{"id":"https://openalex.org/W4392824269","doi":"https://doi.org/10.1109/jbhi.2024.3377362","title":"PTransIPs: Identification of Phosphorylation Sites Enhanced by Protein PLM Embeddings","display_name":"PTransIPs: Identification of Phosphorylation Sites Enhanced by Protein PLM Embeddings","publication_year":2024,"publication_date":"2024-03-14","ids":{"openalex":"https://openalex.org/W4392824269","doi":"https://doi.org/10.1109/jbhi.2024.3377362","pmid":"https://pubmed.ncbi.nlm.nih.gov/38483806"},"language":"en","primary_location":{"id":"doi:10.1109/jbhi.2024.3377362","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2024.3377362","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"is_oa":false,"is_in_doaj":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Journal of Biomedical and Health Informatics","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":"https://openalex.org/A5035857292","display_name":"Ziyang Xu","orcid":"https://orcid.org/0009-0008-5334-1155"},"institutions":[{"id":"https://openalex.org/I4210152533","display_name":"Lanzhou University of Finance and Economics","ror":"https://ror.org/04v7yv031","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210152533"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Ziyang Xu","raw_affiliation_strings":["School of Mathematics and Statistics, Lanzhou University, Lanzhou, China"],"affiliations":[{"raw_affiliation_string":"School of Mathematics and Statistics, Lanzhou University, Lanzhou, China","institution_ids":["https://openalex.org/I4210152533"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100770290","display_name":"Haitian Zhong","orcid":"https://orcid.org/0009-0002-4741-3411"},"institutions":[{"id":"https://openalex.org/I76214153","display_name":"Lanzhou University","ror":"https://ror.org/01mkqqe32","country_code":"CN","type":"education","lineage":["https://openalex.org/I76214153"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Haitian Zhong","raw_affiliation_strings":["Cuiying Honors College, Lanzhou University, Lanzhou, China"],"affiliations":[{"raw_affiliation_string":"Cuiying Honors College, Lanzhou University, Lanzhou, China","institution_ids":["https://openalex.org/I76214153"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101670131","display_name":"Bingrui He","orcid":"https://orcid.org/0009-0000-1306-2276"},"institutions":[{"id":"https://openalex.org/I4210126065","display_name":"Shanghai Electric (China)","ror":"https://ror.org/0314qy595","country_code":"CN","type":"company","lineage":["https://openalex.org/I4210126065"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Bingrui He","raw_affiliation_strings":["Lanzhou Power Supply Company, State Grid Gansu Electric Power Company, Ltd., Lanzhou, China"],"affiliations":[{"raw_affiliation_string":"Lanzhou Power Supply Company, State Grid Gansu Electric Power Company, Ltd., Lanzhou, China","institution_ids":["https://openalex.org/I4210126065"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100425326","display_name":"Xueying Wang","orcid":"https://orcid.org/0000-0001-8979-3737"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]},{"id":"https://openalex.org/I4210124427","display_name":"City College of Dongguan University of Technology","ror":"https://ror.org/02vdh2x09","country_code":"CN","type":"education","lineage":["https://openalex.org/I2799850029","https://openalex.org/I4210124427"]}],"countries":["CN","HK"],"is_corresponding":false,"raw_author_name":"Xueying Wang","raw_affiliation_strings":["Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong","Department of Computer Science, City University of Hong Kong (Dongguan), Dongguan, China","Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong SAR"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong","institution_ids":["https://openalex.org/I168719708"]},{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong (Dongguan), Dongguan, China","institution_ids":["https://openalex.org/I4210124427","https://openalex.org/I168719708"]},{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong SAR","institution_ids":["https://openalex.org/I168719708"]}]},{"author_position":"last","author":{"id":null,"display_name":"Tianchi Lu","orcid":"https://orcid.org/0009-0004-0193-8479"},"institutions":[{"id":"https://openalex.org/I168719708","display_name":"City University of Hong Kong","ror":"https://ror.org/03q8dnn23","country_code":"HK","type":"education","lineage":["https://openalex.org/I168719708"]},{"id":"https://openalex.org/I4210152533","display_name":"Lanzhou University of Finance and Economics","ror":"https://ror.org/04v7yv031","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210152533"]}],"countries":["CN","HK"],"is_corresponding":false,"raw_author_name":"Tianchi Lu","raw_affiliation_strings":["Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong","School of Mathematics and Statistics, Lanzhou University, Lanzhou, China","Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong SAR","Suzhou Xuying Technology Co., Ltd., Suzhou, China"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong","institution_ids":["https://openalex.org/I168719708"]},{"raw_affiliation_string":"School of Mathematics and Statistics, Lanzhou University, Lanzhou, China","institution_ids":["https://openalex.org/I4210152533"]},{"raw_affiliation_string":"Department