{"id":"https://openalex.org/W2574163688","doi":"https://doi.org/10.1109/bibm.2016.7822792","title":"A novel scoring estimator to screening for oncogenic chimeric transcripts in cancer transcriptome sequencing","display_name":"A novel scoring estimator to screening for oncogenic chimeric transcripts in cancer transcriptome sequencing","publication_year":2016,"publication_date":"2016-12-01","ids":{"openalex":"https://openalex.org/W2574163688","doi":"https://doi.org/10.1109/bibm.2016.7822792","mag":"2574163688"},"language":"en","primary_location":{"id":"doi:10.1109/bibm.2016.7822792","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2016.7822792","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"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/A5061896206","display_name":"Jianlei Gu","orcid":"https://orcid.org/0000-0002-9337-5017"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jian-lei Gu","raw_affiliation_strings":["Key Laboratory of Molecular Embryology, Ministry of Health & Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China","SJTU-Yale Joint Center for Biostatistics, Shanghai Jiao Tong University, Shanghai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Molecular Embryology, Ministry of Health & Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China","institution_ids":[]},{"raw_affiliation_string":"SJTU-Yale Joint Center for Biostatistics, Shanghai Jiao Tong University, Shanghai, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100334844","display_name":"Yao L\u00fc","orcid":"https://orcid.org/0000-0002-3380-7762"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yao Lu","raw_affiliation_strings":["Key Laboratory of Molecular Embryology, Ministry of Health & Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China","SJTU-Yale Joint Center for Biostatistics, Shanghai Jiao Tong University, Shanghai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Molecular Embryology, Ministry of Health & Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China","institution_ids":[]},{"raw_affiliation_string":"SJTU-Yale Joint Center for Biostatistics, Shanghai Jiao Tong University, Shanghai, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100736545","display_name":"Shiyi Liu","orcid":"https://orcid.org/0000-0002-2157-8667"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shi-yi Liu","raw_affiliation_strings":["SJTU-Yale Joint Center for Biostatistics, Shanghai Jiao Tong University, Shanghai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"SJTU-Yale Joint Center for Biostatistics, Shanghai Jiao Tong University, Shanghai, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100988713","display_name":"Cong Liu","orcid":"https://orcid.org/0000-0002-5694-1139"},"institutions":[{"id":"https://openalex.org/I39422238","display_name":"University of Illinois Chicago","ror":"https://ror.org/02mpq6x41","country_code":"US","type":"education","lineage":["https://openalex.org/I39422238"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Cong Liu","raw_affiliation_strings":["Department of Bioengineering, University of Illinois at Chicago, Chicago, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of Illinois at Chicago, Chicago, USA","institution_ids":["https://openalex.org/I39422238"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5108053236","display_name":"Hui Lu","orcid":"https://orcid.org/0000-0002-2405-6127"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hui Lu","raw_affiliation_strings":["Key Laboratory of Molecular Embryology, Ministry of Health & Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China","SJTU-Yale Joint Center for Biostatistics, Shanghai Jiao Tong University, Shanghai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Key Laboratory of Molecular Embryology, Ministry of Health & Shanghai Key Laboratory of Embryo and Reproduction Engineering, Shanghai, China","institution_ids":[]},{"raw_affiliation_string":"SJTU-Yale Joint Center for Biostatistics, Shanghai Jiao Tong