{"id":"https://openalex.org/W2132933693","doi":"https://doi.org/10.1109/ssp.2012.6319801","title":"Statistical assessment of gene fusion detection algorithms using RNA Sequencing Data","display_name":"Statistical assessment of gene fusion detection algorithms using RNA Sequencing Data","publication_year":2012,"publication_date":"2012-08-01","ids":{"openalex":"https://openalex.org/W2132933693","doi":"https://doi.org/10.1109/ssp.2012.6319801","mag":"2132933693"},"language":"en","primary_location":{"id":"doi:10.1109/ssp.2012.6319801","is_oa":false,"landing_page_url":"https://doi.org/10.1109/ssp.2012.6319801","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE Statistical Signal Processing Workshop (SSP)","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://resolver.tudelft.nl/uuid:9a6823d0-2cd6-4f5c-85c9-f6f42ac62bb5","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5005628876","display_name":"Vinay Varadan","orcid":"https://orcid.org/0000-0003-1520-1967"},"institutions":[{"id":"https://openalex.org/I1329325741","display_name":"Philips (Finland)","ror":"https://ror.org/01g4jev56","country_code":"FI","type":"company","lineage":["https://openalex.org/I1329325741","https://openalex.org/I4210122849"]},{"id":"https://openalex.org/I4210131230","display_name":"Philips (United States)","ror":"https://ror.org/03kw6wr76","country_code":"US","type":"company","lineage":["https://openalex.org/I4210122849","https://openalex.org/I4210131230"]},{"id":"https://openalex.org/I4210157667","display_name":"IPS Research (United States)","ror":"https://ror.org/04q43a127","country_code":"US","type":"company","lineage":["https://openalex.org/I4210157667"]}],"countries":["FI","US"],"is_corresponding":false,"raw_author_name":"Vinay Varadan","raw_affiliation_strings":["Philips Research North America, Briarcliff Manor, NY, USA","Philips Research North America-Briarcliff Manor, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Philips Research North America, Briarcliff Manor, NY, USA","institution_ids":["https://openalex.org/I4210131230"]},{"raw_affiliation_string":"Philips Research North America-Briarcliff Manor, NY, USA","institution_ids":["https://openalex.org/I4210157667","https://openalex.org/I1329325741"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027223643","display_name":"Angel Janevski","orcid":"https://orcid.org/0000-0003-2324-8976"},"institutions":[{"id":"https://openalex.org/I1329325741","display_name":"Philips (Finland)","ror":"https://ror.org/01g4jev56","country_code":"FI","type":"company","lineage":["https://openalex.org/I1329325741","https://openalex.org/I4210122849"]},{"id":"https://openalex.org/I4210131230","display_name":"Philips (United States)","ror":"https://ror.org/03kw6wr76","country_code":"US","type":"company","lineage":["https://openalex.org/I4210122849","https://openalex.org/I4210131230"]},{"id":"https://openalex.org/I4210157667","display_name":"IPS Research (United States)","ror":"https://ror.org/04q43a127","country_code":"US","type":"company","lineage":["https://openalex.org/I4210157667"]}],"countries":["FI","US"],"is_corresponding":false,"raw_author_name":"Angel Janevski","raw_affiliation_strings":["Philips Research North America, Briarcliff Manor, NY, USA","Philips Research North America-Briarcliff Manor, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Philips Research North America, Briarcliff Manor, NY, USA","institution_ids":["https://openalex.org/I4210131230"]},{"raw_affiliation_string":"Philips Research North America-Briarcliff Manor, NY, USA","institution_ids":["https://openalex.org/I4210157667","https://openalex.org/I1329325741"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003078936","display_name":"Sitharthan Kamalakaran","orcid":null},"institutions":[{"id":"https://openalex.org/I1329325741","display_name":"Philips (Finland)","ror":"https://ror.org/01g4jev56","country_code":"FI","type":"company","lineage":["https://openalex.org/I1329325741","https://openalex.org/I4210122849"]},{"id":"https://openalex.org/I4210131230","display_name":"Philips (United