{"id":"https://openalex.org/W2965052449","doi":"https://doi.org/10.1093/bioinformatics/btz613","title":"ArtiFuse\u2014computational validation of fusion gene detection tools without relying on simulated reads","display_name":"ArtiFuse\u2014computational validation of fusion gene detection tools without relying on simulated reads","publication_year":2019,"publication_date":"2019-08-01","ids":{"openalex":"https://openalex.org/W2965052449","doi":"https://doi.org/10.1093/bioinformatics/btz613","mag":"2965052449","pmid":"https://pubmed.ncbi.nlm.nih.gov/31373612"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btz613","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz613","pdf_url":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5014590973","display_name":"Patrick Sorn","orcid":"https://orcid.org/0000-0001-6179-3014"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]},{"id":"https://openalex.org/I4210094062","display_name":"University Medical Center of the Johannes Gutenberg University Mainz","ror":"https://ror.org/00q1fsf04","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210094062"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Patrick Sorn","raw_affiliation_strings":["TRON \u2013 Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH , Mainz 55131, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"TRON \u2013 Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH , Mainz 55131, Germany","institution_ids":["https://openalex.org/I4210094062","https://openalex.org/I197323543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018000763","display_name":"Christoph Holtstr\u00e4ter","orcid":null},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]},{"id":"https://openalex.org/I4210094062","display_name":"University Medical Center of the Johannes Gutenberg University Mainz","ror":"https://ror.org/00q1fsf04","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210094062"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Christoph Holtstr\u00e4ter","raw_affiliation_strings":["TRON \u2013 Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH , Mainz 55131, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"TRON \u2013 Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH , Mainz 55131, Germany","institution_ids":["https://openalex.org/I4210094062","https://openalex.org/I197323543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111467155","display_name":"Martin L\u00f6wer","orcid":null},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]},{"id":"https://openalex.org/I4210094062","display_name":"University Medical Center of the Johannes Gutenberg University Mainz","ror":"https://ror.org/00q1fsf04","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210094062"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Martin L\u00f6wer","raw_affiliation_strings":["TRON \u2013 Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH , Mainz 55131, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"TRON \u2013 Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH , Mainz 55131, Germany","institution_ids":["https://openalex.org/I4210094062","https://openalex.org/I197323543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075617216","display_name":"U\u011fur \u015eahin","orcid":"https://orcid.org/0000-0003-0363-1564"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]},{"id":"https://openalex.org/I4210094062","display_name":"University Medical Center of the Johannes Gutenberg University Mainz","ror":"https://ror.org/00q1fsf04","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210094062"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Ugur Sahin","raw_affiliation_strings":["TRON \u2013 Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH , Mainz 55131, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"TRON \u2013 Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH , Mainz 55131, Germany","institution_ids":["https://openalex.org/I4210094062","https://openalex.org/I197323543"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5081468498","display_name":"David Weber","orcid":"https://orcid.org/0000-0001-9631-8459"},"institutions":[{"id":"https://openalex.org/I197323543","display_name":"Johannes Gutenberg University Mainz","ror":"https://ror.org/023b0x485","country_code":"DE","type":"education","lineage":["https://openalex.org/I197323543"]},{"id":"https://openalex.org/I4210094062","display_name":"University Medical Center of the Johannes Gutenberg University Mainz","ror":"https://ror.org/00q1fsf04","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I4210094062"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"David Weber","raw_affiliation_strings":["TRON \u2013 Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH , Mainz 55131, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"TRON \u2013 Translational Oncology at the University Medical Center of Johannes Gutenberg University Mainz gGmbH , Mainz 55131, Germany","institution_ids":["https://openalex.org/I4210094062","https://openalex.org/I197323543"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5081468498"],"corresponding_institution_ids":["https://openalex.org/I197323543","https://openalex.org/I4210094062"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.2563,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.56396058,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"36","issue":"2","first_page":"373","last_page":"379"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.319599986076355,"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":0.319599986076355,"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/T10885","display_name":"Gene expression and cancer classification","score":0.22439999878406525,"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":0.1282999962568283,"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":0.5751709342002869},{"id":"https://openalex.org/keywords/fusion-gene","display_name":"Fusion gene","score":0.5506606698036194},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5450674295425415},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5294845700263977},{"id":"https://openalex.org/keywords/benchmark","display_name":"Benchmark (surveying)","score":0.5131924748420715},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.5100422501564026},{"id":"https://openalex.org/keywords/gene-prediction","display_name":"Gene prediction","score":0.48824742436408997},{"id":"https://openalex.org/keywords/precision-and-recall","display_name":"Precision and recall","score":0.4459097981452942},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.43806716799736023},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3926010727882385},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3717215359210968},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3022124767303467},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.23560509085655212},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.1996576488018036},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.1415543556213379},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.08856552839279175}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5751709342002869},{"id":"https://openalex.org/C111829193","wikidata":"https://www.wikidata.org/wiki/Q1108970","display_name":"Fusion