{"id":"https://openalex.org/W2773943265","doi":"https://doi.org/10.1093/bioinformatics/btx807","title":"Computational identification of micro-structural variations and their proteogenomic consequences in cancer","display_name":"Computational identification of micro-structural variations and their proteogenomic consequences in cancer","publication_year":2017,"publication_date":"2017-12-15","ids":{"openalex":"https://openalex.org/W2773943265","doi":"https://doi.org/10.1093/bioinformatics/btx807","mag":"2773943265","pmid":"https://pubmed.ncbi.nlm.nih.gov/29267878"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btx807","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx807","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/10/1672/25118258/btx807.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/34/10/1672/25118258/btx807.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5112341917","display_name":"Yen-Yi Lin","orcid":null},"institutions":[{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Yen-Yi Lin","raw_affiliation_strings":["School of Computing Science, Simon Fraser University, Burnaby, BC, Canada","Vancouver Prostate Centre, Vancouver, BC, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing Science, Simon Fraser University, Burnaby, BC, Canada","institution_ids":["https://openalex.org/I18014758"]},{"raw_affiliation_string":"Vancouver Prostate Centre, Vancouver, BC, Canada","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084563414","display_name":"Alexander Gawronski","orcid":"https://orcid.org/0000-0002-8068-6422"},"institutions":[{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Alexander Gawronski","raw_affiliation_strings":["School of Computing Science, Simon Fraser University, Burnaby, BC, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing Science, Simon Fraser University, Burnaby, BC, Canada","institution_ids":["https://openalex.org/I18014758"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5006644128","display_name":"Faraz Hach","orcid":"https://orcid.org/0000-0003-1143-0172"},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]},{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Faraz Hach","raw_affiliation_strings":["Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada","School of Computing Science, Simon Fraser University, Burnaby, BC, Canada","Vancouver Prostate Centre, Vancouver, BC, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada","institution_ids":["https://openalex.org/I141945490"]},{"raw_affiliation_string":"School of Computing Science, Simon Fraser University, Burnaby, BC, Canada","institution_ids":["https://openalex.org/I18014758"]},{"raw_affiliation_string":"Vancouver Prostate Centre, Vancouver, BC, Canada","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041639230","display_name":"Sujun Li","orcid":"https://orcid.org/0000-0001-5233-2005"},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Sujun Li","raw_affiliation_strings":["Department of Computer Science, Indiana University, Bloomington, IN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Indiana University, Bloomington, IN, USA","institution_ids":["https://openalex.org/I4210119109"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060847860","display_name":"Ibrahim Numanagi\u0107","orcid":"https://orcid.org/0000-0002-2970-7937"},"institutions":[{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Ibrahim Numanagi\u0107","raw_affiliation_strings":["School of Computing Science, Simon Fraser University, Burnaby, BC, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing Science, Simon Fraser University, Burnaby, BC, Canada","institution_ids":["https://openalex.org/I18014758"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085865605","display_name":"Iman Sarrafi","orcid":null},"institutions":[{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Iman Sarrafi","raw_affiliation_strings":["School of Computing Science, Simon Fraser University, Burnaby, BC, Canada","Vancouver Prostate Centre, Vancouver, BC, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing Science, Simon Fraser University, Burnaby, BC, Canada","institution_ids":["https://openalex.org/I18014758"]},{"raw_affiliation_string":"Vancouver Prostate Centre, Vancouver, BC, Canada","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024025157","display_name":"Swati Mishra","orcid":"https://orcid.org/0000-0002-6123-8712"},"institutions":[{"id":"https://openalex.org/I55769427","display_name":"Indiana University \u2013 Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08","country_code":"US","type":"education","lineage":["https://openalex.org/I55769427","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Swati Mishra","raw_affiliation_strings":["Department of Surgery, Indiana University, School of Medicine, Indianapolis, IN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Surgery, Indiana University, School of Medicine, Indianapolis, IN, USA","institution_ids":["https://openalex.org/I55769427"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050657151","display_name":"Andrew