{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,5,15]],"date-time":"2025-05-15T06:44:58Z","timestamp":1747291498895},"reference-count":20,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2013,1,16]],"date-time":"2013-01-16T00:00:00Z","timestamp":1358294400000},"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":[[2013,12]]},"DOI":"10.1186\/1471-2105-14-13","type":"journal-article","created":{"date-parts":[[2013,1,16]],"date-time":"2013-01-16T06:21:55Z","timestamp":1358317315000},"source":"Crossref","is-referenced-by-count":15,"title":["FUSIM: a software tool for simulating fusion transcripts"],"prefix":"10.1186","volume":"14","author":[{"given":"Andrew E","family":"Bruno","sequence":"first","affiliation":[]},{"given":"Jeffrey C","family":"Miecznikowski","sequence":"additional","affiliation":[]},{"given":"Maochun","family":"Qin","sequence":"additional","affiliation":[]},{"given":"Jianmin","family":"Wang","sequence":"additional","affiliation":[]},{"given":"Song","family":"Liu","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2013,1,16]]},"reference":[{"issue":"4","key":"5827_CR1","doi-asserted-by":"publisher","first-page":"233","DOI":"10.1038\/nrc2091","volume":"7","author":"F Mitelman","year":"2007","unstructured":"Mitelman F, Johansson B, Mertens F: The impact of translocations and gene fusions on cancer causation. Nat Rev Cancer 2007,7(4):233-245. 10.1038\/nrc2091","journal-title":"Nat Rev Cancer"},{"issue":"5748","key":"5827_CR2","doi-asserted-by":"publisher","first-page":"644","DOI":"10.1126\/science.1117679","volume":"310","author":"SA Tomlins","year":"2005","unstructured":"Tomlins SA, Rhodes DR, Perner S, Dhanasekaran SM, Mehra R, Sun XW, Varambally S, Cao X, Tchinda J, Kuefer R, Lee C, Montie JE, Shah RB, Pienta KJ, Rubin MA, Chinnaiyan AM: Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science 2005,310(5748):644-648. 10.1126\/science.1117679","journal-title":"Science"},{"issue":"7153","key":"5827_CR3","doi-asserted-by":"publisher","first-page":"561","DOI":"10.1038\/nature05945","volume":"448","author":"M Soda","year":"2007","unstructured":"Soda M, Choi YL, Enomoto M, Takada S, Yamashita Y, Ishikawa S, ichiro Fujiwara S, Watanabe H, Kurashina K, Hatanaka H, Bando M, Ohno S, Ishikawa Y, Aburatani H, Niki T, Sohara Y, Sugiyama Y, Mano H: Identification of the transforming EML4-ALK fusion gene in non-small-cell lung cancer. Nature 2007,448(7153):561-566. 10.1038\/nature05945","journal-title":"Nature"},{"issue":"3","key":"5827_CR4","doi-asserted-by":"publisher","first-page":"245","DOI":"10.1038\/35106108","volume":"1","author":"JD Rowley","year":"2001","unstructured":"Rowley JD: Chromosome translocations: dangerous liaisons revisited. Nat Rev Cancer 2001,1(3):245-250. 10.1038\/35106108","journal-title":"Nat Rev Cancer"},{"issue":"7234","key":"5827_CR5","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":"20","key":"5827_CR6","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":"5827_CR7","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 MGF, Griffith M, Moussavi AH, Senz J, Melnyk N, Pacheco M, Marra MA, Hirst M, Nielsen TO, Sahinalp SC, Huntsman D, Shah SP: deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data. PLoS Comput Biol 2011,7(5):e1001138. 10.1371\/journal.pcbi.1001138","journal-title":"PLoS Comput Biol"},{"issue":"14","key":"5827_CR8","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":"15","key":"5827_CR9","doi-asserted-by":"publisher","first-page":"e100","DOI":"10.1093\/nar\/gkr362","volume":"39","author":"YW Asmann","year":"2011","unstructured":"Asmann YW, Hossain A, Necela BM, Middha S, Kalari KR, Sun Z, Chai HS, Williamson DW, Radisky D, Schroth GP, Kocher JPA, Perez EA, Thompson EA: A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines. Nucleic Acids Res 2011,39(15):e100. 