{"id":"https://openalex.org/W3108149956","doi":"https://doi.org/10.1371/journal.pcbi.1007578","title":"Accurate prediction of kinase-substrate networks using knowledge graphs","display_name":"Accurate prediction of kinase-substrate networks using knowledge graphs","publication_year":2020,"publication_date":"2020-12-03","ids":{"openalex":"https://openalex.org/W3108149956","doi":"https://doi.org/10.1371/journal.pcbi.1007578","mag":"3108149956","pmid":"https://pubmed.ncbi.nlm.nih.gov/33270624"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1007578","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007578","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1371/journal.pcbi.1007578","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102905135","display_name":"V\u00edt Nov\u00e1\u010dek","orcid":"https://orcid.org/0000-0003-4687-6043"},"institutions":[{"id":"https://openalex.org/I188760350","display_name":"Ollscoil na Gaillimhe \u2013 University of Galway","ror":"https://ror.org/03bea9k73","country_code":"IE","type":"education","lineage":["https://openalex.org/I188760350"]},{"id":"https://openalex.org/I21449261","display_name":"Masaryk University","ror":"https://ror.org/02j46qs45","country_code":"CZ","type":"education","lineage":["https://openalex.org/I21449261"]}],"countries":["CZ","IE"],"is_corresponding":true,"raw_author_name":"V\u00edt Nov\u00e1\u010dek","raw_affiliation_strings":["Data Science Institute, National University of Ireland Galway, Ireland","Faculty of Informatics, Masaryk University, Brno, Czech Republic"],"raw_orcid":"https://orcid.org/0000-0003-4687-6043","affiliations":[{"raw_affiliation_string":"Data Science Institute, National University of Ireland Galway, Ireland","institution_ids":["https://openalex.org/I188760350"]},{"raw_affiliation_string":"Faculty of Informatics, Masaryk University, Brno, Czech Republic","institution_ids":["https://openalex.org/I21449261"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038052597","display_name":"Gavin McGauran","orcid":"https://orcid.org/0000-0001-5427-4697"},"institutions":[{"id":"https://openalex.org/I100930933","display_name":"University College Dublin","ror":"https://ror.org/05m7pjf47","country_code":"IE","type":"education","lineage":["https://openalex.org/I100930933"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"Gavin McGauran","raw_affiliation_strings":["Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland"],"raw_orcid":"https://orcid.org/0000-0001-5427-4697","affiliations":[{"raw_affiliation_string":"Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland","institution_ids":["https://openalex.org/I100930933"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091893851","display_name":"David Matallanas","orcid":"https://orcid.org/0000-0002-2360-3141"},"institutions":[{"id":"https://openalex.org/I100930933","display_name":"University College Dublin","ror":"https://ror.org/05m7pjf47","country_code":"IE","type":"education","lineage":["https://openalex.org/I100930933"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"David Matallanas","raw_affiliation_strings":["Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland"],"raw_orcid":"https://orcid.org/0000-0002-2360-3141","affiliations":[{"raw_affiliation_string":"Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland","institution_ids":["https://openalex.org/I100930933"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042660964","display_name":"Alfonso Blanco","orcid":"https://orcid.org/0000-0003-0439-0838"},"institutions":[{"id":"https://openalex.org/I100930933","display_name":"University College Dublin","ror":"https://ror.org/05m7pjf47","country_code":"IE","type":"education","lineage":["https://openalex.org/I100930933"]},{"id":"https://openalex.org/I88155538","display_name":"Universidad de Navarra","ror":"https://ror.org/02rxc7m23","country_code":"ES","type":"education","lineage":["https://openalex.org/I88155538"]}],"countries":["ES","IE"],"is_corresponding":false,"raw_author_name":"Adri\u00e1n Vallejo Blanco","raw_affiliation_strings":["Department of Oncology, Universidad de Navarra, Pamplona, Spain","Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Oncology, Universidad de Navarra, Pamplona, Spain","institution_ids":["https://openalex.org/I88155538"]},{"raw_affiliation_string":"Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland","institution_ids":["https://openalex.org/I100930933"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016346216","display_name":"Piero Conca","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Piero