McPherson","orcid":"https://orcid.org/0000-0002-5654-5101"},"institutions":[{"id":"https://openalex.org/I18014758","display_name":"Simon Fraser University","ror":"https://ror.org/0213rcc28","country_code":"CA","type":"education","lineage":["https://openalex.org/I18014758"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Andrew McPherson","raw_affiliation_strings":["School of Computing Science, Simon Fraser University, Burnaby, BC, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computing Science, Simon Fraser University, Burnaby, BC, Canada","institution_ids":["https://openalex.org/I18014758"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5050325886","display_name":"Colin C. Collins","orcid":"https://orcid.org/0000-0001-6148-6110"},"institutions":[{"id":"https://openalex.org/I141945490","display_name":"University of British Columbia","ror":"https://ror.org/03rmrcq20","country_code":"CA","type":"education","lineage":["https://openalex.org/I141945490"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Colin C Collins","raw_affiliation_strings":["Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada","Vancouver Prostate Centre, Vancouver, BC, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada","institution_ids":["https://openalex.org/I141945490"]},{"raw_affiliation_string":"Vancouver Prostate Centre, Vancouver, BC, Canada","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5049097819","display_name":"Milan Radovich","orcid":"https://orcid.org/0000-0001-9667-156X"},"institutions":[{"id":"https://openalex.org/I55769427","display_name":"Indiana University \u2013 Purdue University Indianapolis","ror":"https://ror.org/05gxnyn08","country_code":"US","type":"education","lineage":["https://openalex.org/I55769427","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Milan Radovich","raw_affiliation_strings":["Department of Surgery, Indiana University, School of Medicine, Indianapolis, IN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Surgery, Indiana University, School of Medicine, Indianapolis, IN, USA","institution_ids":["https://openalex.org/I55769427"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078007096","display_name":"Haixu Tang","orcid":"https://orcid.org/0000-0001-8963-8155"},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Haixu Tang","raw_affiliation_strings":["Department of Computer Science, Indiana University, Bloomington, IN, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Indiana University, Bloomington, IN, USA","institution_ids":["https://openalex.org/I4210119109"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5042282214","display_name":"S. Cenk \u015eahinalp","orcid":"https://orcid.org/0000-0002-5050-0682"},"institutions":[{"id":"https://openalex.org/I4210119109","display_name":"Indiana University Bloomington","ror":"https://ror.org/02k40bc56","country_code":"US","type":"education","lineage":["https://openalex.org/I4210119109","https://openalex.org/I592451"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"S Cenk Sahinalp","raw_affiliation_strings":["Department of Computer Science, Indiana University, Bloomington, IN, USA","Vancouver Prostate Centre, Vancouver, BC, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Indiana University, Bloomington, IN, USA","institution_ids":["https://openalex.org/I4210119109"]},{"raw_affiliation_string":"Vancouver Prostate Centre, Vancouver, BC, Canada","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5042282214"],"corresponding_institution_ids":["https://openalex.org/I4210119109"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.4282,"has_fulltext":false,"cited_by_count":13,"citation_normalized_percentile":{"value":0.59353487,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"34","issue":"10","first_page":"1672","last_page":"1681"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.6327000260353088,"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":0.6327000260353088,"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/T12576","display_name":"vaccines and immunoinformatics approaches","score":0.11190000176429749,"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":0.05620000138878822,"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/identification","display_name":"Identification (biology)","score":0.7744319438934326},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5901088118553162},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5615261793136597},{"id":"https://openalex.org/keywords/proteogenomics","display_name":"Proteogenomics","score":0.4393446743488312},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3487306833267212},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2612990736961365},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.17813122272491455},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.12698271870613098},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.1136903166770935},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.07078707218170166}],"concepts":[{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