{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,22]],"date-time":"2026-01-22T04:46:51Z","timestamp":1769057211214,"version":"3.49.0"},"reference-count":12,"publisher":"Oxford University Press (OUP)","issue":"20","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Next generation sequencing (NGS) technologies have enabled de novo gene fusion discovery that could reveal candidates with therapeutic significance in cancer. Here we present an open-source software package, ChimeraScan, for the discovery of chimeric transcription between two independent transcripts in high-throughput transcriptome sequencing data.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/chimerascan.googlecode.com<\/jats:p>\n               <jats:p>Contact: \u00a0cmaher@dom.wustl.edu<\/jats:p>\n               <jats:p>Supplementary Information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btr467","type":"journal-article","created":{"date-parts":[[2011,8,13]],"date-time":"2011-08-13T00:26:20Z","timestamp":1313195180000},"page":"2903-2904","source":"Crossref","is-referenced-by-count":233,"title":["ChimeraScan: a tool for identifying chimeric transcription in sequencing data"],"prefix":"10.1093","volume":"27","author":[{"given":"Matthew K.","family":"Iyer","sequence":"first","affiliation":[{"name":"1 Michigan Center for Translational Pathology, 2Center for Computational Medicine and Biology, 3Department of Pathology, 4Howard Hughes Medical Institute and 5Department of Urology, University of Michigan Medical School, Ann Arbor, MI 48109, USA"},{"name":"1 Michigan Center for Translational Pathology, 2Center for Computational Medicine and Biology, 3Department of Pathology, 4Howard Hughes Medical Institute and 5Department of Urology, University of Michigan Medical School, Ann Arbor, MI 48109, USA"}]},{"given":"Arul M.","family":"Chinnaiyan","sequence":"additional","affiliation":[{"name":"1 Michigan Center for Translational Pathology, 2Center for Computational Medicine and Biology, 3Department of Pathology, 4Howard Hughes Medical Institute and 5Department of Urology, University of Michigan Medical School, Ann Arbor, MI 48109, USA"},{"name":"1 Michigan Center for Translational Pathology, 2Center for Computational Medicine and Biology, 3Department of Pathology, 4Howard Hughes Medical Institute and 5Department of Urology, University of Michigan Medical School, Ann Arbor, MI 48109, USA"},{"name":"1 Michigan Center for Translational Pathology, 2Center for Computational Medicine and Biology, 3Department of Pathology, 4Howard Hughes Medical Institute and 5Department of Urology, University of Michigan Medical School, Ann Arbor, MI 48109, USA"},{"name":"1 Michigan Center for Translational Pathology, 2Center for Computational Medicine and Biology, 3Department of Pathology, 4Howard Hughes Medical Institute and 5Department of Urology, University of Michigan Medical School, Ann Arbor, MI 48109, USA"},{"name":"1 Michigan Center for Translational Pathology, 2Center for Computational Medicine and Biology, 3Department of Pathology, 4Howard Hughes Medical Institute and 5Department of Urology, University of Michigan Medical School, Ann Arbor, MI 48109, USA"}]},{"given":"Christopher A.","family":"Maher","sequence":"additional","affiliation":[{"name":"1 Michigan Center for Translational Pathology, 2Center for Computational Medicine and Biology, 3Department of Pathology, 4Howard Hughes Medical Institute and 5Department of Urology, University of Michigan Medical School, Ann Arbor, MI 48109, USA"},{"name":"1 Michigan Center for Translational Pathology, 2Center for Computational Medicine and Biology, 3Department of Pathology, 4Howard Hughes Medical Institute and 5Department of Urology, University of Michigan Medical School, Ann Arbor, MI 48109, USA"},{"name":"1 Michigan Center for Translational Pathology, 2Center for Computational Medicine and Biology, 3Department of Pathology, 4Howard Hughes Medical Institute and 5Department of Urology, University of Michigan Medical School, Ann Arbor, MI 48109, USA"}]}],"member":"286","published-online":{"date-parts":[[2011,8,11]]},"reference":[{"key":"2023012512014081200_B1","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1101\/gr.080259.108","article-title":"A sequence-level map of chromosomal breakpoints in the MCF-7 breast cancer cell line yields insights into the evolution of a cancer genome","volume":"19","author":"Hampton","year":"2009","journal-title":"Genome Res."