States)","ror":"https://ror.org/03kw6wr76","country_code":"US","type":"company","lineage":["https://openalex.org/I4210122849","https://openalex.org/I4210131230"]},{"id":"https://openalex.org/I4210157667","display_name":"IPS Research (United States)","ror":"https://ror.org/04q43a127","country_code":"US","type":"company","lineage":["https://openalex.org/I4210157667"]}],"countries":["FI","US"],"is_corresponding":false,"raw_author_name":"Sitharthan Kamalakaran","raw_affiliation_strings":["Philips Research North America, Briarcliff Manor, NY, USA","Philips Research North America-Briarcliff Manor, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Philips Research North America, Briarcliff Manor, NY, USA","institution_ids":["https://openalex.org/I4210131230"]},{"raw_affiliation_string":"Philips Research North America-Briarcliff Manor, NY, USA","institution_ids":["https://openalex.org/I4210157667","https://openalex.org/I1329325741"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053205624","display_name":"Nilanjana Banerjee","orcid":"https://orcid.org/0000-0001-8022-8598"},"institutions":[{"id":"https://openalex.org/I1329325741","display_name":"Philips (Finland)","ror":"https://ror.org/01g4jev56","country_code":"FI","type":"company","lineage":["https://openalex.org/I1329325741","https://openalex.org/I4210122849"]},{"id":"https://openalex.org/I4210131230","display_name":"Philips (United States)","ror":"https://ror.org/03kw6wr76","country_code":"US","type":"company","lineage":["https://openalex.org/I4210122849","https://openalex.org/I4210131230"]},{"id":"https://openalex.org/I4210157667","display_name":"IPS Research (United States)","ror":"https://ror.org/04q43a127","country_code":"US","type":"company","lineage":["https://openalex.org/I4210157667"]}],"countries":["FI","US"],"is_corresponding":false,"raw_author_name":"Nilanjana Banerjee","raw_affiliation_strings":["Philips Research North America, Briarcliff Manor, NY, USA","Philips Research North America-Briarcliff Manor, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Philips Research North America, Briarcliff Manor, NY, USA","institution_ids":["https://openalex.org/I4210131230"]},{"raw_affiliation_string":"Philips Research North America-Briarcliff Manor, NY, USA","institution_ids":["https://openalex.org/I4210157667","https://openalex.org/I1329325741"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017119312","display_name":"Nevenka Dimitrova","orcid":"https://orcid.org/0000-0003-4091-9233"},"institutions":[{"id":"https://openalex.org/I1329325741","display_name":"Philips (Finland)","ror":"https://ror.org/01g4jev56","country_code":"FI","type":"company","lineage":["https://openalex.org/I1329325741","https://openalex.org/I4210122849"]},{"id":"https://openalex.org/I4210131230","display_name":"Philips (United States)","ror":"https://ror.org/03kw6wr76","country_code":"US","type":"company","lineage":["https://openalex.org/I4210122849","https://openalex.org/I4210131230"]},{"id":"https://openalex.org/I4210157667","display_name":"IPS Research (United States)","ror":"https://ror.org/04q43a127","country_code":"US","type":"company","lineage":["https://openalex.org/I4210157667"]}],"countries":["FI","US"],"is_corresponding":false,"raw_author_name":"Nevenka Dimitrova","raw_affiliation_strings":["Philips Research North America, Briarcliff Manor, NY, USA","Philips Research North America-Briarcliff Manor, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Philips Research North America, Briarcliff Manor, NY, USA","institution_ids":["https://openalex.org/I4210131230"]},{"raw_affiliation_string":"Philips Research North America-Briarcliff Manor, NY, USA","institution_ids":["https://openalex.org/I4210157667","https://openalex.org/I1329325741"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5021514634","display_name":"Lyndsay N. Harris","orcid":"https://orcid.org/0000-0002-9774-6719"},"institutions":[{"id":"https://openalex.org/I4210108791","display_name":"University Hospitals Cleveland Medical Center","ror":"https://ror.org/01gc0wp38","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799343972","https://openalex.org/I4210108791"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lyndsay