{"id":"https://openalex.org/W2972992298","doi":"https://doi.org/10.1145/3307339.3342621","title":"CoPhosK","display_name":"CoPhosK","publication_year":2019,"publication_date":"2019-09-04","ids":{"openalex":"https://openalex.org/W2972992298","doi":"https://doi.org/10.1145/3307339.3342621","mag":"2972992298"},"language":"en","primary_location":{"id":"doi:10.1145/3307339.3342621","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3307339.3342621","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"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/A5051701852","display_name":"Marzieh Ayati","orcid":"https://orcid.org/0000-0002-5280-5738"},"institutions":[{"id":"https://openalex.org/I2802326326","display_name":"The University of Texas Rio Grande Valley","ror":"https://ror.org/02p5xjf12","country_code":"US","type":"education","lineage":["https://openalex.org/I2802326326"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Marzieh Ayati","raw_affiliation_strings":["University of Texas Rio Grande Valley, Edinburg, TX, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Texas Rio Grande Valley, Edinburg, TX, USA","institution_ids":["https://openalex.org/I2802326326"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5038773259","display_name":"Danica Wiredja","orcid":null},"institutions":[{"id":"https://openalex.org/I58956616","display_name":"Case Western Reserve University","ror":"https://ror.org/051fd9666","country_code":"US","type":"education","lineage":["https://openalex.org/I58956616"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Danica Wiredja","raw_affiliation_strings":["Case Western Reserve University, Cleveland, OH, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Case Western Reserve University, Cleveland, OH, USA","institution_ids":["https://openalex.org/I58956616"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070544062","display_name":"Daniela Schlatzer","orcid":"https://orcid.org/0000-0001-7151-594X"},"institutions":[{"id":"https://openalex.org/I58956616","display_name":"Case Western Reserve University","ror":"https://ror.org/051fd9666","country_code":"US","type":"education","lineage":["https://openalex.org/I58956616"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniela Schlatzer","raw_affiliation_strings":["Case Western Reserve University, Cleveland, OH, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Case Western Reserve University, Cleveland, OH, USA","institution_ids":["https://openalex.org/I58956616"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055430350","display_name":"Sean Maxwell","orcid":"https://orcid.org/0000-0002-8924-8111"},"institutions":[{"id":"https://openalex.org/I58956616","display_name":"Case Western Reserve University","ror":"https://ror.org/051fd9666","country_code":"US","type":"education","lineage":["https://openalex.org/I58956616"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sean Maxwell","raw_affiliation_strings":["Case Western Reserve University, Cleveland, OH, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Case Western Reserve University, Cleveland, OH, USA","institution_ids":["https://openalex.org/I58956616"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100351339","display_name":"Ming Li","orcid":"https://orcid.org/0000-0001-8270-2070"},"institutions":[{"id":"https://openalex.org/I58956616","display_name":"Case Western Reserve University","ror":"https://ror.org/051fd9666","country_code":"US","type":"education","lineage":["https://openalex.org/I58956616"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ming Li","raw_affiliation_strings":["Case Western Reserve University, Cleveland, OH, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Case Western Reserve University, Cleveland, OH, USA","institution_ids":["https://openalex.org/I58956616"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035558591","display_name":"Mehmet Koyut\u00fcrk","orcid":"https://orcid.org/0000-0002-3434-5512"},"institutions":[{"id":"https://openalex.org/I58956616","display_name":"Case Western Reserve University","ror":"https://ror.org/051fd9666","country_code":"US","type":"education","lineage":["https://openalex.org/I58956616"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mehmet Koyut\u00fcrk","raw_affiliation_strings":["Case Western Reserve University, Cleveland, OH, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Case Western Reserve University, Cleveland, OH, USA","institution_ids":["https://openalex.org/I58956616"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5071940002","display_name":"Mark R. Chance","orcid":"https://orcid.org/0000-0002-2991-6405"},"institutions":[{"id":"https://openalex.org/I58956616","display_name":"Case Western Reserve