{"id":"https://openalex.org/W4360993110","doi":"https://doi.org/10.1109/tcbb.2023.3262119","title":"Predator: Predicting the Impact of Cancer Somatic Mutations on Protein-Protein Interactions","display_name":"Predator: Predicting the Impact of Cancer Somatic Mutations on Protein-Protein Interactions","publication_year":2023,"publication_date":"2023-03-27","ids":{"openalex":"https://openalex.org/W4360993110","doi":"https://doi.org/10.1109/tcbb.2023.3262119","pmid":"https://pubmed.ncbi.nlm.nih.gov/37030791"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2023.3262119","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2023.3262119","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","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/A5025103194","display_name":"\u0130brahim Berber","orcid":"https://orcid.org/0000-0003-0198-549X"},"institutions":[{"id":"https://openalex.org/I4210100577","display_name":"Antalya Bilim University","ror":"https://ror.org/013sqra93","country_code":"TR","type":"education","lineage":["https://openalex.org/I4210100577"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Ibrahim Berber","raw_affiliation_strings":["Department of Electrical and Computer Engineering Graduate Program, Antalya Bilim University, Antalya, Turkey"],"raw_orcid":"https://orcid.org/0000-0003-0198-549X","affiliations":[{"raw_affiliation_string":"Department of Electrical and Computer Engineering Graduate Program, Antalya Bilim University, Antalya, Turkey","institution_ids":["https://openalex.org/I4210100577"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066274617","display_name":"Cesim Erten","orcid":"https://orcid.org/0000-0002-8149-7113"},"institutions":[{"id":"https://openalex.org/I4210100577","display_name":"Antalya Bilim University","ror":"https://ror.org/013sqra93","country_code":"TR","type":"education","lineage":["https://openalex.org/I4210100577"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Cesim Erten","raw_affiliation_strings":["Department of Computer Engineering, Antalya Bilim University, Antalya, Turkey"],"raw_orcid":"https://orcid.org/0000-0002-8149-7113","affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Antalya Bilim University, Antalya, Turkey","institution_ids":["https://openalex.org/I4210100577"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074332682","display_name":"Hilal Kazan","orcid":"https://orcid.org/0000-0003-2461-4579"},"institutions":[{"id":"https://openalex.org/I4210100577","display_name":"Antalya Bilim University","ror":"https://ror.org/013sqra93","country_code":"TR","type":"education","lineage":["https://openalex.org/I4210100577"]}],"countries":["TR"],"is_corresponding":false,"raw_author_name":"Hilal Kazan","raw_affiliation_strings":["Department of Computer Engineering, Antalya Bilim University, Antalya, Turkey"],"raw_orcid":"https://orcid.org/0000-0003-2461-4579","affiliations":[{"raw_affiliation_string":"Department of Computer Engineering, Antalya Bilim University, Antalya, Turkey","institution_ids":["https://openalex.org/I4210100577"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I4210100577"],"apc_list":null,"apc_paid":null,"fwci":0.8437,"has_fulltext":false,"cited_by_count":6,"citation_normalized_percentile":{"value":0.73400963,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"20","issue":"5","first_page":"3163","last_page":"3172"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9995999932289124,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9896000027656555,"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.9872000217437744,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.6119043231010437},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.6027619242668152},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5317318439483643},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5307117700576782},{"id":"https://openalex.org/keywords/germline-mutation","display_name":"Germline mutation","score":0.5109202265739441},{"id":"https://openalex.org/keywords/predator","display_name":"Predator","score":0.4971368610858917},{"id":"https://openalex.org/keywords/protein\u2013protein-interaction","display_name":"Protein\u2013protein