},{"key":"2023012512014081200_B2","doi-asserted-by":"crossref","first-page":"1068","DOI":"10.1093\/bioinformatics\/btr085","article-title":"Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs","volume":"27","author":"Kinsella","year":"2011","journal-title":"Bioinformatics"},{"key":"2023012512014081200_B3","doi-asserted-by":"crossref","first-page":"R25","DOI":"10.1186\/gb-2009-10-3-r25","article-title":"Ultrafast and memory-efficient alignment of short DNA sequences to the human genome","volume":"10","author":"Langmead","year":"2009","journal-title":"Genome Biol."},{"key":"2023012512014081200_B4","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1038\/nature07638","article-title":"Transcriptome sequencing to detect gene fusions in cancer","volume":"458","author":"Maher","year":"2009","journal-title":"Nature"},{"key":"2023012512014081200_B5","doi-asserted-by":"crossref","first-page":"12353","DOI":"10.1073\/pnas.0904720106","article-title":"Chimeric transcript discovery by paired-end transcriptome sequencing","volume":"106","author":"Maher","year":"2009","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"2023012512014081200_B6","doi-asserted-by":"crossref","first-page":"e1001138","DOI":"10.1371\/journal.pcbi.1001138","article-title":"deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data","volume":"7","author":"McPherson","year":"2011","journal-title":"PLoS Comput. Biol."},{"key":"2023012512014081200_B7","doi-asserted-by":"crossref","first-page":"793","DOI":"10.1038\/nm.2166","article-title":"Rearrangements of the RAF kinase pathway in prostate cancer, gastric cancer and melanoma","volume":"16","author":"Palanisamy","year":"2010","journal-title":"Nat. Med."},{"key":"2023012512014081200_B8","doi-asserted-by":"crossref","first-page":"828","DOI":"10.1101\/gr.6018607","article-title":"Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs)","volume":"17","author":"Ruan","year":"2007","journal-title":"Genome Res."},{"key":"2023012512014081200_B9","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1038\/nature09754","article-title":"MHC class II transactivator CIITA is a recurrent gene fusion partner in lymphoid cancers","volume":"471","author":"Steidl","year":"2011","journal-title":"Nature"},{"key":"2023012512014081200_B10","doi-asserted-by":"crossref","first-page":"644","DOI":"10.1126\/science.1117679","article-title":"Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer","volume":"310","author":"Tomlins","year":"2005","journal-title":"Science"},{"key":"2023012512014081200_B11","doi-asserted-by":"crossref","first-page":"394","DOI":"10.1101\/gr.4247306","article-title":"Decoding the fine-scale structure of a breast cancer genome and transcriptome","volume":"16","author":"Volik","year":"2006","journal-title":"Genome Res."},{"key":"2023012512014081200_B12","doi-asserted-by":"crossref","first-page":"e178","DOI":"10.1093\/nar\/gkq622","article-title":"MapSplice: accurate mapping of RNA-seq reads for splice junction discovery","volume":"38","author":"Wang","year":"2010","journal-title":"Nucleic Acids Res."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/20\/2903\/48874224\/bioinformatics_27_20_2903.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/27\/20\/2903\/48874224\/bioinformatics_27_20_2903.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,25]],"date-time":"2023-01-25T14:12:48Z","timestamp":1674655968000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/27\/20\/2903\/201441"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011,8,11]]},"references-count":12,"journal-issue":{"issue":"20","published-print":{"date-parts":[[2011,10,15]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btr467","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2011,10,15]]},"published":{"date-parts":[[2011,8,11]]}}}