Conca","raw_affiliation_strings":["Fujitsu Ireland Ltd., Co. Dublin, Ireland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Fujitsu Ireland Ltd., Co. Dublin, Ireland","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073333928","display_name":"Emir Mu\u00f1oz","orcid":"https://orcid.org/0000-0002-0089-8135"},"institutions":[{"id":"https://openalex.org/I188760350","display_name":"Ollscoil na Gaillimhe \u2013 University of Galway","ror":"https://ror.org/03bea9k73","country_code":"IE","type":"education","lineage":["https://openalex.org/I188760350"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"Emir Mu\u00f1oz","raw_affiliation_strings":["Data Science Institute, National University of Ireland Galway, Ireland","Fujitsu Ireland Ltd., Co. Dublin, Ireland"],"raw_orcid":"https://orcid.org/0000-0002-0089-8135","affiliations":[{"raw_affiliation_string":"Data Science Institute, National University of Ireland Galway, Ireland","institution_ids":["https://openalex.org/I188760350"]},{"raw_affiliation_string":"Fujitsu Ireland Ltd., Co. Dublin, Ireland","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042660358","display_name":"Luca Costabello","orcid":"https://orcid.org/0000-0002-0720-9347"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Luca Costabello","raw_affiliation_strings":["Fujitsu Ireland Ltd., Co. Dublin, Ireland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Fujitsu Ireland Ltd., Co. Dublin, Ireland","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5062494146","display_name":"Kamalesh Kanakaraj","orcid":null},"institutions":[{"id":"https://openalex.org/I188760350","display_name":"Ollscoil na Gaillimhe \u2013 University of Galway","ror":"https://ror.org/03bea9k73","country_code":"IE","type":"education","lineage":["https://openalex.org/I188760350"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"Kamalesh Kanakaraj","raw_affiliation_strings":["Data Science Institute, National University of Ireland Galway, Ireland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Data Science Institute, National University of Ireland Galway, Ireland","institution_ids":["https://openalex.org/I188760350"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103278064","display_name":"Zeeshan Nawaz","orcid":"https://orcid.org/0000-0002-8107-337X"},"institutions":[{"id":"https://openalex.org/I188760350","display_name":"Ollscoil na Gaillimhe \u2013 University of Galway","ror":"https://ror.org/03bea9k73","country_code":"IE","type":"education","lineage":["https://openalex.org/I188760350"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"Zeeshan Nawaz","raw_affiliation_strings":["Data Science Institute, National University of Ireland Galway, Ireland"],"raw_orcid":"https://orcid.org/0000-0002-8107-337X","affiliations":[{"raw_affiliation_string":"Data Science Institute, National University of Ireland Galway, Ireland","institution_ids":["https://openalex.org/I188760350"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102791364","display_name":"Brian Walsh","orcid":"https://orcid.org/0000-0002-8640-2187"},"institutions":[{"id":"https://openalex.org/I188760350","display_name":"Ollscoil na Gaillimhe \u2013 University of Galway","ror":"https://ror.org/03bea9k73","country_code":"IE","type":"education","lineage":["https://openalex.org/I188760350"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"Brian Walsh","raw_affiliation_strings":["Data Science Institute, National University of Ireland Galway, Ireland"],"raw_orcid":"https://orcid.org/0000-0002-8640-2187","affiliations":[{"raw_affiliation_string":"Data Science Institute, National University of Ireland Galway, Ireland","institution_ids":["https://openalex.org/I188760350"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051014805","display_name":"Sameh K. Mohamed","orcid":"https://orcid.org/0000-0003-2659-2406"},"institutions":[{"id":"https://openalex.org/I188760350","display_name":"Ollscoil na Gaillimhe \u2013 University of Galway","ror":"https://ror.org/03bea9k73","country_code":"IE","type":"education","lineage":["https://openalex.org/I188760350"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"Sameh K. Mohamed","raw_affiliation_strings":["Data Science Institute, National University of Ireland Galway, Ireland"],"raw_orcid":"https://orcid.org/0000-0003-2659-2406","affiliations":[{"raw_affiliation_string":"Data Science Institute, National University of Ireland Galway, Ireland","institution_ids":["https://openalex.org/I188760350"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024897727","display_name":"Pierre-Yves