N. Harris","raw_affiliation_strings":["Division of Hematology and Oncology, University Hospitals Case Medical Center, Cleveland, OH, USA","Division of Hematology and Oncology, University Hospitals Case Medical Center, Cleveland, Ohio 44106, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Hematology and Oncology, University Hospitals Case Medical Center, Cleveland, OH, USA","institution_ids":["https://openalex.org/I4210108791"]},{"raw_affiliation_string":"Division of Hematology and Oncology, University Hospitals Case Medical Center, Cleveland, Ohio 44106, USA","institution_ids":["https://openalex.org/I4210108791"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"708","last_page":"711"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9994000196456909,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9994000196456909,"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":0.9983000159263611,"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9955999851226807,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/fusion-gene","display_name":"Fusion gene","score":0.6729663014411926},{"id":"https://openalex.org/keywords/fusion","display_name":"Fusion","score":0.6669973134994507},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.5686935186386108},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.45680588483810425},{"id":"https://openalex.org/keywords/fusion-transcript","display_name":"Fusion transcript","score":0.4419418275356293},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.43781599402427673},{"id":"https://openalex.org/keywords/concordance","display_name":"Concordance","score":0.41875866055488586},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3726467788219452},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3502238988876343},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.26392292976379395},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.1803417205810547}],"concepts":[{"id":"https://openalex.org/C111829193","wikidata":"https://www.wikidata.org/wiki/Q1108970","display_name":"Fusion gene","level":3,"score":0.6729663014411926},{"id":"https://openalex.org/C158525013","wikidata":"https://www.wikidata.org/wiki/Q2593739","display_name":"Fusion","level":2,"score":0.6669973134994507},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.5686935186386108},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.45680588483810425},{"id":"https://openalex.org/C2778274637","wikidata":"https://www.wikidata.org/wiki/Q5510282","display_name":"Fusion transcript","level":4,"score":0.4419418275356293},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.43781599402427673},{"id":"https://openalex.org/C160798450","wikidata":"https://www.wikidata.org/wiki/Q4230870","display_name":"Concordance","level":2,"score":0.41875866055488586},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3726467788219452},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3502238988876343},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.26392292976379395},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.1803417205810547},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"doi:10.1109/ssp.2012.6319801","is_oa":false,"landing_page_url":"https://doi.org/10.1109/ssp.2012.6319801","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE Statistical Signal Processing Workshop (SSP)","raw_type":"proceedings-article"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.831.9405","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.831.9405","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://repository.tudelft.nl/assets/uuid%3A9a6823d0-2cd6-4f5c-85c9-f6f42ac62bb5/MS-33.366.pdf","raw_type":"text"},{"id":"pmh:philips:oai:tudelft.nl:uuid:9a6823d0-2cd6-4f5c-85c9-f6f42ac62bb5","is_oa":true,"landing_page_url":"http://resolver.tudelft.nl/uuid:9a6823d0-2cd6-4f5c-85c9-f6f42ac62bb5","pdf_url":null,"source":{"id":"https://openalex.org/S4306401843","display_name":"Data Archiving and Networked Services (DANS)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1322597698","host_organization_name":"Royal Netherlands Academy of Arts and