{"id":"https://openalex.org/W4417337766","doi":"https://doi.org/10.1109/tcbbio.2025.3643930","title":"DeepNhKcr: Explainable Deep Learning Framework for the Prediction of Crotonylation Sites of Non-Histone Lysine in Plants Based on Pre-Trained Protein Language Model","display_name":"DeepNhKcr: Explainable Deep Learning Framework for the Prediction of Crotonylation Sites of Non-Histone Lysine in Plants Based on Pre-Trained Protein Language Model","publication_year":2025,"publication_date":"2025-12-15","ids":{"openalex":"https://openalex.org/W4417337766","doi":"https://doi.org/10.1109/tcbbio.2025.3643930","pmid":"https://pubmed.ncbi.nlm.nih.gov/41396754"},"language":"en","primary_location":{"id":"doi:10.1109/tcbbio.2025.3643930","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3643930","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"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":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Jinwei Wang","orcid":"https://orcid.org/0009-0000-0772-0375"},"institutions":[{"id":"https://openalex.org/I20942203","display_name":"Hainan University","ror":"https://ror.org/03q648j11","country_code":"CN","type":"education","lineage":["https://openalex.org/I20942203"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Jinwei Wang","raw_affiliation_strings":["School of Computer Science and Technology, Hainan University, Haikou, China"],"raw_orcid":"https://orcid.org/0009-0000-0772-0375","affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Hainan University, Haikou, China","institution_ids":["https://openalex.org/I20942203"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Zhenjie Luo","orcid":"https://orcid.org/0009-0008-7198-6387"},"institutions":[{"id":"https://openalex.org/I20942203","display_name":"Hainan University","ror":"https://ror.org/03q648j11","country_code":"CN","type":"education","lineage":["https://openalex.org/I20942203"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhenjie Luo","raw_affiliation_strings":["School of Computer Science and Technology, Hainan University, Haikou, China"],"raw_orcid":"https://orcid.org/0009-0008-7198-6387","affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Hainan University, Haikou, China","institution_ids":["https://openalex.org/I20942203"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5114270411","display_name":"Aoyun Geng","orcid":"https://orcid.org/0009-0004-9716-9415"},"institutions":[{"id":"https://openalex.org/I20942203","display_name":"Hainan University","ror":"https://ror.org/03q648j11","country_code":"CN","type":"education","lineage":["https://openalex.org/I20942203"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Aoyun Geng","raw_affiliation_strings":["School of Computer Science and Technology, Hainan University, Haikou, China"],"raw_orcid":"https://orcid.org/0009-0004-9716-9415","affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Hainan University, Haikou, China","institution_ids":["https://openalex.org/I20942203"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066469263","display_name":"Junlin Xu","orcid":"https://orcid.org/0000-0003-1057-1504"},"institutions":[{"id":"https://openalex.org/I43922553","display_name":"Wuhan University of Science and Technology","ror":"https://ror.org/00e4hrk88","country_code":"CN","type":"education","lineage":["https://openalex.org/I43922553"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Junlin Xu","raw_affiliation_strings":["School of Computer Science and Technology, Wuhan University of Science and Technology, Wuhan, China","School of Computer Science and Technology, Wuhan University of Science and Technology, Wuhan, Hubei, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Wuhan University of Science and Technology, Wuhan, China","institution_ids":["https://openalex.org/I43922553"]},{"raw_affiliation_string":"School of Computer Science and Technology, Wuhan University of Science and Technology, Wuhan, Hubei, China","institution_ids":["https://openalex.org/I43922553"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006543131","display_name":"Yajie Meng","orcid":"https://orcid.org/0000-0002-2384-1158"},"institutions":[{"id":"https://openalex.org/I4210119942","display_name":"Wuhan Textile University","ror":"https://ror.org/02jgsf398","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210119942"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yajie Meng","raw_affiliation_strings":["School of Computer Science and Artificial Intelligence, Wuhan Textile University, Wuhan, China","School of Computer Science and Artificial Intelligence, Wuhan Textile University, Wuhan, Hubei, China"],"raw_orcid":"https://orcid.org/0000-0002-2384-1158","affiliations":[{"raw_affiliation_string":"School of Computer Science and Artificial Intelligence, Wuhan Textile University, Wuhan, China","institution_ids":["https://openalex.org/I4210119942"]},{"raw_affiliation_string":"School of Computer Science and Artificial Intelligence, Wuhan Textile University, Wuhan, Hubei, China","institution_ids":["https://openalex.org/I4210119942"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016741865","display_name":"Shankai