Vandenbussche","orcid":"https://orcid.org/0000-0003-0591-6109"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Pierre-Yves Vandenbussche","raw_affiliation_strings":["Fujitsu Ireland Ltd., Co. Dublin, Ireland"],"raw_orcid":"https://orcid.org/0000-0003-0591-6109","affiliations":[{"raw_affiliation_string":"Fujitsu Ireland Ltd., Co. Dublin, Ireland","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029812789","display_name":"Colm J. Ryan","orcid":"https://orcid.org/0000-0003-2750-9854"},"institutions":[{"id":"https://openalex.org/I100930933","display_name":"University College Dublin","ror":"https://ror.org/05m7pjf47","country_code":"IE","type":"education","lineage":["https://openalex.org/I100930933"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"Colm J. Ryan","raw_affiliation_strings":["Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland"],"raw_orcid":"https://orcid.org/0000-0003-2750-9854","affiliations":[{"raw_affiliation_string":"Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland","institution_ids":["https://openalex.org/I100930933"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036674933","display_name":"Walter K\u00f6lch","orcid":null},"institutions":[{"id":"https://openalex.org/I100930933","display_name":"University College Dublin","ror":"https://ror.org/05m7pjf47","country_code":"IE","type":"education","lineage":["https://openalex.org/I100930933"]}],"countries":["IE"],"is_corresponding":false,"raw_author_name":"Walter Kolch","raw_affiliation_strings":["Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland","School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland","Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Conway Institute of Biomolecular & Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland","institution_ids":["https://openalex.org/I100930933"]},{"raw_affiliation_string":"School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland","institution_ids":["https://openalex.org/I100930933"]},{"raw_affiliation_string":"Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland","institution_ids":["https://openalex.org/I100930933"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5077163269","display_name":"Dirk Fey","orcid":"https://orcid.org/0000-0002-5558-0167"},"institutions":[{"id":"https://openalex.org/I100930933","display_name":"University College Dublin","ror":"https://ror.org/05m7pjf47","country_code":"IE","type":"education","lineage":["https://openalex.org/I100930933"]}],"countries":["IE"],"is_corresponding":true,"raw_author_name":"Dirk Fey","raw_affiliation_strings":["School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland","Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland"],"raw_orcid":"https://orcid.org/0000-0002-5558-0167","affiliations":[{"raw_affiliation_string":"School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland","institution_ids":["https://openalex.org/I100930933"]},{"raw_affiliation_string":"Systems Biology Ireland, University College Dublin, Belfield, Dublin 4, Ireland","institution_ids":["https://openalex.org/I100930933"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":15,"corresponding_author_ids":["https://openalex.org/A5077163269","https://openalex.org/A5102905135"],"corresponding_institution_ids":["https://openalex.org/I100930933","https://openalex.org/I188760350","https://openalex.org/I21449261"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":1.5883,"has_fulltext":false,"cited_by_count":29,"citation_normalized_percentile":{"value":0.83689399,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"16","issue":"12","first_page":"e1007578","last_page":"e1007578"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998999834060669,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998999834060669,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9977999925613403,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9976999759674072,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/kinome","display_name":"Kinome","score":0.9655468463897705},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7090631723403931},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.6166324019432068},{"id":"https://openalex.org/keywords/kinase","display_name":"Kinase","score":0.45483487844467163},{"id":"https://openalex.org/keywords/phosphorylation","display_name":"Phosphorylation","score":0.42982199788093567},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.40348100662231445},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3373011648654938},