University, Shanghai, China","institution_ids":["https://openalex.org/I183067930"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":"62","issue":null,"first_page":"1800","last_page":"1805"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9998000264167786,"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"}},"topics":[{"id":"https://openalex.org/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.9998000264167786,"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"}},{"id":"https://openalex.org/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9983999729156494,"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/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9977999925613403,"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/biology","display_name":"Biology","score":0.6966923475265503},{"id":"https://openalex.org/keywords/carcinogenesis","display_name":"Carcinogenesis","score":0.669852614402771},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.660270094871521},{"id":"https://openalex.org/keywords/fusion-gene","display_name":"Fusion gene","score":0.6509911417961121},{"id":"https://openalex.org/keywords/clone","display_name":"clone (Java method)","score":0.5805081129074097},{"id":"https://openalex.org/keywords/cancer","display_name":"Cancer","score":0.5538206100463867},{"id":"https://openalex.org/keywords/chromothripsis","display_name":"Chromothripsis","score":0.5414308309555054},{"id":"https://openalex.org/keywords/chimeric-gene","display_name":"Chimeric gene","score":0.4784929156303406},{"id":"https://openalex.org/keywords/cancer-research","display_name":"Cancer research","score":0.47256961464881897},{"id":"https://openalex.org/keywords/chromoplexy","display_name":"Chromoplexy","score":0.4669695198535919},{"id":"https://openalex.org/keywords/prostate-cancer","display_name":"Prostate cancer","score":0.4346855580806732},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4316740334033966},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.4245617985725403},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.40490975975990295},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.37260979413986206},{"id":"https://openalex.org/keywords/genome-instability","display_name":"Genome instability","score":0.21909186244010925},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.14810696244239807},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.12059438228607178},{"id":"https://openalex.org/keywords/pca3","display_name":"PCA3","score":0.10298308730125427},{"id":"https://openalex.org/keywords/dna-damage","display_name":"DNA damage","score":0.0638323724269867}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6966923475265503},{"id":"https://openalex.org/C555283112","wikidata":"https://www.wikidata.org/wiki/Q1637543","display_name":"Carcinogenesis","level":3,"score":0.669852614402771},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.660270094871521},{"id":"https://openalex.org/C111829193","wikidata":"https://www.wikidata.org/wiki/Q1108970","display_name":"Fusion gene","level":3,"score":0.6509911417961121},{"id":"https://openalex.org/C81089528","wikidata":"https://www.wikidata.org/wiki/Q5134986","display_name":"clone (Java method)","level":3,"score":0.5805081129074097},{"id":"https://openalex.org/C121608353","wikidata":"https://www.wikidata.org/wiki/Q12078","display_name":"Cancer","level":2,"score":0.5538206100463867},{"id":"https://openalex.org/C99983632","wikidata":"https://www.wikidata.org/wiki/Q1087765","display_name":"Chromothripsis","level":5,"score":0.5414308309555054},{"id":"https://openalex.org/C26260077","wikidata":"https://www.wikidata.org/wiki/Q5099361","display_name":"Chimeric gene","level":4,"score":0.4784929156303406},{"id":"https://openalex.org/C502942594","wikidata":"https://www.wikidata.org/wiki/Q3421914","display_name":"Cancer research","level":1,"score":0.47256961464881897},{"id":"https://openalex.org/C205003668","wikidata":"https://www.wikidata.org/wiki/Q17113442","display_name":"Chromoplexy","level":5,"score":0.4669695198535919},{"id":"https://openalex.org/C2780192828","wikidata":"https://www.wikidata.org/wiki/Q181257","display_name":"Prostate cancer","level":3,"score":0.4346855580806732},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4316740334033966},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.4245617985725403},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.40490975975990295},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.37260979413986206},{"id":"https://openalex.org/C178169997","wikidata":"https://www.wikidata.org/wiki/Q2892636","display_name":"Genome