{"id":"https://openalex.org/W4390415411","doi":"https://doi.org/10.1093/bib/bbad480","title":"VIPpred: a novel model for predicting variant impact on phosphorylation events driving carcinogenesis","display_name":"VIPpred: a novel model for predicting variant impact on phosphorylation events driving carcinogenesis","publication_year":2023,"publication_date":"2023-11-22","ids":{"openalex":"https://openalex.org/W4390415411","doi":"https://doi.org/10.1093/bib/bbad480","pmid":"https://pubmed.ncbi.nlm.nih.gov/38156562"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad480","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad480","pdf_url":"https://academic.oup.com/bib/article-pdf/25/1/bbad480/54920768/bbad480.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bib/article-pdf/25/1/bbad480/54920768/bbad480.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102405133","display_name":"Xiaofeng Xu","orcid":null},"institutions":[{"id":"https://openalex.org/I183519381","display_name":"Capital Medical University","ror":"https://ror.org/013xs5b60","country_code":"CN","type":"education","lineage":["https://openalex.org/I183519381"]},{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xiaofeng Xu","raw_affiliation_strings":["Department of Medical Bioinformatics , School of Basic Medical Sciences, , Beijing 100191 , China","Peking University Health Science Center , School of Basic Medical Sciences, , Beijing 100191 , China","Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China"],"affiliations":[{"raw_affiliation_string":"Department of Medical Bioinformatics , School of Basic Medical Sciences, , Beijing 100191 , China","institution_ids":["https://openalex.org/I183519381"]},{"raw_affiliation_string":"Peking University Health Science Center , School of Basic Medical Sciences, , Beijing 100191 , China","institution_ids":["https://openalex.org/I20231570"]},{"raw_affiliation_string":"Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103240178","display_name":"Y Li","orcid":"https://orcid.org/0009-0009-5236-6745"},"institutions":[{"id":"https://openalex.org/I9086337","display_name":"Taiyuan University of Technology","ror":"https://ror.org/03kv08d37","country_code":"CN","type":"education","lineage":["https://openalex.org/I9086337"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ying Li","raw_affiliation_strings":["Department of Computer Science and Technology, Taiyuan University of Technology , Taiyuan, Shanxi 030024 , China"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Technology, Taiyuan University of Technology , Taiyuan, Shanxi 030024 , China","institution_ids":["https://openalex.org/I9086337"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054171297","display_name":"Taoyu Chen","orcid":"https://orcid.org/0000-0002-8966-1264"},"institutions":[{"id":"https://openalex.org/I183519381","display_name":"Capital Medical University","ror":"https://ror.org/013xs5b60","country_code":"CN","type":"education","lineage":["https://openalex.org/I183519381"]},{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Taoyu Chen","raw_affiliation_strings":["Department of Medical Bioinformatics , School of Basic Medical Sciences, , Beijing 100191 , China","Peking University Health Science Center , School of Basic Medical Sciences, , Beijing 100191 , China","Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China"],"affiliations":[{"raw_affiliation_string":"Department of Medical Bioinformatics , School of Basic Medical Sciences, , Beijing 100191 , China","institution_ids":["https://openalex.org/I183519381"]},{"raw_affiliation_string":"Peking University Health Science Center , School of Basic Medical Sciences, , Beijing 100191 , China","institution_ids":["https://openalex.org/I20231570"]},{"raw_affiliation_string":"Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062769133","display_name":"Chao Hou","orcid":"https://orcid.org/0000-0003-4806-7637"},"institutions":[{"id":"https://openalex.org/I183519381","display_name":"Capital Medical University","ror":"https://ror.org/013xs5b60","country_code":"CN","type":"education","lineage":["https://openalex.org/I183519381"]},{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chao Hou","raw_affiliation_strings":["Department of Medical Bioinformatics , School of Basic Medical Sciences, , Beijing 100191 , China","Peking University Health Science Center , School of Basic Medical Sciences, , Beijing 100191 , China","Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China"],"affiliations":[{"raw_affiliation_string":"Department of Medical Bioinformatics , School of Basic Medical Sciences, , Beijing 100191 , China","institution_ids":["https://openalex.org/I183519381"]},{"raw_affiliation_string":"Peking