{"id":"https://openalex.org/W4412488751","doi":"https://doi.org/10.1371/journal.pcbi.1013268","title":"EUP: Enhanced cross-species prediction of ubiquitination sites via a conditional variational autoencoder network based on ESM2","display_name":"EUP: Enhanced cross-species prediction of ubiquitination sites via a conditional variational autoencoder network based on ESM2","publication_year":2025,"publication_date":"2025-07-16","ids":{"openalex":"https://openalex.org/W4412488751","doi":"https://doi.org/10.1371/journal.pcbi.1013268","pmid":"https://pubmed.ncbi.nlm.nih.gov/40668800"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1013268","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013268","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1013268&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1013268&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100725207","display_name":"Junhao Liu","orcid":"https://orcid.org/0009-0004-8535-4349"},"institutions":[{"id":"https://openalex.org/I126924076","display_name":"Chongqing Normal University","ror":"https://ror.org/01dcw5w74","country_code":"CN","type":"education","lineage":["https://openalex.org/I126924076"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Junhao Liu","raw_affiliation_strings":["College of Life Science, Chongqing Normal University, Chongqing, P.R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Life Science, Chongqing Normal University, Chongqing, P.R. China","institution_ids":["https://openalex.org/I126924076"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101920182","display_name":"Zeyu Luo","orcid":"https://orcid.org/0000-0001-6650-9975"},"institutions":[{"id":"https://openalex.org/I126924076","display_name":"Chongqing Normal University","ror":"https://ror.org/01dcw5w74","country_code":"CN","type":"education","lineage":["https://openalex.org/I126924076"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zeyu Luo","raw_affiliation_strings":["College of Life Science, Chongqing Normal University, Chongqing, P.R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Life Science, Chongqing Normal University, Chongqing, P.R. China","institution_ids":["https://openalex.org/I126924076"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5092030203","display_name":"Rui Wang","orcid":"https://orcid.org/0009-0004-4099-2267"},"institutions":[{"id":"https://openalex.org/I126924076","display_name":"Chongqing Normal University","ror":"https://ror.org/01dcw5w74","country_code":"CN","type":"education","lineage":["https://openalex.org/I126924076"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Rui Wang","raw_affiliation_strings":["College of Life Science, Chongqing Normal University, Chongqing, P.R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Life Science, Chongqing Normal University, Chongqing, P.R. China","institution_ids":["https://openalex.org/I126924076"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108148511","display_name":"Xin Li","orcid":"https://orcid.org/0009-0003-2751-1169"},"institutions":[{"id":"https://openalex.org/I126924076","display_name":"Chongqing Normal University","ror":"https://ror.org/01dcw5w74","country_code":"CN","type":"education","lineage":["https://openalex.org/I126924076"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xin Li","raw_affiliation_strings":["College of Life Science, Chongqing Normal University, Chongqing, P.R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Life Science, Chongqing Normal University, Chongqing, P.R. China","institution_ids":["https://openalex.org/I126924076"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101494206","display_name":"Yawen Sun","orcid":"https://orcid.org/0009-0001-8955-6333"},"institutions":[{"id":"https://openalex.org/I126924076","display_name":"Chongqing Normal University","ror":"https://ror.org/01dcw5w74","country_code":"CN","type":"education","lineage":["https://openalex.org/I126924076"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yawen Sun","raw_affiliation_strings":["College of Life Science, Chongqing Normal University, Chongqing, P.R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Life Science, Chongqing Normal University, Chongqing, P.R. China","institution_ids":["https://openalex.org/I126924076"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Zongqing Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I126924076","display_name":"Chongqing Normal University","ror":"https://ror.org/01dcw5w74","country_code":"CN","type":"education","lineage":["https://openalex.org/I126924076"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zongqing Chen","raw_affiliation_strings":["School of Mathematical Sciences; Chongqing Key Lab of Cognitive Intelligence and Intelligent Finance, Chongqing Normal University, Chongqing, P.R. China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Mathematical Sciences; Chongqing Key Lab of Cognitive Intelligence and Intelligent Finance, Chongqing Normal University, Chongqing, P.R. China","institution_ids":["https://openalex.org/I126924076"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100641285","display_name":"Yu\u2010Juan Zhang","orcid":"https://orcid.org/0000-0001-6361-0840"},"institutions":[{"id":"https://openalex.org/I126924076","display_name":"Chongqing Normal