{"id":"https://openalex.org/W2919709896","doi":"https://doi.org/10.1186/s12859-019-2677-9","title":"DeepUbi: a deep learning framework for prediction of ubiquitination sites in proteins","display_name":"DeepUbi: a deep learning framework for prediction of ubiquitination sites in proteins","publication_year":2019,"publication_date":"2019-02-18","ids":{"openalex":"https://openalex.org/W2919709896","doi":"https://doi.org/10.1186/s12859-019-2677-9","mag":"2919709896","pmid":"https://pubmed.ncbi.nlm.nih.gov/30777029"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-019-2677-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2677-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2677-9","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2677-9","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5071489179","display_name":"Hongli Fu","orcid":"https://orcid.org/0000-0002-6962-2671"},"institutions":[{"id":"https://openalex.org/I92403157","display_name":"University of Science and Technology Beijing","ror":"https://ror.org/02egmk993","country_code":"CN","type":"education","lineage":["https://openalex.org/I92403157"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hongli Fu","raw_affiliation_strings":["Department of Information and Computing Science, University of Science and Technology Beijing, Beijing, 100083, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Information and Computing Science, University of Science and Technology Beijing, Beijing, 100083, China","institution_ids":["https://openalex.org/I92403157"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5014559891","display_name":"Yingxi Yang","orcid":"https://orcid.org/0000-0001-5153-2769"},"institutions":[{"id":"https://openalex.org/I92403157","display_name":"University of Science and Technology Beijing","ror":"https://ror.org/02egmk993","country_code":"CN","type":"education","lineage":["https://openalex.org/I92403157"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yingxi Yang","raw_affiliation_strings":["Department of Information and Computing Science, University of Science and Technology Beijing, Beijing, 100083, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Information and Computing Science, University of Science and Technology Beijing, Beijing, 100083, China","institution_ids":["https://openalex.org/I92403157"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100410379","display_name":"Xiaobo Wang","orcid":"https://orcid.org/0000-0001-6044-914X"},"institutions":[{"id":"https://openalex.org/I92403157","display_name":"University of Science and Technology Beijing","ror":"https://ror.org/02egmk993","country_code":"CN","type":"education","lineage":["https://openalex.org/I92403157"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaobo Wang","raw_affiliation_strings":["Department of Information and Computing Science, University of Science and Technology Beijing, Beijing, 100083, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Information and Computing Science, University of Science and Technology Beijing, Beijing, 100083, China","institution_ids":["https://openalex.org/I92403157"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100460922","display_name":"Hui Wang","orcid":"https://orcid.org/0000-0003-2791-8981"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"government","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210090176","display_name":"Institute of Computing Technology","ror":"https://ror.org/0090r4d87","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210090176"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hui Wang","raw_affiliation_strings":["Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, China","institution_ids":["https://openalex.org/I4210090176","https://openalex.org/I19820366"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5002586536","display_name":"Yan Xu","orcid":"https://orcid.org/0000-0001-9462-580X"},"institutions":[{"id":"https://openalex.org/I78675632","display_name":"Beijing Information Science & Technology University","ror":"https://ror.org/04xnqep60","country_code":"CN","type":"education","lineage":["https://openalex.org/I78675632"]},{"id":"https://openalex.org/I92403157","display_name":"University of Science and Technology Beijing","ror":"https://ror.org/02egmk993","country_code":"CN","type":"education","lineage":["https://openalex.org/I92403157"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yan Xu","raw_affiliation_strings":["Beijing Key Laboratory for Magneto-photoelectrical Composite and Interface Science, University of Science and Technology Beijing, Beijing, 100083, China. xuyan@ustb.edu.cn","Department of Information and Computing Science, University of Science and Technology Beijing, Beijing, 100083, China. xuyan@ustb.edu.cn","Beijing Key Laboratory for Magneto-photoelectrical Composite and Interface Science, University of Science and Technology Beijing, Beijing, 100083, China"],"raw_orcid":"https://orcid.org/0000-0001-9462-580X","affiliations":[{"raw_affiliation_string":"Beijing Key Laboratory for Magneto-photoelectrical Composite and Interface Science, University of Science and Technology Beijing, Beijing, 100083, China. xuyan@ustb.edu.cn","institution_ids":["https://openalex.org/I78675632","https://openalex.org/I92403157"]},{"raw_affiliation_string":"Department of Information and Computing Science, University of Science and Technology Beijing, Beijing, 