{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,5]],"date-time":"2026-04-05T08:41:02Z","timestamp":1775378462460,"version":"3.50.1"},"reference-count":22,"publisher":"Springer Science and Business Media LLC","issue":"S7","license":[{"start":{"date-parts":[[2013,4,1]],"date-time":"2013-04-01T00:00:00Z","timestamp":1364774400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Bioinformatics"],"published-print":{"date-parts":[[2013,4]]},"DOI":"10.1186\/1471-2105-14-s7-s2","type":"journal-article","created":{"date-parts":[[2013,4,22]],"date-time":"2013-04-22T06:15:13Z","timestamp":1366611313000},"source":"Crossref","is-referenced-by-count":56,"title":["State of art fusion-finder algorithms are suitable to detect transcription-induced chimeras in normal tissues?"],"prefix":"10.1186","volume":"14","author":[{"given":"Matteo","family":"Carrara","sequence":"first","affiliation":[]},{"given":"Marco","family":"Beccuti","sequence":"additional","affiliation":[]},{"given":"Federica","family":"Cavallo","sequence":"additional","affiliation":[]},{"given":"Susanna","family":"Donatelli","sequence":"additional","affiliation":[]},{"given":"Fulvio","family":"Lazzarato","sequence":"additional","affiliation":[]},{"given":"Francesca","family":"Cordero","sequence":"additional","affiliation":[]},{"given":"Raffaele A","family":"Calogero","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2013,4,22]]},"reference":[{"issue":"7","key":"5812_CR1","doi-asserted-by":"publisher","first-page":"621","DOI":"10.1038\/nmeth.1226","volume":"5","author":"A Mortazavi","year":"2008","unstructured":"Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B: Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature methods. 2008, 5 (7): 621-628. 10.1038\/nmeth.1226.","journal-title":"Nature methods"},{"issue":"7234","key":"5812_CR2","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1038\/nature07638","volume":"458","author":"CA Maher","year":"2009","unstructured":"Maher CA, Kumar-Sinha C, Cao X, Kalyana-Sundaram S, Han B, Jing X, Sam L, Barrette T, Palanisamy N, Chinnaiyan AM: Transcriptome sequencing to detect gene fusions in cancer. Nature. 2009, 458 (7234): 97-101. 10.1038\/nature07638.","journal-title":"Nature"},{"issue":"26","key":"5812_CR3","doi-asserted-by":"publisher","first-page":"16005","DOI":"10.1074\/jbc.273.26.16005","volume":"273","author":"F Magrangeas","year":"1998","unstructured":"Magrangeas F, Pitiot G, Dubois S, Bragado-Nilsson E, Cherel M, Jobert S, Lebeau B, Boisteau O, Lethe B, Mallet J: Cotranscription and intergenic splicing of human galactose-1-phosphate uridylyltransferase and interleukin-11 receptor alpha-chain genes generate a fusion mRNA in normal cells. Implication for the production of multidomain proteins during evolution. The Journal of biological chemistry. 1998, 273 (26): 16005-16010. 10.1074\/jbc.273.26.16005.","journal-title":"The Journal of biological chemistry"},{"issue":"1","key":"5812_CR4","doi-asserted-by":"publisher","first-page":"30","DOI":"10.1101\/gr.4137606","volume":"16","author":"P Akiva","year":"2006","unstructured":"Akiva P, Toporik A, Edelheit S, Peretz Y, Diber A, Shemesh R, Novik A, Sorek R: Transcription-mediated gene fusion in the human genome. Genome research. 2006, 16 (1): 30-36.","journal-title":"Genome research"},{"issue":"1","key":"5812_CR5","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1101\/gr.4145906","volume":"16","author":"G Parra","year":"2006","unstructured":"Parra G, Reymond A, Dabbouseh N, Dermitzakis ET, Castelo R, Thomson TM, Antonarakis SE, Guigo R: Tandem chimerism as a means to increase protein complexity in the human genome. Genome research. 