Sciences","host_organization_lineage":["https://openalex.org/I1322597698"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/conferencepaper"}],"best_oa_location":{"id":"pmh:philips:oai:tudelft.nl:uuid:9a6823d0-2cd6-4f5c-85c9-f6f42ac62bb5","is_oa":true,"landing_page_url":"http://resolver.tudelft.nl/uuid:9a6823d0-2cd6-4f5c-85c9-f6f42ac62bb5","pdf_url":null,"source":{"id":"https://openalex.org/S4306401843","display_name":"Data Archiving and Networked Services (DANS)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1322597698","host_organization_name":"Royal Netherlands Academy of Arts and Sciences","host_organization_lineage":["https://openalex.org/I1322597698"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/conferencepaper"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","score":0.5099999904632568,"display_name":"Good health and well-being"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":16,"referenced_works":["https://openalex.org/W1966822396","https://openalex.org/W2018336040","https://openalex.org/W2029623390","https://openalex.org/W2052297191","https://openalex.org/W2064469303","https://openalex.org/W2082534286","https://openalex.org/W2103569192","https://openalex.org/W2112044462","https://openalex.org/W2112888168","https://openalex.org/W2114289944","https://openalex.org/W2124985265","https://openalex.org/W2129495613","https://openalex.org/W2136145671","https://openalex.org/W2139399606","https://openalex.org/W2157160484","https://openalex.org/W2329648702"],"related_works":["https://openalex.org/W1501720035","https://openalex.org/W2010507532","https://openalex.org/W2116011569","https://openalex.org/W2911167977","https://openalex.org/W2350670584","https://openalex.org/W59832779","https://openalex.org/W2321864840","https://openalex.org/W2489687894","https://openalex.org/W2161099760","https://openalex.org/W1986850084"],"abstract_inverted_index":{"The":[0,51],"detection":[1,36],"and":[2,10,20,39,48,79,95,194],"quantification":[3],"of":[4,24,67,87,123,160,163],"fusion":[5,25,35,61,89,165,173],"transcripts":[6,174],"has":[7],"both":[8],"biological":[9],"clinical":[11],"implications.":[12],"RNA":[13],"sequencing":[14],"provides":[15,155],"a":[16,65,156],"means":[17],"for":[18,103,150],"unbiased":[19],"high":[21,192],"resolution":[22],"characterization":[23],"transcript":[26],"information":[27],"in":[28,132],"tissue":[29],"samples.":[30],"We":[31,83],"evaluated":[32,84],"two":[33,52,93,115],"gene":[34,88],"algorithms,":[37],"TopHat-Fusion":[38,63,147,167],"deFuse,":[40],"using":[41],"transcriptomes":[42],"derived":[43],"from":[44],"breast":[45],"cancer":[46],"biopsies":[47],"cell":[49],"line.":[50],"algorithms":[53,94,116,186],"use":[54],"different":[55],"strategies":[56],"to":[57,77,128,137,170,184],"reduce":[58],"false":[59],"positive":[60],"calls:":[62],"uses":[64],"cascade":[66],"heuristically":[68],"designed":[69],"filters":[70],"while":[71],"deFuse":[72,126,141,154],"relies":[73],"on":[74],"statistical":[75],"methodologies":[76],"assess":[78],"prune":[80],"potential":[81],"fusions.":[82,106,152],"the":[85,92,97,104,111,114,161,164],"concordance":[86,112],"calls":[90],"between":[91,113],"characterized":[96],"evidence":[98,149],"generated":[99],"by":[100,178],"each":[101],"methodology":[102],"common":[105],"Our":[107],"results":[108],"show":[109],"that":[110,175,187],"is":[117,168,182],"about":[118],"6%":[119],"at":[120],"comparable":[121],"number":[122],"fusions":[124,134,190],"detected.":[125],"tends":[127],"be":[129],"more":[130,144,157],"sensitive":[131],"detecting":[133],"when":[135],"compared":[136],"TopHat-Fusion.":[138],"On":[139],"average,":[140],"identifies":[142],"proportionally":[143],"reads":[145],"than":[146],"as":[148],"concordant":[151],"While":[153],"quantitative":[158],"summary":[159],"reliability":[162],"calls,":[166],"able":[169],"detect":[171,189],"additional":[172],"were":[176],"missed":[177],"deFuse.":[179],"Further":[180],"research":[181],"required":[183],"develop":[185],"can":[188],"with":[191],"sensitivity":[193],"specificity.":[195]},"counts_by_year":[{"year":2013,"cited_by_count":1}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