University Health Science Center , School of Basic Medical Sciences, , Beijing 100191 , China","institution_ids":["https://openalex.org/I20231570"]},{"raw_affiliation_string":"Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101352623","display_name":"Liang Yang","orcid":null},"institutions":[{"id":"https://openalex.org/I183519381","display_name":"Capital Medical University","ror":"https://ror.org/013xs5b60","country_code":"CN","type":"education","lineage":["https://openalex.org/I183519381"]},{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Liang Yang","raw_affiliation_strings":["Department of Medical Bioinformatics , School of Basic Medical Sciences, , Beijing 100191 , China","Peking University Health Science Center , School of Basic Medical Sciences, , Beijing 100191 , China","Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China"],"affiliations":[{"raw_affiliation_string":"Department of Medical Bioinformatics , School of Basic Medical Sciences, , Beijing 100191 , China","institution_ids":["https://openalex.org/I183519381"]},{"raw_affiliation_string":"Peking University Health Science Center , School of Basic Medical Sciences, , Beijing 100191 , China","institution_ids":["https://openalex.org/I20231570"]},{"raw_affiliation_string":"Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046307619","display_name":"Peiyu Zhu","orcid":null},"institutions":[{"id":"https://openalex.org/I183519381","display_name":"Capital Medical University","ror":"https://ror.org/013xs5b60","country_code":"CN","type":"education","lineage":["https://openalex.org/I183519381"]},{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Peiyu Zhu","raw_affiliation_strings":["Department of Medical Bioinformatics , School of Basic Medical Sciences, , Beijing 100191 , China","Peking University Health Science Center , School of Basic Medical Sciences, , Beijing 100191 , China","Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China"],"affiliations":[{"raw_affiliation_string":"Department of Medical Bioinformatics , School of Basic Medical Sciences, , Beijing 100191 , China","institution_ids":["https://openalex.org/I183519381"]},{"raw_affiliation_string":"Peking University Health Science Center , School of Basic Medical Sciences, , Beijing 100191 , China","institution_ids":["https://openalex.org/I20231570"]},{"raw_affiliation_string":"Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100388020","display_name":"Yi Zhang","orcid":"https://orcid.org/0000-0001-5388-1276"},"institutions":[{"id":"https://openalex.org/I183519381","display_name":"Capital Medical University","ror":"https://ror.org/013xs5b60","country_code":"CN","type":"education","lineage":["https://openalex.org/I183519381"]},{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yi Zhang","raw_affiliation_strings":["Department of Medical Bioinformatics , School of Basic Medical Sciences, , Beijing 100191 , China","Peking University Health Science Center , School of Basic Medical Sciences, , Beijing 100191 , China","Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China"],"affiliations":[{"raw_affiliation_string":"Department of Medical Bioinformatics , School of Basic Medical Sciences, , Beijing 100191 , China","institution_ids":["https://openalex.org/I183519381"]},{"raw_affiliation_string":"Peking University Health Science Center , School of Basic Medical Sciences, , Beijing 100191 , China","institution_ids":["https://openalex.org/I20231570"]},{"raw_affiliation_string":"Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100416506","display_name":"Tingting Li","orcid":"https://orcid.org/0000-0003-4266-0317"},"institutions":[{"id":"https://openalex.org/I183519381","display_name":"Capital Medical University","ror":"https://ror.org/013xs5b60","country_code":"CN","type":"education","lineage":["https://openalex.org/I183519381"]},{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]},{"id":"https://openalex.org/I271893122","display_name":"National Health and Family Planning Commission","ror":"https://ror.org/052eegr76","country_code":"CN","type":"government","lineage":["https://openalex.org/I271893122","https://openalex.org/I4210127390"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tingting Li","raw_affiliation_strings":["Department of Medical Bioinformatics , School of Basic Medical Sciences, , Beijing 100191 , China","Key Laboratory for Neuroscience , Ministry of Education/National Health Commission of China, , Beijing 100191 , China","Peking University , Ministry of Education/National Health Commission of China, , Beijing 100191 , China","Peking University Health Science Center , School of Basic Medical Sciences, , Beijing 100191 , China","Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, Peking