interaction","score":0.48225051164627075},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.48097503185272217},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.4309615194797516},{"id":"https://openalex.org/keywords/cohort","display_name":"Cohort","score":0.4220839738845825},{"id":"https://openalex.org/keywords/evolutionary-biology","display_name":"Evolutionary biology","score":0.38517385721206665},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3326740562915802},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.14841264486312866},{"id":"https://openalex.org/keywords/ecology","display_name":"Ecology","score":0.11236453056335449}],"concepts":[{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.6119043231010437},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6027619242668152},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5317318439483643},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5307117700576782},{"id":"https://openalex.org/C13514818","wikidata":"https://www.wikidata.org/wiki/Q5552256","display_name":"Germline mutation","level":4,"score":0.5109202265739441},{"id":"https://openalex.org/C96857902","wikidata":"https://www.wikidata.org/wiki/Q2138108","display_name":"Predator","level":3,"score":0.4971368610858917},{"id":"https://openalex.org/C11804247","wikidata":"https://www.wikidata.org/wiki/Q896177","display_name":"Protein\u2013protein interaction","level":2,"score":0.48225051164627075},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.48097503185272217},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.4309615194797516},{"id":"https://openalex.org/C72563966","wikidata":"https://www.wikidata.org/wiki/Q1303415","display_name":"Cohort","level":2,"score":0.4220839738845825},{"id":"https://openalex.org/C78458016","wikidata":"https://www.wikidata.org/wiki/Q840400","display_name":"Evolutionary biology","level":1,"score":0.38517385721206665},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3326740562915802},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.14841264486312866},{"id":"https://openalex.org/C18903297","wikidata":"https://www.wikidata.org/wiki/Q7150","display_name":"Ecology","level":1,"score":0.11236453056335449},{"id":"https://openalex.org/C188382862","wikidata":"https://www.wikidata.org/wiki/Q170430","display_name":"Predation","level":2,"score":0.0},{"id":"https://openalex.org/C126322002","wikidata":"https://www.wikidata.org/wiki/Q11180","display_name":"Internal medicine","level":1,"score":0.0}],"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":"D009154","descriptor_name":"Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbb.2023.3262119","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2023.3262119","pdf_url":null,"source":{"id":"https://openalex.org/S36029991","display_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","issn_l":"1545-5963","issn":["1545-5963","1557-9964","2374-0043"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319808","host_organization_name":"Institute of Electrical and Electronics Engineers","host_organization_lineage":["https://openalex.org/P4310319808"],"host_organization_lineage_names":["Institute of Electrical and Electronics Engineers"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37030791","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37030791","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE/ACM transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G595578521","display_name":null,"funder_award_id":"2019-TA-01-4069","funder_id":"https://openalex.org/F4320319756","funder_display_name":"T\u00fcrkiye Sa\u011fl\u0131k Enstit\u00fcleri Ba\u015fkanl\u0131\u011f\u0131"}],"funders":[{"id":"https://openalex.org/F4320319756","display_name":"T\u00fcrkiye Sa\u011fl\u0131k Enstit\u00fcleri