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22261613607406616},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.11885792016983032}],"concepts":[{"id":"https://openalex.org/C54174078","wikidata":"https://www.wikidata.org/wiki/Q3197188","display_name":"Kinome","level":3,"score":0.9655468463897705},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7090631723403931},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6166324019432068},{"id":"https://openalex.org/C184235292","wikidata":"https://www.wikidata.org/wiki/Q421851","display_name":"Kinase","level":2,"score":0.45483487844467163},{"id":"https://openalex.org/C11960822","wikidata":"https://www.wikidata.org/wiki/Q242736","display_name":"Phosphorylation","level":2,"score":0.42982199788093567},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.40348100662231445},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3373011648654938},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22261613607406616},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.11885792016983032},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":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":"D013379","descriptor_name":"Substrate Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013379","descriptor_name":"Substrate Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013379","descriptor_name":"Substrate Specificity","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D047428","descriptor_name":"Protein Kinase Inhibitors","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D047428","descriptor_name":"Protein Kinase Inhibitors","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false},{"descriptor_ui":"D047428","descriptor_name":"Protein Kinase Inhibitors","qualifier_ui":"Q000494","qualifier_name":"pharmacology","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1007578","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007578","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:33270624","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33270624","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:RePEc:plo:pcbi00:1007578","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007578","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},{"id":"pmh:oai:doaj.org/article:25d2415552804e8fa21e45dbf2bf6550","is_oa":true,"landing_page_url":"https://doaj.org/article/25d2415552804e8fa21e45dbf2bf6550","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 16, Iss 12, p e1007578 (2020)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7738173","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7738173","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"},{"id":"pmh:oai:researchrepository.ucd.ie:10197/25159","is_oa":true,"landing_page_url":"http://hdl.handle.net/10197/25159","pdf_url":null,"source":{"id":"https://openalex.org/S4306402280","display_name":"Research Repository UCD (University College Dublin)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I100930933","host_organization_name":"University College Dublin","host_organization_lineage":["https://openalex.org/I100930933"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1007578","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1007578","pdf_url":null,"source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/17","display_name":"Partnerships for the goals","score":0.4099999964237213}],"awards":[{"id":"https://openalex.org/G3989894238","display_name":null,"funder_award_id":"12/RC/2289","funder_id":"https://openalex.org/F4320331354","funder_display_name":"Insight SFI Research Centre for Data Analytics"},{"id":"https://openalex.org/G5098725405","display_name":null,"funder_award_id":"12/RC/","funder_id":"https://openalex.org/F4320320847","funder_display_name":"Science Foundation Ireland"},{"id":"https://openalex.org/G7362007176","display_name":null,"funder_award_id":"12/RC/2289","funder_id":"https://openalex.org/F4320320847","funder_display_name":"Science Foundation Ireland"},{"id":"https://openalex.org/G7696909983","display_name":null,"funder_award_id":"14/IA/2395","funder_id":"https://openalex.org/F4320320847","funder_display_name":"Science Foundation Ireland"},{"id":"https://openalex.org/G8112075043","display_name":null,"funder_award_id":"875160","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320311521","display_name":"National University of Ireland","ror":"https://ror.org/00shsf120"},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320320847","display_name":"Science Foundation