Yan","orcid":"https://orcid.org/0000-0003-0369-4979"},"institutions":[{"id":"https://openalex.org/I20942203","display_name":"Hainan University","ror":"https://ror.org/03q648j11","country_code":"CN","type":"education","lineage":["https://openalex.org/I20942203"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shankai Yan","raw_affiliation_strings":["School of Computer Science and Technology, Hainan University, Haikou, China"],"raw_orcid":"https://orcid.org/0000-0003-0369-4979","affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Hainan University, Haikou, China","institution_ids":["https://openalex.org/I20942203"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033232360","display_name":"Leyi Wei","orcid":"https://orcid.org/0000-0003-1444-190X"},"institutions":[{"id":"https://openalex.org/I49835588","display_name":"Macao Polytechnic University","ror":"https://ror.org/02sf5td35","country_code":"MO","type":"education","lineage":["https://openalex.org/I49835588"]}],"countries":["MO"],"is_corresponding":false,"raw_author_name":"Leyi Wei","raw_affiliation_strings":["Centre for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Science, Macao Polytechnic University, Macao, SAR, China","Centre for Artificial Intelligence driven Drug Discovery, Faculty of Applied Science, Macao Polytechnic University, Macao, China"],"raw_orcid":"https://orcid.org/0000-0003-1444-190X","affiliations":[{"raw_affiliation_string":"Centre for Artificial Intelligence Driven Drug Discovery, Faculty of Applied Science, Macao Polytechnic University, Macao, SAR, China","institution_ids":["https://openalex.org/I49835588"]},{"raw_affiliation_string":"Centre for Artificial Intelligence driven Drug Discovery, Faculty of Applied Science, Macao Polytechnic University, Macao, China","institution_ids":["https://openalex.org/I49835588"]}]},{"author_position":"middle","author":{"id":null,"display_name":"Zilong Zhang","orcid":"https://orcid.org/0000-0002-4934-1258"},"institutions":[{"id":"https://openalex.org/I20942203","display_name":"Hainan University","ror":"https://ror.org/03q648j11","country_code":"CN","type":"education","lineage":["https://openalex.org/I20942203"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zilong Zhang","raw_affiliation_strings":["School of Computer Science and Technology, Hainan University, Haikou, China"],"raw_orcid":"https://orcid.org/0000-0002-4934-1258","affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Hainan University, Haikou, China","institution_ids":["https://openalex.org/I20942203"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101829682","display_name":"Qingchen Zhang","orcid":"https://orcid.org/0000-0001-5525-687X"},"institutions":[{"id":"https://openalex.org/I20942203","display_name":"Hainan University","ror":"https://ror.org/03q648j11","country_code":"CN","type":"education","lineage":["https://openalex.org/I20942203"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qingchen Zhang","raw_affiliation_strings":["School of Computer Science and Technology, Hainan University, Haikou, China"],"raw_orcid":"https://orcid.org/0000-0001-5525-687X","affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Hainan University, Haikou, China","institution_ids":["https://openalex.org/I20942203"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017426085","display_name":"Quan Zou","orcid":"https://orcid.org/0000-0001-6406-1142"},"institutions":[{"id":"https://openalex.org/I150229711","display_name":"University of Electronic Science and Technology of China","ror":"https://ror.org/04qr3zq92","country_code":"CN","type":"education","lineage":["https://openalex.org/I150229711"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Quan Zou","raw_affiliation_strings":["Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China"],"raw_orcid":"https://orcid.org/0000-0001-6406-1142","affiliations":[{"raw_affiliation_string":"Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, Chengdu, China","institution_ids":["https://openalex.org/I150229711"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5061028143","display_name":"Feifei Cui","orcid":"https://orcid.org/0000-0001-7055-3813"},"institutions":[{"id":"https://openalex.org/I20942203","display_name":"Hainan University","ror":"https://ror.org/03q648j11","country_code":"CN","type":"education","lineage":["https://openalex.org/I20942203"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Feifei Cui","raw_affiliation_strings":["School of Computer Science and Technology, Hainan University, Haikou, China"],"raw_orcid":"https://orcid.org/0000-0001-7055-3813","affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, Hainan