University","ror":"https://ror.org/01dcw5w74","country_code":"CN","type":"education","lineage":["https://openalex.org/I126924076"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yu-Juan Zhang","raw_affiliation_strings":["College of Life Science, Chongqing Normal University, Chongqing, P.R. China"],"raw_orcid":"https://orcid.org/0000-0001-6361-0840","affiliations":[{"raw_affiliation_string":"College of Life Science, Chongqing Normal University, Chongqing, P.R. China","institution_ids":["https://openalex.org/I126924076"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5100641285"],"corresponding_institution_ids":["https://openalex.org/I126924076"],"apc_list":{"value":3043,"currency":"USD","value_usd":3043},"apc_paid":{"value":3043,"currency":"USD","value_usd":3043},"fwci":0.7566,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.69788998,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":97},"biblio":{"volume":"21","issue":"7","first_page":"e1013268","last_page":"e1013268"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9897000193595886,"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":0.9897000193595886,"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":0.9890000224113464,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9854999780654907,"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/autoencoder","display_name":"Autoencoder","score":0.7207862734794617},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.6394546627998352},{"id":"https://openalex.org/keywords/interpretability","display_name":"Interpretability","score":0.6129180192947388},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.6111963987350464},{"id":"https://openalex.org/keywords/ubiquitin","display_name":"Ubiquitin","score":0.5702686905860901},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5358980894088745},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5287123322486877},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.4534187912940979},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.43600213527679443},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.36227309703826904},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.28393006324768066},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.10959893465042114}],"concepts":[{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.7207862734794617},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.6394546627998352},{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.6129180192947388},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.6111963987350464},{"id":"https://openalex.org/C25602115","wikidata":"https://www.wikidata.org/wiki/Q407111","display_name":"Ubiquitin","level":3,"score":0.5702686905860901},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5358980894088745},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5287123322486877},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.4534187912940979},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.43600213527679443},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.36227309703826904},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.28393006324768066},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10959893465042114},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","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},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098446","descriptor_name":"Autoencoder","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098446","descriptor_name":"Autoencoder","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098446","descriptor_name":"Autoencoder","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000098446","descriptor_name":"Autoencoder","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013045","descriptor_name":"Species Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013045","descriptor_name":"Species Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013045","descriptor_name":"Species Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013045","descriptor_name":"Species Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","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":"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}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1013268","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013268","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1013268&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:40668800","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40668800","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":"PLoS computational biology","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12266453","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12266453","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":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:doaj.org/article:b1f49471ee704883a22758074bc235b1","is_oa":true,"landing_page_url":"https://doaj.org/article/b1f49471ee704883a22758074bc235b1","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":"PLoS Computational Biology, Vol 21, Iss 7, p e1013268 (2025)","raw_type":"article"},{"id":"pmh:oai:doaj.org/article:e90b36230d7c4a5880e1792ab585e62f","is_oa":true,"landing_page_url":"https://doaj.org/article/e90b36230d7c4a5880e1792ab585e62f","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":"PLoS