Ireland","ror":"https://ror.org/0271asj38"},{"id":"https://openalex.org/F4320320861","display_name":"University of Galway","ror":"https://ror.org/03bea9k73"},{"id":"https://openalex.org/F4320331354","display_name":"Insight SFI Research Centre for Data Analytics","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":41,"referenced_works":["https://openalex.org/W1529533208","https://openalex.org/W1533230146","https://openalex.org/W1608710587","https://openalex.org/W1826266252","https://openalex.org/W1966285532","https://openalex.org/W1976526581","https://openalex.org/W1995989434","https://openalex.org/W2021019297","https://openalex.org/W2026926544","https://openalex.org/W2027928327","https://openalex.org/W2030205108","https://openalex.org/W2038663416","https://openalex.org/W2043274355","https://openalex.org/W2044868069","https://openalex.org/W2054318449","https://openalex.org/W2071141381","https://openalex.org/W2074172901","https://openalex.org/W2085037886","https://openalex.org/W2097998348","https://openalex.org/W2104244040","https://openalex.org/W2114969712","https://openalex.org/W2127230663","https://openalex.org/W2127795553","https://openalex.org/W2129242642","https://openalex.org/W2139180993","https://openalex.org/W2140397999","https://openalex.org/W2147054306","https://openalex.org/W2157658519","https://openalex.org/W2162172965","https://openalex.org/W2165460636","https://openalex.org/W2432356473","https://openalex.org/W2443568108","https://openalex.org/W2554266282","https://openalex.org/W2604272474","https://openalex.org/W2737403359","https://openalex.org/W2759136286","https://openalex.org/W2794211762","https://openalex.org/W2912820434","https://openalex.org/W2950069446","https://openalex.org/W3000075214","https://openalex.org/W6674385629"],"related_works":["https://openalex.org/W2991424847","https://openalex.org/W3043167921","https://openalex.org/W3088289817","https://openalex.org/W4296741799","https://openalex.org/W2948125847","https://openalex.org/W2167618007","https://openalex.org/W2608811481","https://openalex.org/W3015170184","https://openalex.org/W4298137444","https://openalex.org/W3035584768"],"abstract_inverted_index":{"Phosphorylation":[0],"of":[1,79,100,129,156],"specific":[2,22],"substrates":[3],"by":[4,133],"protein":[5],"kinases":[6,140],"is":[7,25,146],"a":[8,86,97],"key":[9],"control":[10],"mechanism":[11],"for":[12,91,148],"vital":[13],"cell-fate":[14],"decisions":[15],"and":[16,27,47,111,138,152],"other":[17,121],"cellular":[18],"processes.":[19],"However,":[20],"discovering":[21],"kinase-substrate":[23],"relationships":[24],"time-consuming":[26],"often":[28],"rather":[29],"serendipitous.":[30],"Computational":[31],"predictions":[32,116,128],"alleviate":[33],"these":[34,63],"challenges,":[35],"but":[36],"the":[37,107,120,134,154],"current":[38],"approaches":[39],"suffer":[40],"from":[41],"limitations":[42],"like":[43],"restricted":[44],"kinome":[45,109],"coverage":[46,110],"inaccuracy.":[48],"They":[49],"also":[50],"typically":[51],"utilise":[52],"only":[53],"local":[54],"features":[55],"without":[56],"reflecting":[57],"broader":[58],"interaction":[59],"context.":[60],"To":[61],"address":[62],"limitations,":[64],"we":[65,124],"have":[66,125],"developed":[67],"an":[68,167],"alternative":[69],"predictive":[70],"model.":[71],"It":[72],"uses":[73],"statistical":[74],"relational":[75],"learning":[76],"on":[77],"top":[78],"phosphorylation":[80,158],"networks":[81],"interpreted":[82],"as":[83],"knowledge":[84],"graphs,":[85],"simple":[87],"yet":[88],"robust":[89],"model":[90,105,161],"representing":[92],"networked":[93],"knowledge.":[94],"Compared":[95],"to":[96],"representative":[98],"selection":[99],"six":[101],"existing":[102],"systems,":[103],"our":[104,144],"has":[106],"highest":[108],"produces":[112],"biologically":[113],"valid":[114],"high-confidence":[115],"not":[117],"possible":[118],"with":[119],"tools.":[122],"Specifically,":[123],"experimentally":[126],"validated":[127],"previously":[130],"unknown":[131],"phosphorylations":[132],"LATS1,":[135],"AKT1,":[136],"PKA":[137],"MST2":[139],"in":[141],"human.":[142],"Thus,":[143],"tool":[145],"useful":[147],"focusing":[149],"phosphoproteomic":[150],"experiments,":[151],"facilitates":[153],"discovery":[155],"new":[157],"reactions.":[159],"Our":[160],"can":[162],"be":[163],"accessed":[164],"publicly":[165],"via":[166],"easy-to-use":[168],"web":[169],"interface":[170],"(LinkPhinder).":[171]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":3},{"year":2022,"cited_by_count":15},{"year":2021,"cited_by_count":1}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