University, Haikou, China","institution_ids":["https://openalex.org/I20942203"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":11,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I20942203"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.34697304,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"23","issue":"1","first_page":"326","last_page":"340"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9810000061988831,"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":0.9810000061988831,"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":0.003100000089034438,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.00139999995008111,"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/interpretability","display_name":"Interpretability","score":0.9096999764442444},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.7450000047683716},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.49309998750686646},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.44040000438690186},{"id":"https://openalex.org/keywords/sequence","display_name":"Sequence (biology)","score":0.40209999680519104},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.4009999930858612},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.3734000027179718},{"id":"https://openalex.org/keywords/encoding","display_name":"Encoding (memory)","score":0.34709998965263367}],"concepts":[{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.9096999764442444},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.7455999851226807},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.7450000047683716},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6656000018119812},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5123999714851379},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.49309998750686646},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.44040000438690186},{"id":"https://openalex.org/C2778112365","wikidata":"https://www.wikidata.org/wiki/Q3511065","display_name":"Sequence (biology)","level":2,"score":0.40209999680519104},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.4009999930858612},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.3734000027179718},{"id":"https://openalex.org/C125411270","wikidata":"https://www.wikidata.org/wiki/Q18653","display_name":"Encoding (memory)","level":2,"score":0.34709998965263367},{"id":"https://openalex.org/C149364088","wikidata":"https://www.wikidata.org/wiki/Q185917","display_name":"Translation (biology)","level":4,"score":0.3409999907016754},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.3276999890804291},{"id":"https://openalex.org/C10010492","wikidata":"https://www.wikidata.org/wiki/Q3142557","display_name":"Protein sequencing","level":4,"score":0.3075000047683716},{"id":"https://openalex.org/C40506919","wikidata":"https://www.wikidata.org/wiki/Q7452469","display_name":"Sequence learning","level":2,"score":0.3046000003814697},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.3012999892234802},{"id":"https://openalex.org/C52622490","wikidata":"https://www.wikidata.org/wiki/Q1026626","display_name":"Feature extraction","level":2,"score":0.2944999933242798},{"id":"https://openalex.org/C136389625","wikidata":"https://www.wikidata.org/wiki/Q334384","display_name":"Supervised learning","level":3,"score":0.2913999855518341},{"id":"https://openalex.org/C204323151","wikidata":"https://www.wikidata.org/wiki/Q905424","display_name":"Range (aeronautics)","level":2,"score":0.28540000319480896},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.2847999930381775},{"id":"https://openalex.org/C137293760","wikidata":"https://www.wikidata.org/wiki/Q3621696","display_name":"Language model","level":2,"score":0.2549999952316284},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.2529999911785126}],"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":"D008239","descriptor_name":"Lysine","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008239","descriptor_name":"Lysine","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D008239","descriptor_name":"Lysine","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D008239","descriptor_name":"Lysine","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010940","descriptor_name":"Plant Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D010940","descriptor_name":"Plant Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D010940","descriptor_name":"Plant Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010940","descriptor_name":"Plant Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D010940","descriptor_name":"Plant Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D010940","descriptor_name":"Plant Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"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}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbbio.2025.3643930","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3643930","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"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":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:41396754","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41396754","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":"IEEE transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G771689064","display_name":null,"funder_award_id":"62450002","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"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":49,"referenced_works":["https://openalex.org/W2097606916","https://openalex.org/W2107882638","https://openalex.org/W2115862579","https://openalex.org/W2131774270","https://openalex.org/W2141818629","https://openalex.org/W2143210482","https://openalex.org/W2163603537","https://openalex.org/W2606879989","https://openalex.org/W2613130271","https://openalex.org/W2621036017","https://openalex.org/W2748860630","https://openalex.org/W2768705872","https://openalex.org/W2805827044","https://openalex.org/W2883294189","https://openalex.org/W2963351448","https://openalex.org/W2991059578","https://openalex.org/W3010697764","https://openalex.org/W3048991675","https://openalex.org/W3094567318","https://openalex.org/W3113678970","https://openalex.org/W3120982625","https://openalex.org/W3129096424","https://openalex.org/W3136291807","https://openalex.org/W3139265997","https://openalex.org/W3162632405","https://openalex.org/W3167718630","https://openalex.org/W3207838037","https://openalex.org/W4200111237","https://openalex.org/W4210810268","https://openalex.org/W4282961683","https://openalex.org/W4297138475","https://openalex.org/W4307645443","https://openalex.org/W4311761046","https://openalex.org/W4312827846","https://openalex.org/W4315619315","https://openalex.org/W4365150857","https://openalex.org/W4376133604","https://openalex.org/W4382680733","https://openalex.org/W4389311889","https://openalex.org/W4391618534","https://openalex.org/W4391844900","https://openalex.org/W4392714934","https://openalex.org/W4393371661","https://openalex.org/W4396572253","https://openalex.org/W4399153512","https://openalex.org/W4401163224","https://openalex.org/W4401171136","https://openalex.org/W4403782367","https://openalex.org/W4414163797"],"related_works":[],"abstract_inverted_index":{"Lysine":[0],"crotonylation":[1],"(Kcr)":[2],"is":[3,51,261],"an":[4,14],"important":[5,239],"protein":[6,117,158],"modification":[7],"occurring":[8],"after":[9],"translation":[10],"in":[11,17,23,101,180,219,256,268],"biology,":[12],"serving":[13],"essential":[15,52],"function":[16],"a":[18,81,89,107,122,249],"range":[19],"of":[20,31,36,43,48,78,98,133,176,183],"biological":[21,56,201,244],"processes":[22],"both":[24,220],"plants":[25],"and":[26,40,68,95,166,199,211,215,223,242,260],"animals,":[27],"including":[28],"the":[29,34,41,46,75,93,116,131,136,139,144,174,192,228,236],"regulation":[30],"gene":[32],"expression,":[33],"maintenance":[35],"cellular":[37],"metabolic":[38],"balance,":[39],"enhancement":[42],"photosynthesis.":[44],"Exploring":[45],"detection":[47,63],"Kcr":[49,79,99,178,254,270],"sites":[50,80,100,179,255],"for":[53,62,92,252],"uncovering":[54],"their":[55,200,243],"functions.":[57],"Nonetheless,":[58],"conventional":[59,140],"experimental":[60],"approaches":[61,155],"are":[64],"often":[65],"time-consuming,":[66],"expensive,":[67],"hindered":[69],"by":[70],"various":[71],"technical":[72],"constraints,":[73],"making":[74],"precise":[76],"identification":[77],"significant":[82],"challenge.":[83],"This":[84,168],"study":[85],"seeks":[86],"to":[87,161,234,263],"develop":[88],"computational":[90],"approach":[91],"rapid":[94],"accurate":[96],"prediction":[97],"plant":[102,257,269],"non-histone":[103,181,258],"proteins.":[104],"We":[105],"introduce":[106],"novel":[108],"deep":[109,153,212],"learning":[110,154,210,213],"framework":[111],"named":[112],"DeepNhKcr,":[113],"which":[114],"integrates":[115,230],"language":[118],"model":[119,137,229],"(ESM2)":[120],"with":[121,143,156],"bidirectional":[123],"long":[124],"short-term":[125],"memory":[126],"(BiLSTM)":[127],"network.":[128],"To":[129],"address":[130],"challenge":[132],"data":[134],"imbalance,":[135],"replaces":[138],"cross-entropy":[141],"loss":[142,146],"focal":[145],"function.":[147],"In":[148],"addition,":[149],"DeepNhKcr":[150,203,246],"combines":[151],"advanced":[152],"traditional":[157],"encoding":[159],"strategies":[160],"enable":[162],"effective":[163],"feature":[164],"extraction":[165],"integration.":[167],"method":[169,251],"not":[170],"only":[171],"significantly":[172],"boosts":[173],"accuracy":[175],"predicting":[177],"proteins":[182,259],"plants.":[184],"but":[185],"also":[186],"provides":[187],"interpretability,":[188],"shedding":[189],"light":[190],"on":[191],"potential":[193],"links":[194],"between":[195,238],"key":[196],"sequence":[197,240],"characteristics":[198],"roles.":[202,245],"delivers":[204],"outstanding":[205],"results,":[206],"surpassing":[207],"existing":[208],"machine":[209],"models,":[214],"demonstrating":[216],"excellent":[217],"performance":[218],"five-fold":[221],"cross-validation":[222],"independent":[224],"test":[225],"experiments.":[226],"Moreover,":[227],"interpretability":[231],"analysis":[232],"techniques":[233],"investigate":[235],"connections":[237],"features":[241],"acts":[247],"as":[248],"powerful":[250],"detecting":[253],"anticipated":[262],"greatly":[264],"advance":[265],"future":[266],"studies":[267],"site":[271],"prediction.":[272]},"counts_by_year":[],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-12-15T00:00:00"}