2006, 16 (1): 37-44.","journal-title":"Genome research"},{"key":"5812_CR6","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1186\/1755-8794-4-11","volume":"4","author":"S Nacu","year":"2011","unstructured":"Nacu S, Yuan W, Kan Z, Bhatt D, Rivers CS, Stinson J, Peters BA, Modrusan Z, Jung K, Seshagiri S: Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples. BMC medical genomics. 2011, 4: 11-10.1186\/1755-8794-4-11.","journal-title":"BMC medical genomics"},{"issue":"7","key":"5812_CR7","doi-asserted-by":"publisher","first-page":"1231","DOI":"10.1101\/gr.130062.111","volume":"22","author":"M Frenkel-Morgenstern","year":"2012","unstructured":"Frenkel-Morgenstern M, Lacroix V, Ezkurdia I, Levin Y, Gabashvili A, Prilusky J, Del Pozo A, Tress M, Johnson R, Guigo R: Chimeras taking shape: Potential functions of proteins encoded by chimeric RNA transcripts. Genome research. 2012, 22 (7): 1231-1242. 10.1101\/gr.130062.111.","journal-title":"Genome research"},{"key":"5812_CR8","first-page":"D34","volume":"33 Database","author":"DA Benson","year":"2005","unstructured":"Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL: GenBank. Nucleic acids research. 2005, D34-38. 33 Database","journal-title":"Nucleic acids research"},{"issue":"20","key":"5812_CR9","doi-asserted-by":"publisher","first-page":"2903","DOI":"10.1093\/bioinformatics\/btr467","volume":"27","author":"MK Iyer","year":"2011","unstructured":"Iyer MK, Chinnaiyan AM, Maher CA: ChimeraScan: a tool for identifying chimeric transcription in sequencing data. Bioinformatics. 2011, 27 (20): 2903-2904. 10.1093\/bioinformatics\/btr467.","journal-title":"Bioinformatics"},{"issue":"5","key":"5812_CR10","doi-asserted-by":"publisher","first-page":"e1001138","DOI":"10.1371\/journal.pcbi.1001138","volume":"7","author":"A McPherson","year":"2011","unstructured":"McPherson A, Hormozdiari F, Zayed A, Giuliany R, Ha G, Sun MG, Griffith M, Heravi Moussavi A, Senz J, Melnyk N: deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data. PLoS computational biology. 2011, 7 (5): e1001138-10.1371\/journal.pcbi.1001138.","journal-title":"PLoS computational biology"},{"issue":"6","key":"5812_CR11","doi-asserted-by":"publisher","first-page":"e39987","DOI":"10.1371\/journal.pone.0039987","volume":"7","author":"RW Francis","year":"2012","unstructured":"Francis RW, Thompson-Wicking K, Carter KW, Anderson D, Kees UR, Beesley AH: FusionFinder: a software tool to identify expressed gene fusion candidates from RNA-Seq data. PloS one. 2012, 7 (6): e39987-10.1371\/journal.pone.0039987.","journal-title":"PloS one"},{"issue":"12","key":"5812_CR12","doi-asserted-by":"publisher","first-page":"1708","DOI":"10.1093\/bioinformatics\/btr265","volume":"27","author":"Y Li","year":"2011","unstructured":"Li Y, Chien J, Smith DI, Ma J: FusionHunter: identifying fusion transcripts in cancer using paired-end RNA-seq. Bioinformatics. 2011, 27 (12): 1708-1710. 10.1093\/bioinformatics\/btr265.","journal-title":"Bioinformatics"},{"issue":"14","key":"5812_CR13","doi-asserted-by":"publisher","first-page":"1922","DOI":"10.1093\/bioinformatics\/btr310","volume":"27","author":"H Ge","year":"2011","unstructured":"Ge H, Liu K, Juan T, Fang F, Newman M, Hoeck W: FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution. Bioinformatics. 2011, 27 (14): 1922-1928. 10.1093\/bioinformatics\/btr310.","journal-title":"Bioinformatics"},{"issue":"18","key":"5812_CR14","doi-asserted-by":"publisher","first-page":"e178","DOI":"10.1093\/nar\/gkq622","volume":"38","author":"K Wang","year":"2010","unstructured":"Wang K, Singh D, Zeng Z, Coleman SJ, Huang Y, Savich GL, He X, Mieczkowski P, Grimm SA, Perou CM: MapSplice: accurate mapping of RNA-seq reads for splice junction discovery. Nucleic acids research. 