{"id":"https://openalex.org/W2970566740","doi":"https://doi.org/10.1089/cmb.2018.0192","title":"Identifying the Impact of Inframe Insertions and Deletions on Protein Function in Cancer","display_name":"Identifying the Impact of Inframe Insertions and Deletions on Protein Function in Cancer","publication_year":2019,"publication_date":"2019-08-28","ids":{"openalex":"https://openalex.org/W2970566740","doi":"https://doi.org/10.1089/cmb.2018.0192","mag":"2970566740","pmid":"https://pubmed.ncbi.nlm.nih.gov/31460787"},"language":"en","primary_location":{"is_oa":false,"landing_page_url":"https://doi.org/10.1089/cmb.2018.0192","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false},"type":"article","type_crossref":"journal-article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://figshare.com/articles/journal_contribution/Identifying_the_impact_of_inframe_insertions_and_deletions_on_protein_function_in_cancer/23474468/1/files/41183612.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5049955748","display_name":"Hanadi M. Baeissa","orcid":null},"institutions":[{"id":"https://openalex.org/I162608824","display_name":"University of Sussex","ror":"https://ror.org/00ayhx656","country_code":"GB","type":"education","lineage":["https://openalex.org/I162608824"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Hanadi M. Baeissa","raw_affiliation_strings":["Bioinformatics Group, School of Life Sciences, University of Sussex, Brighton, United Kingdom."],"affiliations":[{"raw_affiliation_string":"Bioinformatics Group, School of Life Sciences, University of Sussex, Brighton, United Kingdom.","institution_ids":["https://openalex.org/I162608824"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085283148","display_name":"Frances M. G. Pearl","orcid":"https://orcid.org/0000-0002-8210-4393"},"institutions":[{"id":"https://openalex.org/I162608824","display_name":"University of Sussex","ror":"https://ror.org/00ayhx656","country_code":"GB","type":"education","lineage":["https://openalex.org/I162608824"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Frances M.G. Pearl","raw_affiliation_strings":["Bioinformatics Group, School of Life Sciences, University of Sussex, Brighton, United Kingdom."],"affiliations":[{"raw_affiliation_string":"Bioinformatics Group, School of Life Sciences, University of Sussex, Brighton, United Kingdom.","institution_ids":["https://openalex.org/I162608824"]}]}],"institution_assertions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5085283148"],"corresponding_institution_ids":["https://openalex.org/I162608824"],"apc_list":null,"apc_paid":null,"fwci":0.082,"has_fulltext":true,"fulltext_origin":"pdf","cited_by_count":3,"citation_normalized_percentile":{"value":0.446378,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":74,"max":77},"biblio":{"volume":"27","issue":"5","first_page":"786","last_page":"795"},"is_retracted":false,"is_paratext":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9972,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9972,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9969,"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/T11642","display_name":"Genomics and Rare Diseases","score":0.9968,"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/indel","display_name":"Indel","score":0.97624093},{"id":"https://openalex.org/keywords/indel-mutation","display_name":"INDEL Mutation","score":0.66867596},{"id":"https://openalex.org/keywords/insertion","display_name":"Insertion","score":0.43471602}],"concepts":[{"id":"https://openalex.org/C119054055","wikidata":"https://www.wikidata.org/wiki/Q1576681","display_name":"Indel","level":5,"score":0.97624093},{"id":"https://openalex.org/C2910714999","wikidata":"https://www.wikidata.org/wiki/Q1576681","display_name":"INDEL Mutation","level":5,"score":0.66867596},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5900177},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.5162606},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5137933},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5106059},{"id":"https://openalex.org/C118083812","wikidata":"https://www.wikidata.org/wiki/Q1650834","display_name":"Insertion","level":4,"score":0.43471602},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.40236574},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.119619966},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.0}],"mesh":[{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D054643","descriptor_name":"INDEL Mutation","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009363","descriptor_name":"Neoplasm Proteins","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":"D000465","descriptor_name":"Algorithms","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015894","descriptor_name":"Genome, Human","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D054643","descriptor_name":"INDEL Mutation","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009363","descriptor_name":"Neoplasm Proteins","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000473","qualifier_name":"pathology","is_major_topic":false},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009857","descriptor_name":"Oncogenes","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009857","descriptor_name":"Oncogenes","qualifier_ui":"","qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"is_oa":false,"landing_page_url":"https://doi.org/10.1089/cmb.2018.0192","pdf_url":null,"source":{"id":"https://openalex.org/S78571599","display_name":"Journal of Computational Biology","issn_l":"1066-5277","issn":["1066-5277","1557-8666"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320443","host_organization_name":"Mary Ann Liebert, Inc.","host_organization_lineage":["https://openalex.org/P4310320443"],"host_organization_lineage_names":["Mary Ann Liebert, Inc."],"type":"journal"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false},{"is_oa":true,"landing_page_url":"https://figshare.com/articles/journal_contribution/Identifying_the_impact_of_inframe_insertions_and_deletions_on_protein_function_in_cancer/23474468","pdf_url":"https://figshare.com/articles/journal_contribution/Identifying_the_impact_of_inframe_insertions_and_deletions_on_protein_function_in_cancer/23474468/1/files/41183612.pdf","source":{"id":"https://openalex.org/S4306402621","display_name":"INDIGO (University of Illinois at Chicago)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I39422238","host_organization_name":"University of Illinois Chicago","host_organization_lineage":["https://openalex.org/I39422238"],"host_organization_lineage_names":["University of Illinois Chicago"],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true},{"is_oa":true,"landing_page_url":"http://sro.sussex.ac.uk/id/eprint/89224/3/__smbhome.uscs.susx.ac.uk_tjk30_Documents_INDELS_BMCfpSRO.pdf","pdf_url":"https://sussex.figshare.com/articles/journal_contribution/Identifying_the_impact_of_inframe_insertions_and_deletions_on_protein_function_in_cancer/23474468/1/files/41183612.pdf","source":{"id":"https://openalex.org/S4306400129","display_name":"Sussex Research Online (University of Sussex)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I162608824","host_organization_name":"University of Sussex","host_organization_lineage":["https://openalex.org/I162608824"],"host_organization_lineage_names":["University of Sussex"],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"acceptedVersion","is_accepted":true,"is_published":false},{"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31460787","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":["National Institutes of Health"],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false}],"best_oa_location":{"is_oa":true,"landing_page_url":"https://figshare.com/articles/journal_contribution/Identifying_the_impact_of_inframe_insertions_and_deletions_on_protein_function_in_cancer/23474468","pdf_url":"https://figshare.com/articles/journal_contribution/Identifying_the_impact_of_inframe_insertions_and_deletions_on_protein_function_in_cancer/23474468/1/files/41183612.pdf","source":{"id":"https://openalex.org/S4306402621","display_name":"INDIGO (University of Illinois at Chicago)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I39422238","host_organization_name":"University of Illinois Chicago","host_organization_lineage":["https://openalex.org/I39422238"],"host_organization_lineage_names":["University of Illinois Chicago"],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true},"sustainable_development_goals":[{"score":0.73,"id":"https://metadata.un.org/sdg/10","display_name":"Reduced inequalities"}],"grants":[],"datasets":[],"versions":[],"referenced_works_count":34,"referenced_works":["https://openalex.org/W1596717185","https://openalex.org/W1900984040","https://openalex.org/W1927517816","https://openalex.org/W1980370800","https://openalex.org/W1987754412","https://openalex.org/W1992192857","https://openalex.org/W1992880766","https://openalex.org/W1995162107","https://openalex.org/W1996031526","https://openalex.org/W1999083393","https://openalex.org/W2000025256","https://openalex.org/W2002218976","https://openalex.org/W2023568503","https://openalex.org/W2024405748","https://openalex.org/W2030356048","https://openalex.org/W2047433619","https://openalex.org/W2056777053","https://openalex.org/W2085344563","https://openalex.org/W2086775982","https://openalex.org/W2097152766","https://openalex.org/W2102140136","https://openalex.org/W2117446594","https://openalex.org/W2118286367","https://openalex.org/W2125003131","https://openalex.org/W2137297899","https://openalex.org/W2139086914","https://openalex.org/W2154595610","https://openalex.org/W2154866190","https://openalex.org/W2155845523","https://openalex.org/W2158116492","https://openalex.org/W2160515792","https://openalex.org/W2160995259","https://openalex.org/W2171777347","https://openalex.org/W2174602966"],"related_works":["https://openalex.org/W4206406917","https://openalex.org/W3015361613","https://openalex.org/W2970566740","https://openalex.org/W2394286786","https://openalex.org/W2167094946","https://openalex.org/W2135846417","https://openalex.org/W2080028493","https://openalex.org/W2046457574","https://openalex.org/W1971376828","https://openalex.org/W1574259053"],"abstract_inverted_index":{"Inframe":[0],"insertion":[1,141],"and":[2,30,53,90,106,117,121,138,142],"deletion":[3,143],"mutations":[4,89,156],"(indels)":[5],"are":[6,34,46],"commonly":[7],"observed":[8],"in":[9,102,157],"cancer":[10,42,87,104,155],"samples":[11],"accounting":[12],"for":[13,86,140],"over":[14],"1%":[15],"of":[16,50,63,76,136],"all":[17],"reported":[18],"mutations.":[19,124],"Few":[20],"somatic":[21],"inframe":[22,64,122,153],"indels":[23,40,45,65,101,107],"have":[24,56],"been":[25,57],"clinically":[26],"documented":[27],"as":[28],"pathogenic":[29],"at":[31],"present":[32],"there":[33],"few":[35],"tools":[36,55,80],"to":[37,59,84,115,150],"predict":[38,60],"which":[39],"drive":[41],"development.":[43],"However,":[44],"a":[47,93,126],"common":[48],"feature":[49],"hereditary":[51],"disease":[52],"several":[54],"developed":[58,114],"the":[61,77,152,158],"impact":[62],"on":[66],"protein":[67],"function.":[68],"In":[69],"this":[70],"study,":[71],"we":[72,147],"test":[73,85],"whether":[74],"six":[75],"popular":[78],"prediction":[79],"can":[81],"be":[82],"adapted":[83],"driver":[88],"then":[91],"develop":[92],"new":[94],"algorithm":[95],"(IndelRF)":[96],"that":[97],"discriminates":[98],"between":[99],"recurrent":[100],"known":[103],"genes":[105],"not":[108],"associated":[109],"with":[110,130],"disease.":[111],"IndelRF":[112,133,149],"was":[113],"try":[116],"identify":[118],"somatic,":[119],"driver,":[120],"indel":[123,154],"Using":[125],"random":[127],"forest":[128],"classifier":[129],"11":[131],"features,":[132],"achieved":[134],"accuracies":[135],"0.995":[137],"0.968":[139],"mutations,":[144],"respectively.":[145],"Finally,":[146],"use":[148],"classify":[151],"MOKCa":[159],"database.":[160]},"cited_by_api_url":"https://api.openalex.org/works?filter=cites:W2970566740","counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1}],"updated_date":"2025-01-18T21:32:53.261515","created_date":"2019-09-05"}