University, Beijing 100191, China","Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China"],"affiliations":[{"raw_affiliation_string":"Department of Medical Bioinformatics , School of Basic Medical Sciences, , Beijing 100191 , China","institution_ids":["https://openalex.org/I183519381"]},{"raw_affiliation_string":"Key Laboratory for Neuroscience , Ministry of Education/National Health Commission of China, , Beijing 100191 , China","institution_ids":["https://openalex.org/I271893122"]},{"raw_affiliation_string":"Peking University , Ministry of Education/National Health Commission of China, , Beijing 100191 , China","institution_ids":["https://openalex.org/I271893122","https://openalex.org/I20231570"]},{"raw_affiliation_string":"Peking University Health Science Center , School of Basic Medical Sciences, , Beijing 100191 , China","institution_ids":["https://openalex.org/I20231570"]},{"raw_affiliation_string":"Key Laboratory for Neuroscience, Ministry of Education/National Health Commission of China, Peking University, Beijing 100191, China","institution_ids":["https://openalex.org/I271893122","https://openalex.org/I20231570"]},{"raw_affiliation_string":"Department of Medical Bioinformatics, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China","institution_ids":["https://openalex.org/I20231570"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5102405133"],"corresponding_institution_ids":["https://openalex.org/I183519381","https://openalex.org/I20231570"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.9436,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.79552225,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"25","issue":"1","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9976000189781189,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9976000189781189,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.9968000054359436,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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":0.9968000054359436,"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/phosphorylation","display_name":"Phosphorylation","score":0.7886536121368408},{"id":"https://openalex.org/keywords/carcinogenesis","display_name":"Carcinogenesis","score":0.7141123414039612},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5371935963630676},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.5131078958511353},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5048344731330872},{"id":"https://openalex.org/keywords/protein-phosphorylation","display_name":"Protein phosphorylation","score":0.47465163469314575},{"id":"https://openalex.org/keywords/suppressor","display_name":"Suppressor","score":0.43963152170181274},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4251061677932739},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3885774612426758},{"id":"https://openalex.org/keywords/cancer-research","display_name":"Cancer research","score":0.3661651313304901},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.24005848169326782},{"id":"https://openalex.org/keywords/protein-kinase-a","display_name":"Protein kinase A","score":0.08228158950805664}],"concepts":[{"id":"https://openalex.org/C11960822","wikidata":"https://www.wikidata.org/wiki/Q242736","display_name":"Phosphorylation","level":2,"score":0.7886536121368408},{"id":"https://openalex.org/C555283112","wikidata":"https://www.wikidata.org/wiki/Q1637543","display_name":"Carcinogenesis","level":3,"score":0.7141123414039612},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5371935963630676},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.5131078958511353},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5048344731330872},{"id":"https://openalex.org/C87325107","wikidata":"https://www.wikidata.org/wiki/Q7251493","display_name":"Protein phosphorylation","level":4,"score":0.47465163469314575},{"id":"https://openalex.org/C179185449","wikidata":"https://www.wikidata.org/wiki/Q219699","display_name":"Suppressor","level":3,"score":0.43963152170181274},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4251061677932739},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3885774612426758},{"id":"https://openalex.org/C502942594","wikidata":"https://www.wikidata.org/wiki/Q3421914","display_name":"Cancer research","level":1,"score":0.3661651313304901},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.24005848169326782},{"id":"https://openalex.org/C97029542","wikidata":"https://www.wikidata.org/wiki/Q281417","display_name":"Protein kinase A","level":3,"score":0.08228158950805664}],"mesh":[{"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":"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":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D009857","descriptor_name":"Oncogenes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009857","descriptor_name":"Oncogenes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009857","descriptor_name":"Oncogenes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009857","descriptor_name":"Oncogenes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009857","descriptor_name":"Oncogenes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009857","descriptor_name":"Oncogenes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009857","descriptor_name":"Oncogenes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009857","descriptor_name":"Oncogenes","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":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":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":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":false},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D040901","descriptor_name":"Proteomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D063646","descriptor_name":"Carcinogenesis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D063646","descriptor_name":"Carcinogenesis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D063646","descriptor_name":"Carcinogenesis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D063646","descriptor_name":"Carcinogenesis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D063646","descriptor_name":"Carcinogenesis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D063646","descriptor_name":"Carcinogenesis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D063646","descriptor_name":"Carcinogenesis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D063646","descriptor_name":"Carcinogenesis","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbad480","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad480","pdf_url":"https://academic.oup.com/bib/article-pdf/25/1/bbad480/54920768/bbad480.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38156562","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38156562","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10782907","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10782907","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10782907/pdf/bbad480.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbad480","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbad480","pdf_url":"https://academic.oup.com/bib/article-pdf/25/1/bbad480/54920768/bbad480.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.6899999976158142,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G1121271761","display_name":null,"funder_award_id":"Program","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2087396116","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3085993365","display_name":null,"funder_award_id":"(Grant No.","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3317480652","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G391238517","display_name":null,"funder_award_id":", and","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G547477281","display_name":null,"funder_award_id":"20210302123092","funder_id":"https://openalex.org/F4320326179","funder_display_name":"Shanxi Province Science Foundation for Youths"},{"id":"https://openalex.org/G5797066792","display_name":null,"funder_award_id":"2021YFF1200900","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G5881942141","display_name":null,"funder_award_id":"202103","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5994120800","display_name":null,"funder_award_id":"Natural","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6258415954","display_name":null,"funder_award_id":"Chinese","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6664801711","display_name":null,"funder_award_id":"32070666","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7657054411","display_name":null,"funder_award_id":"2018YFA0507504","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G7726157001","display_name":null,"funder_award_id":"Grant No.","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/F4320321133","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35"},{"id":"https://openalex.org/F4320324787","display_name":"Peking University","ror":"https://ror.org/02v51f717"},{"id":"https://openalex.org/F4320326179","display_name":"Shanxi Province Science Foundation for