.7744319438934326},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5901088118553162},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5615261793136597},{"id":"https://openalex.org/C145741570","wikidata":"https://www.wikidata.org/wiki/Q7251534","display_name":"Proteogenomics","level":5,"score":0.4393446743488312},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3487306833267212},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2612990736961365},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.17813122272491455},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.12698271870613098},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.1136903166770935},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.07078707218170166},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000071696","descriptor_name":"Proteogenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000071696","descriptor_name":"Proteogenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D000071696","descriptor_name":"Proteogenomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","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":"D009363","descriptor_name":"Neoplasm Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D009363","descriptor_name":"Neoplasm Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D009363","descriptor_name":"Neoplasm Proteins","qualifier_ui":"Q000032","qualifier_name":"analysis","is_major_topic":false},{"descriptor_ui":"D009363","descriptor_name":"Neoplasm Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009363","descriptor_name":"Neoplasm Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D009363","descriptor_name":"Neoplasm Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D013058","descriptor_name":"Mass Spectrometry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D015972","descriptor_name":"Gene Expression Regulation, Neoplastic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015972","descriptor_name":"Gene Expression Regulation, Neoplastic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015972","descriptor_name":"Gene Expression Regulation, Neoplastic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D050939","descriptor_name":"Gene Fusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D050939","descriptor_name":"Gene Fusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D050939","descriptor_name":"Gene Fusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btx807","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx807","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/10/1672/25118258/btx807.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29267878","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29267878","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:europepmc.org:5490467","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5946953","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":"Text"},{"id":"pmh:oai:iu.tind.io:619","is_oa":false,"landing_page_url":"http://iu.tind.io/record/619","pdf_url":null,"source":{"id":"https://openalex.org/S4306402656","display_name":"IUScholarWorks Open (Indiana University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I592451","host_organization_name":"Indiana University","host_organization_lineage":["https://openalex.org/I592451"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://iu.tind.io/record/619","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btx807","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx807","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/10/1672/25118258/btx807.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.5099999904632568,"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being"}],"awards":[{"id":"https://openalex.org/G1759869059","display_name":null,"funder_award_id":"R01 GM103725","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G2734865839","display_name":null,"funder_award_id":"GM108348","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2749735394","display_name":null,"funder_award_id":"R01 GM108348","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G2839081034","display_name":null,"funder_award_id":"R01 GM103725-04","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320309291","display_name":"Indiana University","ror":"https://ror.org/01kg8sb98"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":49,"referenced_works":["https://openalex.org/W1592050624","https://openalex.org/W1592701464","https://openalex.org/W1966651331","https://openalex.org/W1972006807","https://openalex.org/W1982564236","https://openalex.org/W1992251814","https://openalex.org/W2000586119","https://openalex.org/W2012348415","https://openalex.org/W2012900739","https://openalex.org/W2022873228","https://openalex.org/W2024954384","https://openalex.org/W2026433130","https://openalex.org/W2028673251","https://openalex.org/W2029623390","https://openalex.org/W2036145579","https://openalex.org/W2036982348","https://openalex.org/W2043398720","https://openalex.org/W2043951056","https://openalex.org/W2044702943","https://openalex.org/W2050139272","https://openalex.org/W2079187939","https://openalex.org/W2079288054","https://openalex.org/W2082534286","https://openalex.org/W2096057003","https://openalex.org/W2096136407","https://openalex.org/W2096283457","https://openalex.org/W2097420863","https://openalex.org/W2103011829","https://openalex.org/W2107688500","https://openalex.org/W2112226798","https://openalex.org/W2117713095","https://openalex.org/W2118416745","https://openalex.org/W2123128942","https://openalex.org/W2126333123","https://openalex.org/W2131856634","https://openalex.org/W2134761228","https://openalex.org/W2140673900","https://openalex.org/W2142386866","https://openalex.org/W2143307936","https://openalex.org/W2146005104","https://openalex.org/W2154397429","https://openalex.org/W2155320075","https://openalex.org/W2159759316","https://openalex.org/W2201800325","https://openalex.org/W2395887422","https://openalex.org/W2560367415","https://openalex.org/W2803327664","https://openalex.org/W4241803728","https://openalex.org/W6635345608"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2968156700","https://openalex.org/W2061992841","https://openalex.org/W2294474938","https://openalex.org/W2242659647","https://openalex.org/W333403425","https://openalex.org/W2810379953","https://openalex.org/W3048812222"],"abstract_inverted_index":{"Motivation:":[0],"Rapid":[1],"advancement":[2],"in":[3,93,126,136,229,241,251],"high":[4],"throughput":[5],"genome":[6],"and":[7,11,24,101,116,199,221,269,272,281],"transcriptome":[8],"sequencing":[9],"(HTS)":[10],"mass":[12],"spectrometry":[13],"(MS)":[14],"technologies":[15],"has":[16,190],"enabled":[17],"the":[18,21,28,96,113,137,219,230,233,246],"acquisition":[19],"of":[20,44,52,130,218,236,255],"genomic,":[22],"transcriptomic":[23,214],"proteomic":[25,121],"data":[26,46,132,170,292],"from":[27,171,209],"same":[29],"tissue":[30,54],"sample.":[31,55],"We":[32,141],"introduce":[33],"a":[34,48,53,60,77],"computational":[35],"framework,":[36],"ProTIE,":[37],"to":[38,64,146,195],"integratively":[39],"analyze":[40],"all":[41,108,127,147,163],"three":[42,128],"types":[43,129],"omics":[45,131],"for":[47,167,277],"complete":[49],"molecular":[50],"profile":[51,89],"Our":[56],"framework":[57,104,145],"features":[58],"MiStrVar,":[59],"novel":[61,196,207,266],"algorithmic":[62],"method":[63,82],"identify":[65,107],"micro":[66],"structural":[67,124],"variants":[68],"(microSVs)":[69],"on":[70,184,188],"genomic":[71,212],"HTS":[72],"data.":[73],"Coupled":[74],"with":[75,119],"deFuse,":[76,102],"popular":[78],"gene":[79],"fusion":[80],"detection":[81],"we":[83,204,223],"developed":[84],"earlier,":[85],"MiStrVar":[86,100,274],"can":[87,105],"accurately":[88],"structurally":[90],"aberrant":[91],"transcripts":[92],"tumors.":[94],"Given":[95],"breakpoints":[97],"obtained":[98],"by":[99],"our":[103,144],"then":[106],"relevant":[109],"peptides":[110,208],"that":[111,193],"span":[112],"breakpoint":[114],"junctions":[115],"match":[117],"them":[118],"unique":[120],"signatures.":[122],"Observing":[123],"aberrations":[125,257],"validates":[133],"their":[134],"presence":[135],"tumor":[138],"samples.":[139],"Results:":[140],"have":[142,178,225,259],"applied":[143],"The":[148],"Cancer":[149],"Genome":[150,156],"Atlas":[151],"(TCGA)":[152],"breast":[153,252],"cancer":[154],"Whole":[155],"Sequencing":[157],"(WGS)":[158],"and/or":[159],"RNA-Seq":[160],"datasets,":[161],"spanning":[162],"four":[164],"major":[165],"subtypes,":[166],"which":[168],"proteomics":[169],"Clinical":[172],"Proteomic":[173],"Tumor":[174],"Analysis":[175],"Consortium":[176],"(CPTAC)":[177],"been":[179,227],"released.":[180],"A":[181],"recent":[182],"study":[183],"this":[185,202],"dataset":[186],"focusing":[187],"SNVs":[189],"reported":[191,228],"many":[192],"lead":[194],"peptides.":[197],"Complementing":[198],"significantly":[200],"broadening":[201],"study,":[203],"detected":[205],"244":[206],"432":[210],"candidate":[211],"or":[213],"sequence":[215,268],"aberrations.":[216],"Many":[217,254],"fusions":[220,240],"microSVs":[222],"discovered":[224],"not":[226],"literature.":[231],"Interestingly,":[232],"vast":[234],"majority":[235],"these":[237,256],"translated":[238],"aberrations,":[239],"particular,":[242],"were":[243],"private,":[244],"demonstrating":[245],"extensive":[247],"inter-genomic":[248],"heterogeneity":[249],"present":[250],"cancer.":[253],"also":[258],"matching":[260],"out-of-frame":[261],"downstream":[262],"peptides,":[263],"potentially":[264],"indicating":[265],"protein":[267],"structure.":[270],"Availability":[271],"implementation:":[273],"is":[275,283],"available":[276,284,294],"download":[278],"at":[279,285,295],"https://bitbucket.org/compbio/mistrvar,":[280],"ProTIE":[282],"https://bitbucket.org/compbio/protie.":[286],"Contact:":[287],"cenksahi@indiana.edu.":[288],"Supplementary":[289,291],"information:":[290],"are":[293],"Bioinformatics":[296],"online.":[297]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":5},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}