org/W2514430732","https://openalex.org/W2588614855","https://openalex.org/W2593867025","https://openalex.org/W2598495276","https://openalex.org/W2753241613","https://openalex.org/W2762279748","https://openalex.org/W2807186140","https://openalex.org/W2888906255","https://openalex.org/W2900391652","https://openalex.org/W2909409778","https://openalex.org/W2911321166","https://openalex.org/W2911964244","https://openalex.org/W2924066922","https://openalex.org/W2937997287","https://openalex.org/W2965901104","https://openalex.org/W2967960129","https://openalex.org/W6717827561","https://openalex.org/W6735888752"],"related_works":["https://openalex.org/W4367336074","https://openalex.org/W3154045278","https://openalex.org/W4379620016","https://openalex.org/W4393666307","https://openalex.org/W3210764983","https://openalex.org/W4393443811","https://openalex.org/W4367335949","https://openalex.org/W3089416646","https://openalex.org/W4396816114","https://openalex.org/W4380048833"],"abstract_inverted_index":{"Pseudouridine":[0],"(\u03a8)":[1],"is":[2,9,31],"the":[3,18,83,122,126,161],"most":[4],"prevalent":[5],"RNA":[6],"modification,":[7],"which":[8],"formed":[10],"from":[11],"uridine":[12],"through":[13],"an":[14,39,91,153],"isomerization":[15],"reaction.":[16],"With":[17],"increasing":[19],"availability":[20],"of":[21],"genomic":[22],"and":[23,65,86,109,137,152,169],"proteomic":[24],"samples,":[25],"computer-aided":[26],"pseudouridine-synthase-specific":[27],"\u03a8":[28],"site":[29],"recognition":[30],"becoming":[32],"possible.":[33],"In":[34],"this":[35],"paper,":[36],"we":[37],"propose":[38],"ensemble":[40,92],"approach":[41],"to":[42,71,81,115],"identify":[43],"pseudouridine":[44],"sites,":[45],"named":[46],"EnsemPseU.":[47],"First,":[48],"five":[49],"sequence-encoding":[50],"strategies,":[51],"namely,":[52],"kmer,":[53],"binary":[54],"encoding,":[55],"enhanced":[56],"nucleic":[57],"acid":[58],"composition":[59],"(ENAC),":[60],"nucleotide":[61,66],"chemical":[62],"property":[63],"(NCP),":[64],"density":[67],"(ND),":[68],"were":[69],"applied":[70],"extract":[72],"sequence":[73],"information.":[74,89],"Then,":[75],"chi-square":[76,143],"feature":[77,84,144],"selection":[78],"was":[79,113],"used":[80,114],"reduce":[82],"dimensionality":[85],"remove":[87],"redundant":[88],"Finally,":[90],"algorithm":[93],"integrating":[94],"support":[95],"vector":[96],"machine":[97],"(SVM),":[98],"extreme":[99],"gradient":[100],"boosting":[101],"(XGBoost),":[102],"na\u00efve":[103],"Bayes":[104],"(NB),":[105],"k-nearest":[106],"neighbor":[107],"(KNN),":[108],"random":[110],"forest":[111],"(RF)":[112],"build":[116],"our":[117,156],"prediction":[118],"model.":[119,165],"Upon":[120],"testing,":[121],"results":[123],"showed":[124],"that":[125],"accuracy":[127],"improved":[128],"5.3%":[129],"for":[130,134,139],"H.":[131],"sapiens,":[132],"6.09%":[133],"S.":[135],"cerevisiae,":[136],"5.55%":[138],"M.":[140],"musculus":[141],"after":[142],"selection.":[145],"Moreover,":[146],"upon":[147],"evaluation":[148],"via":[149],"10-fold":[150],"cross-validation":[151],"independent":[154],"test,":[155],"proposed":[157],"model":[158],"EnsemPseU":[159],"outperformed":[160],"other":[162],"best":[163],"existing":[164],"The":[166],"source":[167],"code":[168],"data":[170],"sets":[171],"are":[172],"available":[173],"at":[174],"https://github.com/biyue1026/EnsemPseU.":[175]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":5},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":9},{"year":2020,"cited_by_count":2}],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2025-10-10T00:00:00"}