instability","level":4,"score":0.21909186244010925},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.14810696244239807},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.12059438228607178},{"id":"https://openalex.org/C87874733","wikidata":"https://www.wikidata.org/wiki/Q18039844","display_name":"PCA3","level":4,"score":0.10298308730125427},{"id":"https://openalex.org/C143425029","wikidata":"https://www.wikidata.org/wiki/Q5205747","display_name":"DNA damage","level":3,"score":0.0638323724269867}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm.2016.7822792","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm.2016.7822792","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.7699999809265137}],"awards":[],"funders":[{"id":"https://openalex.org/F4320322999","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04"},{"id":"https://openalex.org/F4320326223","display_name":"International Foundation for CDKL5 Research","ror":null}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W1978227858","https://openalex.org/W1980312974","https://openalex.org/W1984740535","https://openalex.org/W1985213868","https://openalex.org/W2023560061","https://openalex.org/W2026099579","https://openalex.org/W2027845674","https://openalex.org/W2029623390","https://openalex.org/W2046233258","https://openalex.org/W2079298594","https://openalex.org/W2082534286","https://openalex.org/W2085807927","https://openalex.org/W2088612061","https://openalex.org/W2102450275","https://openalex.org/W2103569192","https://openalex.org/W2114289944","https://openalex.org/W2116353323","https://openalex.org/W2121158863","https://openalex.org/W2121761025","https://openalex.org/W2124887618","https://openalex.org/W2126144698","https://openalex.org/W2128493216","https://openalex.org/W2135185276","https://openalex.org/W2154431984","https://openalex.org/W2165288212","https://openalex.org/W2346845651","https://openalex.org/W6680105682"],"related_works":["https://openalex.org/W2023006132","https://openalex.org/W2011957420","https://openalex.org/W2091055693","https://openalex.org/W2116532769","https://openalex.org/W2031048481","https://openalex.org/W2319371655","https://openalex.org/W2006944218","https://openalex.org/W2137015585","https://openalex.org/W2562309431","https://openalex.org/W2334842888"],"abstract_inverted_index":{"Based":[0,31],"on":[1,32,110],"various":[2],"genomic":[3],"information":[4],"of":[5,27,87,95,177],"chimeric":[6,19,29,40,57,90,138,182],"transcript,":[7],"recent":[8],"studies":[9],"used":[10],"machine-learning":[11],"methods":[12],"to":[13,45,83,92,144],"predict":[14],"the":[15,52,85,93,124,137,152],"oncogenic":[16,48],"potentials":[17],"for":[18,118,126,179],"transcripts,":[20],"however":[21],"these":[22],"works":[23],"ignored":[24],"transcriptional":[25],"signature":[26],"those":[28],"transcripts.":[30],"clonal":[33,61],"evolution":[34],"theory,":[35],"we":[36,72,106],"hypothesized":[37],"that":[38,136],"a":[39,68,74,174],"transcript":[41],"is":[42],"more":[43],"likely":[44],"be":[46],"an":[47],"`driver'":[49],"mutation,":[50,158],"if":[51],"neoplastic":[53,65,96],"cells":[54,66,97],"harboring":[55],"this":[56],"mutation":[58],"has":[59,161],"larger":[60],"size":[62],"than":[63,149],"other":[64,125],"in":[67,98,140,166,184],"particular":[69],"tumor.":[70],"Here":[71],"proposed":[73],"novel":[75,175],"method,":[76],"called":[77],"iFCR":[78,108,147,164],"(internal":[79],"Fusion":[80],"Clone":[81],"Ratio),":[82],"estimate":[84],"ratio":[86],"subclone":[88],"carrying":[89],"transcripts":[91,139,183],"rest":[94],"transcriptome":[99,114],"sequencing":[100,115],"data.":[101],"To":[102],"evaluate":[103],"our":[104],"hypothesis,":[105],"applied":[107],"method":[109],"two":[111],"public":[112],"cancer":[113,120,156,185],"datasets,":[116],"one":[117],"breast":[119],"cell":[121],"line":[122],"and":[123],"prostate":[127,155],"tumors":[128],"with":[129],"adjacent":[130],"normal":[131,150],"tissues.":[132],"Our":[133,171],"results":[134],"demonstrated":[135],"tumor":[141],"samples":[142],"appear":[143],"have":[145],"higher":[146,163],"value":[148,165],"tissues,":[151],"most":[153],"frequent":[154],"fusion":[157],"TMPRSS2-":[159],"ERG,":[160],"remarkably":[162],"all":[167],"three":[168],"independent":[169],"patients.":[170],"work":[172],"providing":[173],"point":[176],"view":[178],"screening":[180],"oncogenesis":[181],"research.":[186]},"counts_by_year":[],"updated_date":"2026-07-15T18:14:33.161393","created_date":"2025-10-10T00:00:00"}