2010, 38 (18): e178-10.1093\/nar\/gkq622.","journal-title":"Nucleic acids research"},{"issue":"8","key":"5812_CR15","doi-asserted-by":"publisher","first-page":"1068","DOI":"10.1093\/bioinformatics\/btr085","volume":"27","author":"M Kinsella","year":"2011","unstructured":"Kinsella M, Harismendy O, Nakano M, Frazer KA, Bafna V: Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs. Bioinformatics. 2011, 27 (8): 1068-1075. 10.1093\/bioinformatics\/btr085.","journal-title":"Bioinformatics"},{"issue":"8","key":"5812_CR16","doi-asserted-by":"publisher","first-page":"R72","DOI":"10.1186\/gb-2011-12-8-r72","volume":"12","author":"D Kim","year":"2011","unstructured":"Kim D, Salzberg SL: TopHat-Fusion: an algorithm for discovery of novel fusion transcripts. Genome biology. 2011, 12 (8): R72-10.1186\/gb-2011-12-8-r72.","journal-title":"Genome biology"},{"issue":"18","key":"5812_CR17","doi-asserted-by":"crossref","first-page":"2518","DOI":"10.1093\/bioinformatics\/btr427","volume":"27","author":"GR Grant","year":"2011","unstructured":"Grant GR, Farkas MH, Pizarro AD, Lahens NF, Schug J, Brunk BP, Stoeckert CJ, Hogenesch JB, Pierce EA: Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq unified mapper (RUM). Bioinformatics. 2011, 27 (18): 2518-2528.","journal-title":"Bioinformatics"},{"key":"5812_CR18","doi-asserted-by":"crossref","unstructured":"Trapnell C, Pachter L, Salzberg SL: TopHat: discovering splice junctions with RNA-seq. Bioinformatics. 2009, 25 (9): 10.1093\/bioinformatics\/btp120.","DOI":"10.1093\/bioinformatics\/btp120"},{"issue":"10","key":"5812_CR19","doi-asserted-by":"publisher","first-page":"R80","DOI":"10.1186\/gb-2004-5-10-r80","volume":"5","author":"RC Gentleman","year":"2004","unstructured":"Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J: Bioconductor: open software development for computational biology and bioinformatics. Genome biology. 2004, 5 (10): R80-10.1186\/gb-2004-5-10-r80.","journal-title":"Genome biology"},{"issue":"24","key":"5812_CR20","doi-asserted-by":"publisher","first-page":"3406","DOI":"10.1093\/bioinformatics\/btm469","volume":"23","author":"R Sanges","year":"2007","unstructured":"Sanges R, Cordero F, Calogero RA: oneChannelGUI: a graphical interface to Bioconductor tools, designed for life scientists who are not familiar with R language. Bioinformatics. 2007, 23 (24): 3406-3408. 10.1093\/bioinformatics\/btm469.","journal-title":"Bioinformatics"},{"issue":"2","key":"5812_CR21","doi-asserted-by":"publisher","first-page":"218","DOI":"10.4161\/cc.8.2.7358","volume":"8","author":"H Li","year":"2009","unstructured":"Li H, Wang J, Ma X, Sklar J: Gene fusions and RNA trans-splicing in normal and neoplastic human cells. Cell Cycle. 2009, 8 (2): 218-222. 10.4161\/cc.8.2.7358.","journal-title":"Cell Cycle"},{"key":"5812_CR22","doi-asserted-by":"publisher","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","volume":"10","author":"B Langmead","year":"2009","unstructured":"Langmead B, Trapnell C, Pop M, Salzberg SL: Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biolology. 2009, 10: R25-10.1186\/gb-2009-10-3-r25.","journal-title":"Genome Biolology"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-14-S7-S2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-14-S7-S2\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-14-S7-S2.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,22]],"date-time":"2019-01-22T06:09:18Z","timestamp":1548137358000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-14-S7-S2"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,4]]},"references-count":22,"journal-issue":{"issue":"S7","published-print":{"date-parts":[[2013,4]]}},"alternative-id":["5812"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-14-s7-s2","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,4]]},"article-number":"S2"}}