of Computer Science, City University of Hong Kong, Kowloon, Hong Kong SAR","institution_ids":["https://openalex.org/I168719708"]},{"raw_affiliation_string":"Suzhou Xuying Technology Co., Ltd., Suzhou, China","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5035857292"],"corresponding_institution_ids":["https://openalex.org/I4210152533"],"apc_list":null,"apc_paid":null,"fwci":3.1703,"has_fulltext":false,"cited_by_count":14,"citation_normalized_percentile":{"value":0.92064559,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":99},"biblio":{"volume":"28","issue":"6","first_page":"3762","last_page":"3771"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9995999932289124,"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":0.9976999759674072,"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/overfitting","display_name":"Overfitting","score":0.7199367880821228},{"id":"https://openalex.org/keywords/phosphorylation","display_name":"Phosphorylation","score":0.6776679754257202},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6660699248313904},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.6262021064758301},{"id":"https://openalex.org/keywords/convolutional-neural-network","display_name":"Convolutional neural network","score":0.5348061323165894},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.518814742565155},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.505233108997345},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.4863649010658264},{"id":"https://openalex.org/keywords/protein-phosphorylation","display_name":"Protein phosphorylation","score":0.4198872148990631},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.4181840419769287},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.38042646646499634},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.280012845993042},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2613307535648346},{"id":"https://openalex.org/keywords/protein-kinase-a","display_name":"Protein kinase A","score":0.1431492269039154},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.13076022267341614},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.12837418913841248}],"concepts":[{"id":"https://openalex.org/C22019652","wikidata":"https://www.wikidata.org/wiki/Q331309","display_name":"Overfitting","level":3,"score":0.7199367880821228},{"id":"https://openalex.org/C11960822","wikidata":"https://www.wikidata.org/wiki/Q242736","display_name":"Phosphorylation","level":2,"score":0.6776679754257202},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6660699248313904},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.6262021064758301},{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.5348061323165894},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.518814742565155},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.505233108997345},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.4863649010658264},{"id":"https://openalex.org/C87325107","wikidata":"https://www.wikidata.org/wiki/Q7251493","display_name":"Protein phosphorylation","level":4,"score":0.4198872148990631},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.4181840419769287},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.38042646646499634},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.280012845993042},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2613307535648346},{"id":"https://openalex.org/C97029542","wikidata":"https://www.wikidata.org/wiki/Q281417","display_name":"Protein kinase A","level":3,"score":0.1431492269039154},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.13076022267341614},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.12837418913841248},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D000072283","descriptor_name":"A549 Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000072283","descriptor_name":"A549 Cells","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":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":"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":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","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":"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":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010766","descriptor_name":"Phosphorylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010766","descriptor_name":"Phosphorylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010766","descriptor_name":"Phosphorylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010766","descriptor_name":"Phosphorylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D010766","descriptor_name":"Phosphorylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010766","descriptor_name":"Phosphorylation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D016571","descriptor_name":"Neural Networks, Computer","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":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/jbhi.2024.3377362","is_oa":false,"landing_page_url":"https://doi.org/10.1109/jbhi.2024.3377362","pdf_url":null,"source":{"id":"https://openalex.org/S2495854775","display_name":"IEEE Journal of Biomedical and Health