{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,29]],"date-time":"2026-05-29T10:32:22Z","timestamp":1780050742568,"version":"3.53.1"},"reference-count":14,"publisher":"Oxford University Press (OUP)","issue":"14","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2012,7,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Summary: Despite recent progress, computational tools that identify gene fusions from next-generation whole transcriptome sequencing data are often limited in accuracy and scalability. Here, we present a software package, BreakFusion that combines the strength of reference alignment followed by read-pair analysis and de novo assembly to achieve a good balance in sensitivity, specificity and computational efficiency.<\/jats:p>\n               <jats:p>Availability: \u00a0http:\/\/bioinformatics.mdanderson.org\/main\/BreakFusion<\/jats:p>\n               <jats:p>Contact: \u00a0kchen3@mdanderson.org; lding@genome.wustl.edu<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online<\/jats:p>","DOI":"10.1093\/bioinformatics\/bts272","type":"journal-article","created":{"date-parts":[[2012,5,5]],"date-time":"2012-05-05T09:09:30Z","timestamp":1336208970000},"page":"1923-1924","source":"Crossref","is-referenced-by-count":52,"title":["BreakFusion: targeted assembly-based identification of gene fusions in whole transcriptome paired-end sequencing data"],"prefix":"10.1093","volume":"28","author":[{"given":"Ken","family":"Chen","sequence":"first","affiliation":[{"name":"1 Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX, 2The Genome Institute, 3Department of Genetics, Washington University, St Louis, MO, USA, 4Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada and 5Department of Internal Medicine, Division of Oncology, Washington University, St Louis, MO, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John W.","family":"Wallis","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX, 2The Genome Institute, 3Department of Genetics, Washington University, St Louis, MO, USA, 4Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada and 5Department of Internal Medicine, Division of Oncology, Washington University, St Louis, MO, USA"},{"name":"1 Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX, 2The Genome Institute, 3Department of Genetics, Washington University, St Louis, MO, USA, 4Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada and 5Department of Internal Medicine, Division of Oncology, Washington University, St Louis, MO, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cyriac","family":"Kandoth","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX, 2The Genome Institute, 3Department of Genetics, Washington University, St Louis, MO, USA, 4Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada and 5Department of Internal Medicine, Division of Oncology, Washington University, St Louis, MO, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Joelle M.","family":"Kalicki\u2212Veizer","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX, 2The Genome Institute, 3Department of Genetics, Washington University, St Louis, MO, USA, 4Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada and 5Department of Internal Medicine, Division of Oncology, Washington University, St Louis, MO, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karen L.","family":"Mungall","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX, 2The Genome Institute, 3Department of Genetics, Washington University, St Louis, MO, USA, 4Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada and 5Department of Internal Medicine, Division of Oncology, Washington University, St Louis, MO, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew J.","family":"Mungall","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX, 2The Genome Institute, 3Department of Genetics, Washington University, St Louis, MO, USA, 4Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada and 5Department of Internal Medicine, Division of Oncology, Washington University, St Louis, MO, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Steven J.","family":"Jones","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX, 2The Genome Institute, 3Department of Genetics, Washington University, St Louis, MO, USA, 4Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada and 5Department of Internal Medicine, Division of Oncology, Washington University, St Louis, MO, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marco A.","family":"Marra","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX, 2The Genome Institute, 3Department of Genetics, Washington University, St Louis, MO, USA, 4Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada and 5Department of Internal Medicine, Division of Oncology, Washington University, St Louis, MO, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Timothy J.","family":"Ley","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX, 2The Genome Institute, 3Department of Genetics, Washington University, St Louis, MO, USA, 4Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada and 5Department of Internal Medicine, Division of Oncology, Washington University, St Louis, MO, USA"},{"name":"1 Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX, 2The Genome Institute, 3Department of Genetics, Washington University, St Louis, MO, USA, 4Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada and 5Department of Internal Medicine, Division of Oncology, Washington University, St Louis, MO, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elaine R.","family":"Mardis","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX, 2The Genome Institute, 3Department of Genetics, Washington University, St Louis, MO, USA, 4Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada and 5Department of Internal Medicine, Division of Oncology, Washington University, St Louis, MO, USA"},{"name":"1 Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX, 2The Genome Institute, 3Department of Genetics, Washington University, St Louis, MO, USA, 4Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada and 5Department of Internal Medicine, Division of Oncology, Washington University, St Louis, MO, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Richard K.","family":"Wilson","sequence":"additional","affiliation":[{"name":"1 Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX, 2The Genome Institute, 3Department of Genetics, Washington University, St Louis, MO, USA, 4Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada and 5Department 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