{"id":"https://openalex.org/W2289481940","doi":"https://doi.org/10.1142/s0219720015420056","title":"A novel network-based computational method to predict protein phosphorylation on tyrosine sites","display_name":"A novel network-based computational method to predict protein phosphorylation on tyrosine sites","publication_year":2015,"publication_date":"2015-11-23","ids":{"openalex":"https://openalex.org/W2289481940","doi":"https://doi.org/10.1142/s0219720015420056","mag":"2289481940","pmid":"https://pubmed.ncbi.nlm.nih.gov/26781824"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720015420056","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720015420056","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","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/A5101458598","display_name":"Binghua Wang","orcid":"https://orcid.org/0000-0001-9345-7568"},"institutions":[{"id":"https://openalex.org/I126520041","display_name":"University of Science and Technology of China","ror":"https://ror.org/04c4dkn09","country_code":"CN","type":"education","lineage":["https://openalex.org/I126520041","https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Binghua Wang","raw_affiliation_strings":["School of Information Science and Technology, University of Science and Technology of China, Hefei 230027, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Science and Technology, University of Science and Technology of China, Hefei 230027, China","institution_ids":["https://openalex.org/I126520041"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100376897","display_name":"Minghui Wang","orcid":"https://orcid.org/0000-0002-0181-8467"},"institutions":[{"id":"https://openalex.org/I126520041","display_name":"University of Science and Technology of China","ror":"https://ror.org/04c4dkn09","country_code":"CN","type":"education","lineage":["https://openalex.org/I126520041","https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Minghui Wang","raw_affiliation_strings":["Centers for Biomedical Engineering, University of Science and Technology of China, Hefei 230027, China","School of Information Science and Technology, University of Science and Technology of China, Hefei 230027, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centers for Biomedical Engineering, University of Science and Technology of China, Hefei 230027, China","institution_ids":["https://openalex.org/I126520041"]},{"raw_affiliation_string":"School of Information Science and Technology, University of Science and Technology of China, Hefei 230027, China","institution_ids":["https://openalex.org/I126520041"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101476541","display_name":"Yujie Jiang","orcid":"https://orcid.org/0000-0003-2199-238X"},"institutions":[{"id":"https://openalex.org/I126520041","display_name":"University of Science and Technology of China","ror":"https://ror.org/04c4dkn09","country_code":"CN","type":"education","lineage":["https://openalex.org/I126520041","https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yujie Jiang","raw_affiliation_strings":["School of Information Science and Technology, University of Science and Technology of China, Hefei 230027, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Science and Technology, University of Science and Technology of China, Hefei 230027, China","institution_ids":["https://openalex.org/I126520041"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100732036","display_name":"Dongdong Sun","orcid":"https://orcid.org/0000-0002-9077-1866"},"institutions":[{"id":"https://openalex.org/I126520041","display_name":"University of Science and Technology of China","ror":"https://ror.org/04c4dkn09","country_code":"CN","type":"education","lineage":["https://openalex.org/I126520041","https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dongdong Sun","raw_affiliation_strings":["School of Information Science and Technology, University of Science and Technology of China, Hefei 230027, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Science and Technology, University of Science and Technology of China, Hefei 230027, China","institution_ids":["https://openalex.org/I126520041"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5028516138","display_name":"Xiaoyi Xu","orcid":"https://orcid.org/0000-0001-8432-6291"},"institutions":[{"id":"https://openalex.org/I126520041","display_name":"University of Science and Technology of China","ror":"https://ror.org/04c4dkn09","country_code":"CN","type":"education","lineage":["https://openalex.org/I126520041","https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiaoyi Xu","raw_affiliation_strings":["School of Information Science and Technology, University of Science and Technology of China, Hefei 230027, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Information Science and Technology, University of Science and Technology of China, Hefei 230027, China","institution_ids":["https://openalex.org/I126520041"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5100376897"],"corresponding_institution_ids":["https://openalex.org/I126520041"],"apc_list":null,"apc_paid":null,"fwci":0.739,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.72435213,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"13","issue":"06","first_page":"1542005","last_page":"1542005"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9988999962806702,"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/T10602","display_name":"Glycosylation and Glycoproteins Research","score":0.9983999729156494,"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":0.6184404492378235},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5737345814704895},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5342686772346497},{"id":"https://openalex.org/keywords/tyrosine","display_name":"Tyrosine","score":0.5287235379219055},{"id":"https://openalex.org/keywords/protein-phosphorylation","display_name":"Protein phosphorylation","score":0.4407830834388733},{"id":"https://openalex.org/keywords/tyrosine-phosphorylation","display_name":"Tyrosine