gene","level":3,"score":0.5506606698036194},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5450674295425415},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5294845700263977},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.5131924748420715},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.5100422501564026},{"id":"https://openalex.org/C105565629","wikidata":"https://www.wikidata.org/wiki/Q1248292","display_name":"Gene prediction","level":4,"score":0.48824742436408997},{"id":"https://openalex.org/C81669768","wikidata":"https://www.wikidata.org/wiki/Q2359161","display_name":"Precision and recall","level":2,"score":0.4459097981452942},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.43806716799736023},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3926010727882385},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3717215359210968},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3022124767303467},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.23560509085655212},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.1996576488018036},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.1415543556213379},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.08856552839279175},{"id":"https://openalex.org/C13280743","wikidata":"https://www.wikidata.org/wiki/Q131089","display_name":"Geodesy","level":1,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C205649164","wikidata":"https://www.wikidata.org/wiki/Q1071","display_name":"Geography","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":null,"qualifier_name":null,"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":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","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":false},{"descriptor_ui":"D050939","descriptor_name":"Gene Fusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D050939","descriptor_name":"Gene Fusion","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D059014","descriptor_name":"High-Throughput Nucleotide Sequencing","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btz613","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btz613","pdf_url":null,"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:31373612","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31373612","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}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17","score":0.4000000059604645}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":22,"referenced_works":["https://openalex.org/W1982538875","https://openalex.org/W2034269086","https://openalex.org/W2045949302","https://openalex.org/W2062819701","https://openalex.org/W2090004346","https://openalex.org/W2091828109","https://openalex.org/W2099530756","https://openalex.org/W2103569192","https://openalex.org/W2126144698","https://openalex.org/W2148802388","https://openalex.org/W2156274673","https://openalex.org/W2157539385","https://openalex.org/W2169456326","https://openalex.org/W2201704194","https://openalex.org/W2256379692","https://openalex.org/W2271526763","https://openalex.org/W2275311108","https://openalex.org/W2557396115","https://openalex.org/W2765689414","https://openalex.org/W2796292093","https://openalex.org/W2949522823","https://openalex.org/W6694207711"],"related_works":["https://openalex.org/W4200033037","https://openalex.org/W3213655218","https://openalex.org/W2391738941","https://openalex.org/W3147425560","https://openalex.org/W2233436997","https://openalex.org/W3018517591","https://openalex.org/W4254856796","https://openalex.org/W2547207246","https://openalex.org/W2790791672","https://openalex.org/W4236119335"],"abstract_inverted_index":{"MOTIVATION:":[0],"Gene":[1],"fusions":[2],"are":[3,59,241,249],"an":[4],"important":[5],"class":[6],"of":[7,32,41,198],"transcriptional":[8],"variants":[9],"that":[10,84,204,211],"can":[11,16,97,212],"influence":[12],"cancer":[13],"development":[14],"and":[15,44,95,135,139,150,173,239],"be":[17,98,213],"predicted":[18],"from":[19,73,182],"RNA":[20],"sequencing":[21],"(RNA-seq)":[22],"data":[23,71,248],"by":[24,88],"multiple":[25],"existing":[26],"tools.":[27],"However,":[28],"the":[29,39,92,105,196],"real-world":[30],"performance":[31,156,180],"these":[33,62],"tools":[34,132,222],"is":[35,184,232],"unclear":[36],"due":[37],"to":[38,50,91,100,159,187,195,215],"lack":[40],"known":[42],"positive":[43],"negative":[45],"events,":[46],"especially":[47],"with":[48,157,175],"regard":[49,158],"fusion":[51,86,121,219],"genes":[52,87,149,169,174],"in":[53,69,170,225,234],"individual":[54],"samples.":[55,75],"Often":[56],"simulated":[57,109,192],"reads":[58],"used,":[60],"but":[61],"cannot":[63],"account":[64],"for":[65,107,119,129,137,167,223],"all":[66,130],"technical":[67],"biases":[68],"RNA-seq":[70,102,117,200],"generated":[72],"real":[74,199],"RESULTS:":[76],"Here,":[77],"we":[78,153,202],"present":[79],"ArtiFuse,":[80],"a":[81,163,207],"novel":[82],"approach":[83,114],"simulates":[85],"sequence":[89],"modification":[90],"genomic":[93],"reference,":[94],"therefore,":[96],"applied":[99],"any":[101,108],"dataset":[103],"without":[104],"need":[106],"reads.":[110,193],"We":[111],"demonstrate":[112],"our":[113],"on":[115,191],"eight":[116],"datasets":[118],"three":[120,131],"gene":[122,220],"prediction":[123,221],"tools:":[124],"average":[125],"recall":[126,165],"values":[127],"peak":[128],"between":[133],"0.4":[134],"0.56":[136],"high-quality":[138],"high-coverage":[140,171],"datasets.":[141],"As":[142],"ArtiFuse":[143,205,231],"affords":[144],"total":[145],"control":[146],"over":[147],"involved":[148],"breakpoint":[151],"position,":[152],"also":[154],"assessed":[155,181],"gene-related":[160],"properties,":[161],"showing":[162],"drop-in":[164],"value":[166],"low-expressed":[168],"samples":[172],"co-expressed":[176],"paralogues.":[177],"Overall":[178],"tool":[179],"ArtiFusions":[183],"lower":[185],"compared":[186],"previously":[188],"reported":[189],"estimates":[190],"Due":[194],"use":[197],"datasets,":[201],"believe":[203],"provides":[206],"more":[208,217],"realistic":[209],"benchmark":[210],"used":[214],"develop":[216],"accurate":[218],"application":[224],"clinical":[226],"settings.":[227],"AVAILABILITY":[228],"AND":[229],"IMPLEMENTATION:":[230],"implemented":[233],"Python.":[235],"The":[236],"source":[237],"code":[238],"documentation":[240],"available":[242,250],"at":[243,251],"https://github.com/TRON-Bioinformatics/ArtiFusion.":[244],"SUPPLEMENTARY":[245],"INFORMATION:":[246],"Supplementary":[247],"Bioinformatics":[252],"online.":[253]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
