{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,9]],"date-time":"2026-09-09T23:41:31Z","timestamp":1788997291813,"version":"build-2803163510"},"reference-count":19,"publisher":"Oxford University Press (OUP)","issue":"23","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2014,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Summary: For practical and robust de novo identification of genomic fusions and breakpoints from targeted paired-end DNA sequencing data, we developed Fusion And Chromosomal Translocation Enumeration and Recovery Algorithm (FACTERA). Our method has minimal external dependencies, works directly on a preexisting Binary Alignment\/Map file and produces easily interpretable output. We demonstrate FACTERA\u2019s ability to rapidly identify breakpoint-resolution fusion events with high sensitivity and specificity in patients with non-small cell lung cancer, including novel rearrangements. We anticipate that FACTERA will be broadly applicable to the discovery and analysis of clinically relevant fusions from both targeted and genome-wide sequencing datasets.<\/jats:p>\n                  <jats:p>Availability and implementation: \u00a0http:\/\/factera.stanford.edu.<\/jats:p>\n                  <jats:p>Contact: \u00a0arasha@stanford.edu or diehn@stanford.edu<\/jats:p>\n                  <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btu549","type":"journal-article","created":{"date-parts":[[2014,8,21]],"date-time":"2014-08-21T00:05:53Z","timestamp":1408579553000},"page":"3390-3393","source":"Crossref","is-referenced-by-count":219,"title":["FACTERA: a practical method for the discovery of genomic rearrangements at breakpoint resolution"],"prefix":"10.1093","volume":"30","author":[{"given":"Aaron M.","family":"Newman","sequence":"first","affiliation":[{"name":"1 Institute for Stem Cell Biology and Regenerative Medicine, 2Division of Oncology, Department of Medicine, 3Department of Radiation Oncology and 4Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA"},{"name":"1 Institute for Stem Cell Biology and Regenerative Medicine, 2Division of Oncology, Department of Medicine, 3Department of Radiation Oncology and 4Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Scott V.","family":"Bratman","sequence":"additional","affiliation":[{"name":"1 Institute for Stem Cell Biology and Regenerative Medicine, 2Division of Oncology, Department of Medicine, 3Department of Radiation Oncology and 4Stanford Cancer Institute, Stanford University, Stanford, CA 94305, USA"},{"name":"1 Institute for Stem Cell Biology and Regenerative Medicine, 2Division of Oncology, Department of Medicine, 3Department of Radiation Oncology and 4Stanford Cancer Institute, Stanford University, 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