phosphorylation","score":0.4176395535469055},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.37779688835144043},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.3446803689002991},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.33729156851768494},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.32838261127471924}],"concepts":[{"id":"https://openalex.org/C11960822","wikidata":"https://www.wikidata.org/wiki/Q242736","display_name":"Phosphorylation","level":2,"score":0.6184404492378235},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5737345814704895},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5342686772346497},{"id":"https://openalex.org/C2776165026","wikidata":"https://www.wikidata.org/wiki/Q188017","display_name":"Tyrosine","level":2,"score":0.5287235379219055},{"id":"https://openalex.org/C87325107","wikidata":"https://www.wikidata.org/wiki/Q7251493","display_name":"Protein phosphorylation","level":4,"score":0.4407830834388733},{"id":"https://openalex.org/C2777553839","wikidata":"https://www.wikidata.org/wiki/Q14330986","display_name":"Tyrosine phosphorylation","level":3,"score":0.4176395535469055},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.37779688835144043},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.3446803689002991},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.33729156851768494},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.32838261127471924},{"id":"https://openalex.org/C97029542","wikidata":"https://www.wikidata.org/wiki/Q281417","display_name":"Protein kinase A","level":3,"score":0.0}],"mesh":[{"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":"D011494","descriptor_name":"Protein Kinases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011494","descriptor_name":"Protein Kinases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011494","descriptor_name":"Protein Kinases","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011499","descriptor_name":"Protein Processing, Post-Translational","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014443","descriptor_name":"Tyrosine","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014443","descriptor_name":"Tyrosine","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014443","descriptor_name":"Tyrosine","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1142/s0219720015420056","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720015420056","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:26781824","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26781824","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":"Journal of bioinformatics and computational biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.6200000047683716,"display_name":"Peace, Justice and strong institutions","id":"https://metadata.un.org/sdg/16"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320309070","display_name":"Brown University","ror":"https://ror.org/05gq02987"},{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":37,"referenced_works":["https://openalex.org/W1570204439","https://openalex.org/W1893639437","https://openalex.org/W1968129408","https://openalex.org/W1972378799","https://openalex.org/W1982511335","https://openalex.org/W1984084871","https://openalex.org/W1993450321","https://openalex.org/W1995240259","https://openalex.org/W1995989434","https://openalex.org/W2003878905","https://openalex.org/W2008491586","https://openalex.org/W2012828386","https://openalex.org/W2018797206","https://openalex.org/W2022274575","https://openalex.org/W2022446852","https://openalex.org/W2030205108","https://openalex.org/W2033500845","https://openalex.org/W2038163496","https://openalex.org/W2052652433","https://openalex.org/W2075184904","https://openalex.org/W2079056345","https://openalex.org/W2091787667","https://openalex.org/W2103404876","https://openalex.org/W2119220491","https://openalex.org/W2122109577","https://openalex.org/W2129137060","https://openalex.org/W2130277691","https://openalex.org/W2132039382","https://openalex.org/W2148853951","https://openalex.org/W2152970345","https://openalex.org/W2153635508","https://openalex.org/W2154390027","https://openalex.org/W2154718035","https://openalex.org/W2158577092","https://openalex.org/W2161062388","https://openalex.org/W2192273339","https://openalex.org/W2546354416"],"related_works":["https://openalex.org/W2072299589","https://openalex.org/W2022006194","https://openalex.org/W2352214813","https://openalex.org/W2403922722","https://openalex.org/W1898795080","https://openalex.org/W2491608603","https://openalex.org/W2505862120","https://openalex.org/W4223412920","https://openalex.org/W1987307749","https://openalex.org/W2030033027"],"abstract_inverted_index":{"Phosphorylation":[0],"plays":[1],"a":[2,7,30,89],"great":[3],"role":[4],"in":[5,55,83,152],"regulating":[6],"variety":[8],"of":[9,15,32,39,64,108,127,149],"cellular":[10],"processes":[11],"and":[12,46,140],"the":[13,23,51,68,77,106,109,124,147],"identification":[14],"tyrosine":[16,52,100,154],"phosphorylation":[17],"sites":[18,53],"is":[19,159],"fundamental":[20],"for":[21],"understanding":[22],"post-translational":[24],"modification":[25,70],"(PTM)":[26],"regulation":[27],"processes.":[28],"Although":[29],"lot":[31],"computational":[33,92,118],"methods":[34,137],"have":[35],"been":[36],"developed,":[37],"most":[38],"them":[40],"only":[41],"concern":[42],"local":[43],"sequence":[44],"information":[45],"few":[47],"studies":[48],"focus":[49],"on":[50,67],"with":[54,115,134],"situ":[56,84],"PTM":[57,65,85],"information,":[58,86],"which":[59],"refers":[60],"to":[61,98,104],"different":[62],"types":[63],"occurring":[66],"same":[69],"site.":[71],"In":[72,102],"this":[73],"study,":[74],"by":[75],"constructing":[76],"site-modification":[78,94,150],"network":[79,151],"that":[80],"efficiently":[81],"incorporates":[82],"we":[87,112,130],"introduce":[88],"novel":[90],"network-based":[91,95,117],"method,":[93,111],"inference":[96],"(SMNBI)":[97],"predict":[99],"phosphorylation.":[101,155],"order":[103],"verify":[105],"effectiveness":[107],"proposed":[110,157],"compare":[113,132],"it":[114],"other":[116,135],"methods.":[119],"The":[120,144,156],"results":[121],"clearly":[122],"show":[123],"superior":[125],"performance":[126],"SMNBI.":[128],"Besides,":[129],"extensively":[131],"SMNBI":[133],"sequence-based":[136],"including":[138],"SVM":[139],"Bayesian":[141],"decision":[142],"theory.":[143],"evaluation":[145],"demonstrates":[146],"power":[148],"predicting":[153],"method":[158],"freely":[160],"available":[161],"at":[162],"http://bioinformatics.ustc.edu.cn/smnbi/.":[163]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