10.1093\/nar\/gkr362","journal-title":"Nucleic Acids Res"},{"issue":"12","key":"5827_CR10","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"},{"key":"5827_CR11","unstructured":"GenePred Table Format [\n                    http:\/\/genome.ucsc.edu\/FAQ\/FAQformat.html#format9\n                    \n                  ] []"},{"key":"5827_CR12","unstructured":"Gene Feature Format [\n                    http:\/\/www.sanger.ac.uk\/resources\/software\/gff\/\n                    \n                  ] []"},{"key":"5827_CR13","unstructured":"Gene Transfer Format [\n                    http:\/\/mblab.wustl.edu\/GTF22.html\n                    \n                  ] []"},{"issue":"8","key":"5827_CR14","doi-asserted-by":"publisher","first-page":"2444","DOI":"10.1073\/pnas.85.8.2444","volume":"85","author":"WR Pearson","year":"1988","unstructured":"Pearson WR, Lipman DJ: Improved tools for biological sequence comparison. Proc Natl Acad Sci U S A 1988,85(8):2444-2448. 10.1073\/pnas.85.8.2444","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"16","key":"5827_CR15","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, Subgroup GPDP: The Sequence Alignment\/Map format and SAMtools. Bioinformatics 2009,25(16):2078-2079. 10.1093\/bioinformatics\/btp352","journal-title":"Bioinformatics"},{"issue":"7","key":"5827_CR16","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. Nat Methods 2008,5(7):621-628. 10.1038\/nmeth.1226","journal-title":"Nat Methods"},{"issue":"4","key":"5827_CR17","doi-asserted-by":"publisher","first-page":"476","DOI":"10.1093\/humupd\/dmr010","volume":"17","author":"F Pellestor","year":"2011","unstructured":"Pellestor F, Anahory T, Lefort G, Puechberty J, Liehr T, H\u00e9don B, Sarda P: Complex chromosomal rearrangements: origin and meiotic behavior. Hum Reprod Update 2011,17(4):476-494. 10.1093\/humupd\/dmr010","journal-title":"Hum Reprod Update"},{"issue":"Database issue","key":"5827_CR18","doi-asserted-by":"publisher","first-page":"D81","DOI":"10.1093\/nar\/gkp982","volume":"38","author":"P Kim","year":"2010","unstructured":"Kim P, Yoon S, Kim N, Lee S, Ko M, Lee H, Kang H, Kim J, Lee S: ChimerDB 2.0-a knowledgebase for fusion genes updated. Nucleic Acids Res 2010,38(Database issue):D81-D85. 10.1093\/nar\/gkp982","journal-title":"Nucleic Acids Res"},{"issue":"6","key":"5827_CR19","doi-asserted-by":"publisher","first-page":"1767","DOI":"10.1093\/nar\/gkp1137","volume":"38","author":"PJA Cock","year":"2010","unstructured":"Cock PJA, Fields CJ, Goto N, Heuer ML, Rice PM: The Sanger FASTQ file format for sequences with quality scores, and the Solexa\/Illumina FASTQ variants. Nucleic Acids Res 2010,38(6):1767-1771. 10.1093\/nar\/gkp1137","journal-title":"Nucleic Acids Res"},{"issue":"4","key":"5827_CR20","doi-asserted-by":"publisher","first-page":"593","DOI":"10.1093\/bioinformatics\/btr708","volume":"28","author":"W Huang","year":"2012","unstructured":"Huang W, Li L, Myers JR, Marth GT: ART: a next-generation sequencing read simulator. Bioinformatics 2012,28(4):593-594. 10.1093\/bioinformatics\/btr708","journal-title":"Bioinformatics"}],"container-title":["BMC Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-14-13.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1471-2105-14-13\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1471-2105-14-13.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,1,22]],"date-time":"2019-01-22T05:30:17Z","timestamp":1548135017000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcbioinformatics.biomedcentral.com\/articles\/10.1186\/1471-2105-14-13"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,1,16]]},"references-count":20,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2013,12]]}},"alternative-id":["5827"],"URL":"https:\/\/doi.org\/10.1186\/1471-2105-14-13","relation":{},"ISSN":["1471-2105"],"issn-type":[{"value":"1471-2105","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,1,16]]},"article-number":"13"}}