Computational Biology, Vol 21, Iss 7 (2025)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1013268","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1013268","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1013268&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15","score":0.7099999785423279}],"awards":[{"id":"https://openalex.org/G2165486229","display_name":null,"funder_award_id":"11991024, 12271071","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5391772797","display_name":null,"funder_award_id":"11991024","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5661824348","display_name":null,"funder_award_id":"12271071","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5842416684","display_name":null,"funder_award_id":"202304500006","funder_id":"https://openalex.org/F4320322725","funder_display_name":"China Scholarship Council"},{"id":"https://openalex.org/G8792734103","display_name":null,"funder_award_id":"No. 202304500006","funder_id":"https://openalex.org/F4320322725","funder_display_name":"China Scholarship Council"}],"funders":[{"id":"https://openalex.org/F4320311970","display_name":"Chongqing Normal University","ror":"https://ror.org/01dcw5w74"},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320322725","display_name":"China Scholarship Council","ror":"https://ror.org/04atp4p48"},{"id":"https://openalex.org/F4320327557","display_name":"National Office for Philosophy and Social Sciences","ror":"https://ror.org/04m0ms912"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4412488751.pdf","grobid_xml":"https://content.openalex.org/works/W4412488751.grobid-xml"},"referenced_works_count":37,"referenced_works":["https://openalex.org/W1583837637","https://openalex.org/W1959608418","https://openalex.org/W2031300832","https://openalex.org/W2042571564","https://openalex.org/W2086831875","https://openalex.org/W2152084880","https://openalex.org/W2156125289","https://openalex.org/W2569814361","https://openalex.org/W2612690371","https://openalex.org/W2765094222","https://openalex.org/W2767152811","https://openalex.org/W2772984056","https://openalex.org/W2921182217","https://openalex.org/W2962772482","https://openalex.org/W3086598145","https://openalex.org/W3156007823","https://openalex.org/W3189220322","https://openalex.org/W3202924278","https://openalex.org/W4205742853","https://openalex.org/W4205773061","https://openalex.org/W4207041005","https://openalex.org/W4214895574","https://openalex.org/W4223644783","https://openalex.org/W4236965008","https://openalex.org/W4281489087","https://openalex.org/W4283746646","https://openalex.org/W4313453665","https://openalex.org/W4315621831","https://openalex.org/W4321214126","https://openalex.org/W4327550249","https://openalex.org/W4361298515","https://openalex.org/W4388094481","https://openalex.org/W4388656332","https://openalex.org/W4389076414","https://openalex.org/W4391280974","https://openalex.org/W4400344236","https://openalex.org/W4406440058"],"related_works":["https://openalex.org/W2905433371","https://openalex.org/W2888392564","https://openalex.org/W4310278675","https://openalex.org/W4388422664","https://openalex.org/W4390569940","https://openalex.org/W4361193272","https://openalex.org/W2669956259","https://openalex.org/W4249005693","https://openalex.org/W4392946183","https://openalex.org/W4405887298"],"abstract_inverted_index":{"Ubiquitination":[0],"is":[1,53,141],"critical":[2],"in":[3,25,94],"biomedical":[4],"research.":[5],"Predicting":[6],"ubiquitination":[7,45,96,110,138],"sites":[8,97,111],"based":[9],"on":[10,85],"deep":[11],"learning":[12],"model":[13,23,48,63,136],"have":[14],"advanced":[15],"the":[16,26,72,131,134],"study":[17],"of":[18,121,133],"ubiquitination.":[19],"However,":[20],"traditional":[21],"supervised":[22],"limits":[24],"scenarios":[27],"where":[28],"labels":[29],"are":[30],"scarcity":[31],"across":[32,98,114],"species.":[33],"To":[34],"address":[35],"this":[36,86],"issue,":[37],"we":[38],"introduce":[39],"EUP,":[40],"an":[41],"online":[42],"webserver":[43],"for":[44,50,108,137],"prediction":[46],"and":[47,117,143],"interpretation":[49],"multi-species.":[51],"EUP":[52,90,135,140],"constructed":[54],"by":[55],"extracting":[56],"lysine":[57],"site-dependent":[58],"features":[59,74,107,124],"from":[60],"pretrained":[61],"language":[62],"ESM2.":[64],"Then,":[65],"utilizing":[66],"conditional":[67],"variational":[68],"inference":[69,103],"to":[70,75],"reduce":[71],"ESM2":[73],"a":[76],"lower-dimensional":[77],"latent":[78,87],"representation.":[79],"By":[80],"constructing":[81],"downstream":[82],"models":[83],"built":[84],"feature":[88],"representation,":[89],"exhibited":[91],"superior":[92],"performance":[93],"predicting":[95,109],"species,":[99],"while":[100],"maintaining":[101],"low":[102],"latency.":[104],"Furthermore,":[105],"key":[106,123],"were":[112],"identified":[113],"animals,":[115],"plants,":[116],"microbes.":[118],"The":[119],"identification":[120],"shared":[122],"that":[125],"capture":[126],"evolutionarily":[127],"conserved":[128],"traits":[129],"enhances":[130],"interpretability":[132],"prediction.":[139],"free":[142],"available":[144],"at":[145],"(https://eup.aibtit.com/).":[146]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1}],"updated_date":"2026-08-25T07:29:55.448023","created_date":"2025-10-10T00:00:00"}
