Searching journal content for articles similar to Drier et al. 23 (2): 228.

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  1. Research: Somatic structural variant formation is guided by and influences genome architecture
    • Nikos Sidiropoulos,
    • Balca R. Mardin,
    • F. Germán Rodríguez-González,
    • Ivan D. Bochkov,
    • Shilpa Garg,
    • Adrian M. Stütz,
    • Jan O. Korbel,
    • Erez Lieberman Aiden,
    • and Joachim Weischenfeldt
    Genome Res. April 2022 32: 643-655; Published in Advance February 17, 2022, doi:10.1101/gr.275790.121
    ...genomic rearrangements in a single cell cycle (Mardin et al. 2015). Dox, a widely used chemotherapeutic, traps Topoisomerase II (TOP2) on DNA and acts as a poison for TOP2 cleavage complexes by inhibiting DNA religation, causing TOP2-linked double-strand breaks (DSBs), which can result in the formation...
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  2. Method: Single-cell sequencing data reveal widespread recurrence and loss of mutational hits in the life histories of tumors
    • Jack Kuipers,
    • Katharina Jahn,
    • Benjamin J. Raphael,
    • and Niko Beerenwinkel
    Genome Res. November 2017 27: 1885-1894; Published in Advance October 13, 2017, doi:10.1101/gr.220707.117
    ...–523. Drier Y, LawrenceMS, Carter SL, Stewart C, Gabriel SB, Lander ES,Meyerson M, Beroukhim R, Getz G. 2013. Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability. Genome Res 23: 228–235. El-Kebir M, Oesper L, Acheson...
  3. Method: SvABA: genome-wide detection of structural variants and indels by local assembly
    • Jeremiah A. Wala,
    • Pratiti Bandopadhayay,
    • Noah F. Greenwald,
    • Ryan O'Rourke,
    • Ted Sharpe,
    • Chip Stewart,
    • Steve Schumacher,
    • Yilong Li,
    • Joachim Weischenfeldt,
    • Xiaotong Yao,
    • Chad Nusbaum,
    • Peter Campbell,
    • Gad Getz,
    • Matthew Meyerson,
    • Cheng-Zhong Zhang,
    • Marcin Imielinski,
    • and Rameen Beroukhim
    Genome Res. April 2018 28: 581-591; Published in Advance March 13, 2018, doi:10.1101/gr.221028.117
    ...papillomavirus (HPV). HPV is a known oncovirus in head and neck cancer and is known to integrate into the of tumor cells (Parfenov et al. 2014). SvABA identified 16 breakpoints across seven samples where viral sequences were fused with genomic DNA (Supplemental Table S5). All of the viral junctions involved...
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