Youths","ror":null},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4390415411.pdf","grobid_xml":"https://content.openalex.org/works/W4390415411.grobid-xml"},"referenced_works_count":59,"referenced_works":["https://openalex.org/W1582734106","https://openalex.org/W1970111367","https://openalex.org/W2015556811","https://openalex.org/W2034269086","https://openalex.org/W2040942754","https://openalex.org/W2043274355","https://openalex.org/W2048280438","https://openalex.org/W2054260164","https://openalex.org/W2085037886","https://openalex.org/W2087588809","https://openalex.org/W2094036688","https://openalex.org/W2094122486","https://openalex.org/W2107889651","https://openalex.org/W2112078820","https://openalex.org/W2117692326","https://openalex.org/W2140638448","https://openalex.org/W2146913682","https://openalex.org/W2156916536","https://openalex.org/W2158485828","https://openalex.org/W2295598076","https://openalex.org/W2587708405","https://openalex.org/W2607310450","https://openalex.org/W2612690371","https://openalex.org/W2767377392","https://openalex.org/W2796153225","https://openalex.org/W2796408191","https://openalex.org/W2806543441","https://openalex.org/W2898789672","https://openalex.org/W2900629010","https://openalex.org/W2907677104","https://openalex.org/W2940627982","https://openalex.org/W2949528721","https://openalex.org/W2956732318","https://openalex.org/W2963066819","https://openalex.org/W2977723521","https://openalex.org/W2982402173","https://openalex.org/W2990857223","https://openalex.org/W2994464657","https://openalex.org/W3006211741","https://openalex.org/W3007245269","https://openalex.org/W3041397352","https://openalex.org/W3043316508","https://openalex.org/W3047825284","https://openalex.org/W3093532012","https://openalex.org/W3095435122","https://openalex.org/W3099641263","https://openalex.org/W3101645555","https://openalex.org/W3107322429","https://openalex.org/W3118409923","https://openalex.org/W3119681293","https://openalex.org/W3131527464","https://openalex.org/W3153473677","https://openalex.org/W3177828909","https://openalex.org/W3188077199","https://openalex.org/W3199725740","https://openalex.org/W3204360192","https://openalex.org/W3213184710","https://openalex.org/W4285388238","https://openalex.org/W4309506674"],"related_works":["https://openalex.org/W2433485935","https://openalex.org/W2352214813","https://openalex.org/W25001789","https://openalex.org/W2491608603","https://openalex.org/W4223412920","https://openalex.org/W2505862120","https://openalex.org/W1973530967","https://openalex.org/W2087084848","https://openalex.org/W2989833656","https://openalex.org/W1970474015"],"abstract_inverted_index":{"Disrupted":[0],"protein":[1,146,154],"phosphorylation":[2,21,53,140],"due":[3,27],"to":[4,28,48,69,143],"genetic":[5],"variation":[6],"is":[7],"a":[8,99,118],"widespread":[9],"phenomenon":[10],"that":[11,107,136],"triggers":[12],"oncogenic":[13],"transformation":[14],"of":[15,34,37,60,121,148],"healthy":[16],"cells.":[17],"However,":[18],"few":[19],"relevant":[20],"disruption":[22],"events":[23,64,92,141],"have":[24],"been":[25],"verified":[26],"limited":[29],"biological":[30],"experimental":[31],"methods.":[32],"Because":[33],"the":[35,58,83,145],"lack":[36],"reliable":[38],"benchmark":[39],"datasets,":[40],"current":[41],"bioinformatics":[42],"methods":[43],"primarily":[44],"use":[45],"sequence-based":[46],"traits":[47],"study":[49],"variant":[50],"impact":[51],"on":[52],"(VIP).":[54],"Here,":[55],"we":[56,96],"increased":[57],"number":[59],"experimentally":[61],"supported":[62],"VIP":[63,91,122],"from":[65,78],"less":[66],"than":[67],"30":[68],"740":[70],"by":[71,82,104],"manually":[72],"curating":[73],"and":[74,130,150],"reanalyzing":[75],"multi-omics":[76],"data":[77],"916":[79],"patients":[80],"provided":[81,117],"Clinical":[84],"Proteomic":[85],"Tumor":[86],"Analysis":[87],"Consortium.":[88],"To":[89],"predict":[90],"in":[93,127,139],"cancer":[94,113,131,163],"cells,":[95],"developed":[97],"VIPpred,":[98],"machine":[100],"learning":[101],"method":[102,116],"characterized":[103],"multidimensional":[105],"features":[106],"exhibits":[108],"robust":[109],"performance":[110],"across":[111],"different":[112],"types.":[114],"Our":[115,156],"pan-cancer":[119],"landscape":[120],"events,":[123],"which":[124],"are":[125],"enriched":[126],"cancer-related":[128],"pathways":[129],"driver":[132],"genes.":[133],"We":[134],"found":[135],"variant-induced":[137],"increases":[138],"tend":[142],"inhibit":[144],"degradation":[147],"oncogenes":[149],"promote":[151],"tumor":[152],"suppressor":[153],"degradation.":[155],"work":[157],"provides":[158],"new":[159],"insights":[160],"into":[161],"phosphorylation-related":[162],"biology":[164],"as":[165,167],"well":[166],"novel":[168],"avenues":[169],"for":[170],"precision":[171],"therapy.":[172]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1}],"updated_date":"2026-04-13T07:58:08.660418","created_date":"2025-10-10T00:00:00"}