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Research

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  Human papillomavirus and the landscape of secondary genetic alterations in oral cancers

  • Maura L. Gillison,
  • Keiko Akagi,
  • Weihong Xiao,
  • Bo Jiang,
  • Robert K.L. Pickard,
  • Jingfeng Li,
  • Benjamin J. Swanson,
  • Amit D. Agrawal,
  • Mark Zucker,
  • Birgit Stache-Crain,
  • Anne-Katrin Emde,
  • Heather M. Geiger,
  • Nicolas Robine,
  • Kevin R. Coombes,
  • and David E. Symer

  Genome Res. January 2019 29: 1-17; Published in Advance December 18, 2018, doi:10.1101/gr.241141.118
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  Rapid reversible changes in compartments and local chromatin organization revealed by hyperosmotic shock

  • Ramon Amat,
  • René Böttcher,
  • François Le Dily,
  • Enrique Vidal,
  • Javier Quilez,
  • Yasmina Cuartero,
  • Miguel Beato,
  • Eulàlia de Nadal,
  • and Francesc Posas

  Genome Res. January 2019 29: 18-28; Published in Advance December 6, 2018, doi:10.1101/gr.238527.118
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  Hormone-control regions mediate steroid receptor–dependent genome organization

  • François Le Dily,
  • Enrique Vidal,
  • Yasmina Cuartero,
  • Javier Quilez,
  • A. Silvina Nacht,
  • Guillermo P. Vicent,
  • José Carbonell-Caballero,
  • Priyanka Sharma,
  • José Luis Villanueva-Cañas,
  • Roberto Ferrari,
  • Lara Isabel De Llobet,
  • Gaetano Verde,
  • Roni H.G. Wright,
  • and Miguel Beato

  Genome Res. January 2019 29: 29-39; Published in Advance December 14, 2018, doi:10.1101/gr.243824.118
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  Widespread roles of enhancer-like transposable elements in cell identity and long-range genomic interactions

  • Yaqiang Cao,
  • Guoyu Chen,
  • Gang Wu,
  • Xiaoli Zhang,
  • Joseph McDermott,
  • Xingwei Chen,
  • Chi Xu,
  • Quanlong Jiang,
  • Zhaoxiong Chen,
  • Yingying Zeng,
  • Daosheng Ai,
  • Yi Huang,
  • and Jing-Dong J. Han

  Genome Res. January 2019 29: 40-52; Published in Advance November 19, 2018, doi:10.1101/gr.235747.118
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  A quantitative framework for characterizing the evolutionary history of mammalian gene expression

  • Jenny Chen,
  • Ross Swofford,
  • Jeremy Johnson,
  • Beryl B. Cummings,
  • Noga Rogel,
  • Kerstin Lindblad-Toh,
  • Wilfried Haerty,
  • Federica di Palma,
  • and Aviv Regev

  Genome Res. January 2019 29: 53-63; Published in Advance December 14, 2018, doi:10.1101/gr.237636.118
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  Accelerated rates of large-scale mutations in the presence of copper and nickel

  • Frédéric J.J. Chain,
  • Jullien M. Flynn,
  • James K. Bull,
  • and Melania E. Cristescu

  Genome Res. January 2019 29: 64-73; Published in Advance November 28, 2018, doi:10.1101/gr.234724.118
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  Nucleosome remodeling at origins of global genome–nucleotide excision repair occurs at the boundaries of higher-order chromatin structure

  • Patrick van Eijk,
  • Shuvro Prokash Nandi,
  • Shirong Yu,
  • Mark Bennett,
  • Matthew Leadbitter,
  • Yumin Teng,
  • and Simon H. Reed

  Genome Res. January 2019 29: 74-84; Published in Advance December 14, 2018, doi:10.1101/gr.237198.118
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  Transposable element insertions in fission yeast drive adaptation to environmental stress

  • Caroline Esnault,
  • Michael Lee,
  • Chloe Ham,
  • and Henry L. Levin

  Genome Res. January 2019 29: 85-95; Published in Advance December 12, 2018, doi:10.1101/gr.239699.118
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  Epigenetic mapping of the Arabidopsis metabolome reveals mediators of the epigenotype-phenotype map

  • Rik Kooke,
  • Lionel Morgado,
  • Frank Becker,
  • Henriëtte van Eekelen,
  • Rashmi Hazarika,
  • Qunfeng Zheng,
  • Ric C.H. de Vos,
  • Frank Johannes,
  • and Joost J.B. Keurentjes

  Genome Res. January 2019 29: 96-106; Published in Advance November 30, 2018, doi:10.1101/gr.232371.117
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