100083, China. xuyan@ustb.edu.cn","institution_ids":["https://openalex.org/I78675632","https://openalex.org/I92403157"]},{"raw_affiliation_string":"Beijing Key Laboratory for Magneto-photoelectrical Composite and Interface Science, University of Science and Technology Beijing, Beijing, 100083, China","institution_ids":["https://openalex.org/I92403157"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5002586536"],"corresponding_institution_ids":["https://openalex.org/I78675632","https://openalex.org/I92403157"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":4.7866,"has_fulltext":true,"cited_by_count":88,"citation_normalized_percentile":{"value":0.96021658,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"20","issue":"1","first_page":"86","last_page":"86"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9789999723434448,"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":0.9789999723434448,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.00559999980032444,"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/T11041","display_name":"Ubiquitin and proteasome pathways","score":0.004900000058114529,"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/ubiquitin","display_name":"Ubiquitin","score":0.7928401231765747},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.6652697324752808},{"id":"https://openalex.org/keywords/regulator","display_name":"Regulator","score":0.5355674028396606},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5328125953674316},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.5199190974235535},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.49898386001586914},{"id":"https://openalex.org/keywords/proteomics","display_name":"Proteomics","score":0.4956592321395874},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.48639658093452454},{"id":"https://openalex.org/keywords/lysine","display_name":"Lysine","score":0.470305860042572},{"id":"https://openalex.org/keywords/proteome","display_name":"Proteome","score":0.46995070576667786},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4602879583835602},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3425953984260559},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3236902952194214},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.20942702889442444}],"concepts":[{"id":"https://openalex.org/C25602115","wikidata":"https://www.wikidata.org/wiki/Q407111","display_name":"Ubiquitin","level":3,"score":0.7928401231765747},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.6652697324752808},{"id":"https://openalex.org/C6929976","wikidata":"https://www.wikidata.org/wiki/Q3771881","display_name":"Regulator","level":3,"score":0.5355674028396606},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5328125953674316},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.5199190974235535},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.49898386001586914},{"id":"https://openalex.org/C46111723","wikidata":"https://www.wikidata.org/wiki/Q471857","display_name":"Proteomics","level":3,"score":0.4956592321395874},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.48639658093452454},{"id":"https://openalex.org/C2776016237","wikidata":"https://www.wikidata.org/wiki/Q178430","display_name":"Lysine","level":3,"score":0.470305860042572},{"id":"https://openalex.org/C104397665","wikidata":"https://www.wikidata.org/wiki/Q860947","display_name":"Proteome","level":2,"score":0.46995070576667786},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4602879583835602},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3425953984260559},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3236902952194214},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.20942702889442444},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C515207424","wikidata":"https://www.wikidata.org/wiki/Q8066","display_name":"Amino acid","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008239","descriptor_name":"Lysine","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008239","descriptor_name":"Lysine","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008239","descriptor_name":"Lysine","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},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","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":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D054875","descriptor_name":"Ubiquitination","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054875","descriptor_name":"Ubiquitination","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D054875","descriptor_name":"Ubiquitination","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D057149","descriptor_name":"Ubiquitinated Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D057149","descriptor_name":"Ubiquitinated Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D057149","descriptor_name":"Ubiquitinated Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-019-2677-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2677-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2677-9","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30777029","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30777029","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:556a406728284254a214c7869244fb57","is_oa":false,"landing_page_url":"https://doaj.org/article/556a406728284254a214c7869244fb57","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 20, Iss 1, Pp 1-10 (2019)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5381589","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC6379983","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:6379983","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6379983","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-019-2677-9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-019-2677-9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-019-2677-9","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3700057763","display_name":null,"funder_award_id":"FRF-TP-17-024A2","funder_id":"https://openalex.org/F4320335787","funder_display_name":"Fundamental Research Funds for the Central Universities"},{"id":"https://openalex.org/G6033847983","display_name":null,"funder_award_id":"11671032","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/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2919709896.pdf","grobid_xml":"https://content.openalex.org/works/W2919709896.grobid-xml"},"referenced_works_count":40,"referenced_works":["https://openalex.org/W66632606","https://openalex.org/W1665214252","https://openalex.org/W1979408355","https://openalex.org/W1984148780","https://openalex.org/W1991634033","https://openalex.org/W1996768014","https://openalex.org/W1999212541","https://openalex.org/W2003204068","https://openalex.org/W2006505144","https://openalex.org/W2006862211","https://openalex.org/W2029093937","https://openalex.org/W2031300832","https://openalex.org/W2034070267","https://openalex.org/W2043338013","https://openalex.org/W2050192820","https://openalex.org/W2053502852","https://openalex.org/W2056775476","https://openalex.org/W2086831875","https://openalex.org/W2095900655","https://openalex.org/W2097606916","https://openalex.org/W2097678794","https://openalex.org/W2101090646","https://openalex.org/W2111524632","https://openalex.org/W2141818629","https://openalex.org/W2145786566","https://openalex.org/W2145957695","https://openalex.org/W2152051829","https://openalex.org/W2152084880","https://openalex.org/W2152339342","https://openalex.org/W2156822612","https://openalex.org/W2164492849","https://openalex.org/W2165618529","https://openalex.org/W2230399809","https://openalex.org/W2257709006","https://openalex.org/W2289712442","https://openalex.org/W2311607323","https://openalex.org/W2344751993","https://openalex.org/W2569814361","https://openalex.org/W2610582292","https://openalex.org/W2745944099"],"related_works":["https://openalex.org/W1982829397","https://openalex.org/W2106414650","https://openalex.org/W4317388196","https://openalex.org/W2347437365","https://openalex.org/W1999412725","https://openalex.org/W4390205769","https://openalex.org/W2974695603","https://openalex.org/W2124137418","https://openalex.org/W2391458050","https://openalex.org/W2086860678"],"abstract_inverted_index":{"BACKGROUND:":[0],"Protein":[1],"ubiquitination":[2,45,65,91,104,194],"occurs":[3],"when":[4],"the":[5,131,147,155],"ubiquitin":[6],"protein":[7,12],"binds":[8],"to":[9,96],"a":[10,47,98,115,137,172],"target":[11,74],"residue":[13],"of":[14,23,152],"lysine":[15,103],"(K),":[16],"and":[17,33,39,54,81,133,154,158],"it":[18],"is":[19],"an":[20,143],"important":[21],"regulator":[22],"many":[24],"cellular":[25],"functions,":[26],"such":[27],"as":[28],"signal":[29],"transduction,":[30],"cell":[31],"division,":[32],"immune":[34],"reactions,":[35],"in":[36,50,57,63,106,192],"eukaryotes.":[37],"Experimental":[38],"clinical":[40],"studies":[41],"have":[42,60],"shown":[43],"that":[44,100,175,187],"plays":[46],"key":[48],"role":[49],"several":[51],"human":[52],"diseases,":[53],"recent":[55],"advances":[56],"proteomic":[58],"technology":[59],"spurred":[61],"interest":[62],"identifying":[64],"sites.":[66],"However,":[67],"most":[68],"current":[69],"computing":[70],"tools":[71],"for":[72],"predicting":[73,193],"sites":[75,92,105],"are":[76,128],"based":[77,120,195],"on":[78,121,196],"small-scale":[79],"data":[80],"shallow":[82],"machine":[83],"learning":[84,117],"algorithms.":[85],"RESULTS:":[86],"As":[87],"more":[88,163],"experimentally":[89],"validated":[90],"emerge,":[93],"we":[94,113],"need":[95],"design":[97],"predictor":[99],"can":[101,176],"identify":[102],"large-scale":[107],"proteome":[108],"data.":[109,198],"In":[110,136],"this":[111],"work,":[112],"propose":[114],"deep":[116],"predictor,":[118],"DeepUbi,":[119],"convolutional":[122],"neural":[123],"networks.":[124],"Four":[125],"different":[126],"features":[127],"adopted":[129],"from":[130,180],"sequences":[132],"physicochemical":[134],"properties.":[135],"10-fold":[138],"cross":[139],"validation,":[140],"DeepUbi":[141,188],"obtains":[142],"AUC":[144],"(area":[145],"under":[146],"Receiver":[148],"Operating":[149],"Characteristic":[150],"curve)":[151],"0.9,":[153],"accuracy,":[156],"sensitivity":[157],"specificity":[159],"exceeded":[160],"85%.":[161],"The":[162],"comprehensive":[164],"indicator,":[165],"MCC,":[166],"reaches":[167],"0.78.":[168],"We":[169],"also":[170],"develop":[171],"software":[173],"package":[174],"be":[177],"freely":[178],"downloaded":[179],"https://github.com/Sunmile/DeepUbi":[181],".":[182],"CONCLUSION:":[183],"Our":[184],"results":[185],"show":[186],"has":[189],"excellent":[190],"performance":[191],"large":[197]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":11},{"year":2024,"cited_by_count":11},{"year":2023,"cited_by_count":7},{"year":2022,"cited_by_count":11},{"year":2021,"cited_by_count":24},{"year":2020,"cited_by_count":17},{"year":2019,"cited_by_count":4}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