University","ror":"https://ror.org/051fd9666","country_code":"US","type":"education","lineage":["https://openalex.org/I58956616"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mark R. Chance","raw_affiliation_strings":["Case Western Reserve University, Cleveland, OH, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Case Western Reserve University, Cleveland, OH, USA","institution_ids":["https://openalex.org/I58956616"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.1237,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.45722226,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"550","last_page":"550"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10683","display_name":"Mass Spectrometry Techniques and Applications","score":0.9980000257492065,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.996999979019165,"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/computer-science","display_name":"Computer science","score":0.6608438491821289},{"id":"https://openalex.org/keywords/phosphopeptide","display_name":"Phosphopeptide","score":0.47222045063972473},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.41292497515678406},{"id":"https://openalex.org/keywords/kinase","display_name":"Kinase","score":0.2918867766857147},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.28945448994636536},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.09891942143440247}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6608438491821289},{"id":"https://openalex.org/C2779933727","wikidata":"https://www.wikidata.org/wiki/Q7187535","display_name":"Phosphopeptide","level":3,"score":0.47222045063972473},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.41292497515678406},{"id":"https://openalex.org/C184235292","wikidata":"https://www.wikidata.org/wiki/Q421851","display_name":"Kinase","level":2,"score":0.2918867766857147},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.28945448994636536},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.09891942143440247}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3307339.3342621","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3307339.3342621","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.6399999856948853}],"awards":[{"id":"https://openalex.org/G5980426603","display_name":null,"funder_award_id":"R01-GM11720801","funder_id":"https://openalex.org/F4320337373","funder_display_name":"Center for Information Technology"}],"funders":[{"id":"https://openalex.org/F4320337373","display_name":"Center for Information Technology","ror":"https://ror.org/03jh5a977"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2748952813","https://openalex.org/W1980037861","https://openalex.org/W241060582","https://openalex.org/W2373312027","https://openalex.org/W1992655966","https://openalex.org/W2403323121","https://openalex.org/W2059286336","https://openalex.org/W2132691927","https://openalex.org/W2917699684"],"abstract_inverted_index":{"We":[0,72],"present":[1],"CoPhosK":[2],"to":[3,29,142],"predict":[4],"kinase-substrate":[5,26,152],"associations":[6,27],"for":[7,39,63,79,128],"phosphopeptide":[8,53],"substrates":[9,47,68],"detected":[10],"by":[11,49],"mass":[12],"spectrometry":[13],"(MS).":[14],"The":[15,104],"tool":[16,57,75],"utilizes":[17],"a":[18,143],"Na\u00efve":[19],"Bayes":[20],"framework":[21],"with":[22],"priors":[23],"of":[24,36,44,52,67,122,148,151],"known":[25],"(KSAs)":[28],"generate":[30],"its":[31],"predictions.":[32],"Through":[33],"the":[34,40,45,56,61,64,74,129,133,137,149],"mining":[35],"MS":[37,95,139],"data":[38,62,140],"collective":[41],"dynamic":[42],"signatures":[43],"kinases'":[46],"revealed":[48],"correlation":[50],"analysis":[51,109],"intensity":[54],"data,":[55,96],"infers":[58],"KSAs":[59,81,134],"in":[60],"considerable":[65],"body":[66],"lacking":[69],"such":[70],"annotations.":[71],"benchmarked":[73],"against":[76],"existing":[77],"approaches":[78],"predicting":[80],"that":[82,107],"rely":[83],"on":[84],"static":[85,116],"information":[86,117],"(e.g.":[87],"sequences,":[88],"structures":[89],"and":[90,100,145],"interactions)":[91],"using":[92],"publically":[93],"available":[94,119,135],"including":[97],"breast,":[98],"colon,":[99],"ovarian":[101],"cancer":[102],"models.":[103],"benchmarking":[105],"reveals":[106],"co-phosphorylation":[108],"can":[110],"significantly":[111],"improve":[112],"prediction":[113],"performance":[114],"when":[115],"is":[118],"(about":[120],"35%":[121],"sites)":[123],"while":[124],"providing":[125,141],"reliable":[126,146],"predictions":[127],"remainder,":[130],"thus":[131],"tripling":[132],"from":[136],"experimental":[138],"comprehensive":[144],"characterization":[147],"landscape":[150],"interactions":[153],"well":[154],"beyond":[155],"current":[156],"limitations.":[157]},"counts_by_year":[{"year":2019,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2019-09-19T00:00:00"}