Informatics","issn_l":"2168-2194","issn":["2168-2194","2168-2208"],"is_oa":false,"is_in_doaj":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Journal of Biomedical and Health Informatics","raw_type":"journal-article"},{"id":"pmid:38483806","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38483806","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 journal of biomedical and health informatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":51,"referenced_works":["https://openalex.org/W1990783034","https://openalex.org/W2043417285","https://openalex.org/W2050039745","https://openalex.org/W2131492087","https://openalex.org/W2133564696","https://openalex.org/W2145402500","https://openalex.org/W2147800946","https://openalex.org/W2156125289","https://openalex.org/W2194775991","https://openalex.org/W2583310064","https://openalex.org/W2742750032","https://openalex.org/W2786672974","https://openalex.org/W2810225085","https://openalex.org/W2896457183","https://openalex.org/W2902652978","https://openalex.org/W2903682118","https://openalex.org/W2906946803","https://openalex.org/W2964686805","https://openalex.org/W3011725683","https://openalex.org/W3020440546","https://openalex.org/W3020511645","https://openalex.org/W3047880613","https://openalex.org/W3048086963","https://openalex.org/W3081382462","https://openalex.org/W3092403777","https://openalex.org/W3096599651","https://openalex.org/W3101668228","https://openalex.org/W3109351054","https://openalex.org/W3119003488","https://openalex.org/W3128571690","https://openalex.org/W3152942277","https://openalex.org/W3154372950","https://openalex.org/W3164698295","https://openalex.org/W3173360330","https://openalex.org/W3177500196","https://openalex.org/W3177828909","https://openalex.org/W3187581192","https://openalex.org/W3216108314","https://openalex.org/W4281291878","https://openalex.org/W4283729532","https://openalex.org/W4310601281","https://openalex.org/W4362657509","https://openalex.org/W4365511327","https://openalex.org/W4385245566","https://openalex.org/W6637373629","https://openalex.org/W6679434410","https://openalex.org/W6684191040","https://openalex.org/W6732958910","https://openalex.org/W6748816842","https://openalex.org/W6766978945","https://openalex.org/W6782534648"],"related_works":["https://openalex.org/W3099765033","https://openalex.org/W4226493464","https://openalex.org/W4312417841","https://openalex.org/W3133861977","https://openalex.org/W2352214813","https://openalex.org/W2951211570","https://openalex.org/W3103566983","https://openalex.org/W2491608603","https://openalex.org/W3029198973","https://openalex.org/W941583161"],"abstract_inverted_index":{"Phosphorylation":[0],"is":[1,28,101,147],"pivotal":[2],"in":[3,13,178,198],"numerous":[4],"fundamental":[5],"cellular":[6],"processes":[7],"and":[8,16,37,82,90,118,123,139,160,170],"plays":[9],"a":[10,56,185],"significant":[11],"role":[12],"the":[14,32,44,62,85,102,131,154],"onset":[15],"progression":[17],"of":[18,24,46,64,80,87,136,156,175,201],"various":[19],"diseases.":[20],"The":[21,173],"accurate":[22],"identification":[23,63,86],"these":[25],"phosphorylation":[26,65],"sites":[27],"crucial":[29],"for":[30,61,84,167,188],"unraveling":[31],"molecular":[33],"mechanisms":[34],"within":[35],"cells":[36],"during":[38],"viral":[39],"infections,":[40],"potentially":[41],"leading":[42],"to":[43,104,112,120,182],"discovery":[45],"novel":[47],"therapeutic":[48],"targets.":[49],"In":[50],"this":[51,113,202],"study,":[52],"we":[53],"develop":[54],"PTransIPs,":[55],"new":[57],"deep":[58],"learning":[59],"framework":[60,187],"sites.":[66],"Independent":[67],"testing":[68],"results":[69],"demonstrate":[70],"that":[71],"PTransIPs":[72,94,100,146,179],"outperforms":[73],"existing":[74],"state-of-the-art":[75],"(SOTA)":[76],"methods,":[77],"achieving":[78],"AUCs":[79],"0.9232":[81],"0.9660":[83],"phosphorylated":[88],"S/T":[89],"Y":[91],"sites,":[92],"respectively.":[93],"contributes":[95],"from":[96],"three":[97],"aspects.":[98],"1)":[99],"first":[103],"apply":[105],"protein":[106],"pre-trained":[107],"language":[108],"model":[109,143,168],"(PLM)":[110],"embeddings":[111],"task.":[114],"It":[115],"utilizes":[116],"ProtTrans":[117],"EMBER2":[119],"extract":[121],"sequence":[122],"structure":[124],"embeddings,":[125],"respectively,":[126],"as":[127,184],"additional":[128],"inputs":[129],"into":[130],"model,":[132],"effectively":[133],"addressing":[134],"issues":[135],"dataset":[137],"size":[138],"overfitting,":[140],"thus":[141],"enhancing":[142],"performance;":[144],"2)":[145],"based":[148],"on":[149],"Transformer":[150],"architecture,":[151],"optimized":[152],"through":[153],"integration":[155],"convolutional":[157],"neural":[158],"networks":[159],"TIM":[161],"loss":[162],"function,":[163],"providing":[164],"practical":[165],"insights":[166],"design":[169],"training;":[171],"3)":[172],"encoding":[174],"amino":[176],"acids":[177],"enables":[180],"it":[181],"serve":[183],"universal":[186],"other":[189],"peptide":[190],"bioactivity":[191],"tasks,":[192],"with":[193],"its":[194],"excellent":[195],"performance":[196],"shown":[197],"extended":[199],"experiments":[200],"paper.":[203]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":4}],"updated_date":"2026-04-16T08:26:57.006410","created_date":"2025-10-10T00:00:00"}