Ba\u015fkanl\u0131\u011f\u0131","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":52,"referenced_works":["https://openalex.org/W1867948347","https://openalex.org/W1964154017","https://openalex.org/W1982993862","https://openalex.org/W1986273621","https://openalex.org/W2006778392","https://openalex.org/W2023490488","https://openalex.org/W2024405748","https://openalex.org/W2044433401","https://openalex.org/W2074549773","https://openalex.org/W2087732778","https://openalex.org/W2088891952","https://openalex.org/W2089335658","https://openalex.org/W2092387745","https://openalex.org/W2107857842","https://openalex.org/W2120010359","https://openalex.org/W2138865250","https://openalex.org/W2139227366","https://openalex.org/W2152176732","https://openalex.org/W2158485828","https://openalex.org/W2192013059","https://openalex.org/W2230320310","https://openalex.org/W2307896283","https://openalex.org/W2341018731","https://openalex.org/W2557187647","https://openalex.org/W2592761229","https://openalex.org/W2768685411","https://openalex.org/W2782910685","https://openalex.org/W2796408191","https://openalex.org/W2797268891","https://openalex.org/W2808064794","https://openalex.org/W2898789672","https://openalex.org/W2905098066","https://openalex.org/W2909255640","https://openalex.org/W2915993617","https://openalex.org/W2945403072","https://openalex.org/W2947811794","https://openalex.org/W2969663251","https://openalex.org/W2973269857","https://openalex.org/W2983394854","https://openalex.org/W2999615587","https://openalex.org/W3007500173","https://openalex.org/W3015602557","https://openalex.org/W3029124060","https://openalex.org/W3045100294","https://openalex.org/W3087367133","https://openalex.org/W3087769169","https://openalex.org/W3111626751","https://openalex.org/W3127041735","https://openalex.org/W3166745938","https://openalex.org/W3215101551","https://openalex.org/W4200321201","https://openalex.org/W4241423335"],"related_works":["https://openalex.org/W2946147833","https://openalex.org/W2728713152","https://openalex.org/W2061023964","https://openalex.org/W3061267761","https://openalex.org/W2168669462","https://openalex.org/W2966158266","https://openalex.org/W2077303587","https://openalex.org/W2050265018","https://openalex.org/W1967223347","https://openalex.org/W2511537300"],"abstract_inverted_index":{"Since":[0],"many":[1],"biological":[2],"processes":[3],"are":[4],"governed":[5],"by":[6,74,158],"protein-protein":[7,103],"interactions,":[8],"understanding":[9],"which":[10],"mutations":[11,56,89,100,146],"lead":[12],"to":[13,148],"a":[14,43,75,150],"disruption":[15,151],"in":[16,112,114,140,152],"these":[17],"interactions":[18,47,69],"is":[19],"profoundly":[20],"important":[21],"for":[22,168],"cancer":[23,126,175,196],"research.":[24],"Most":[25],"of":[26,34,42,63,77,99,116,192],"the":[27,32,35,39,60,64,68,87,96,142,182],"existing":[28,110],"methods":[29],"focus":[30,53],"on":[31,45,54,59,95,101,123,162,165],"stability":[33],"protein":[36,65],"without":[37],"considering":[38],"specific":[40,102],"effects":[41,98],"mutation":[44,76],"its":[46,153],"with":[48],"other":[49],"proteins.":[50],"Here,":[51],"we":[52],"somatic":[55],"that":[57,70,85,107,181],"appear":[58],"interface":[61,88,145],"regions":[62],"and":[66,128,137,185],"predict":[67],"would":[71],"be":[72],"affected":[73],"interest.":[78],"We":[79,105,119],"build":[80],"an":[81],"ensemble":[82],"model,":[83],"Predator,":[84],"classifies":[86],"as":[90,174],"disruptive":[91],"or":[92],"nondisruptive":[93],"based":[94],"predicted":[97],"interactions.":[104,154],"show":[106],"Predator":[108,122,159],"outperforms":[109],"approaches":[111],"literature":[113],"terms":[115],"prediction":[117],"accuracy.":[118],"then":[120],"apply":[121],"various":[124],"TCGA":[125],"cohorts":[127,197],"perform":[129],"comprehensive":[130],"analysis":[131],"at":[132],"cohort":[133,170],"level,":[134,136],"patient":[135],"gene":[138],"level":[139],"determining":[141],"genes":[143,167,184],"whose":[144],"tend":[147],"yield":[149],"The":[155],"predictions":[156],"obtained":[157],"shed":[160],"light":[161],"interesting":[163],"patterns":[164,191],"several":[166],"each":[169],"regarding":[171],"their":[172,186],"potential":[173],"drivers.":[176],"Our":[177],"analyses":[178],"further":[179],"reveal":[180],"identified":[183],"frequently":[187],"disrupted":[188],"partners":[189],"exhibit":[190],"mutually":[193],"exclusivity":[194],"across":[195],"under":[198],"study.":[199]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1}],"updated_date":"2026-06-26T08:34:08.712188","created_date":"2025-10-10T00:00:00"}
