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  1. Method: HIT'nDRIVE: patient-specific multidriver gene prioritization for precision oncology
    • Raunak Shrestha,
    • Ermin Hodzic,
    • Thomas Sauerwald,
    • Phuong Dao,
    • Kendric Wang,
    • Jake Yeung,
    • Shawn Anderson,
    • Fabio Vandin,
    • Gholamreza Haffari,
    • Colin C. Collins,
    • and S. Cenk Sahinalp
    Genome Res. September 2017 27: 1573-1588; Published in Advance July 18, 2017, doi:10.1101/gr.221218.117
  2. Research: Imprints and DPPA3 are bypassed during pluripotency- and differentiation-coupled methylation reprogramming in testicular germ cell tumors
    • J. Keith Killian,
    • Lambert C.J. Dorssers,
    • Britton Trabert,
    • Ad J.M. Gillis,
    • Michael B. Cook,
    • Yonghong Wang,
    • Joshua J. Waterfall,
    • Holly Stevenson,
    • William I. Smith, Jr.,
    • Natalia Noyes,
    • Parvathy Retnakumar,
    • J. Hans Stoop,
    • J. Wolter Oosterhuis,
    • Paul S. Meltzer,
    • Katherine A. McGlynn,
    • and Leendert H.J. Looijenga
    Genome Res. November 2016 26: 1490-1504; Published in Advance October 20, 2016, doi:10.1101/gr.201293.115
    ...Imprints and DPPA3 are bypassed during pluripotency- and differentiation-coupled methylation reprogramming in testicular germ cell tumors J. Keith Killian 1 , Lambert C.J. Dorssers 2 , Britton Trabert 3 , Ad J.M. Gillis 2 , Michael B. Cook 3 ...
  3. Research: Specific down-regulation of spermatogenesis genes targeted by 22G RNAs in hybrid sterile males associated with an X-Chromosome introgression
    • Runsheng Li,
    • Xiaoliang Ren,
    • Yu Bi,
    • Vincy Wing Sze Ho,
    • Chia-Ling Hsieh,
    • Amanda Young,
    • Zhihong Zhang,
    • Tingting Lin,
    • Yanmei Zhao,
    • Long Miao,
    • Peter Sarkies,
    • and Zhongying Zhao
    Genome Res. September 2016 26: 1219-1232; Published in Advance May 18, 2016, doi:10.1101/gr.204479.116
  4. Resource: The EnteroBase user's guide, with case studies on Salmonella transmissions, Yersinia pestis phylogeny, and Escherichia core genomic diversity
    • Zhemin Zhou,
    • Nabil-Fareed Alikhan,
    • Khaled Mohamed,
    • Yulei Fan,
    • the Agama Study Group,
    • and Mark Achtman
    Genome Res. January 2020 30: 138-152; Published in Advance December 6, 2019, doi:10.1101/gr.251678.119
    OPEN ACCESS ARTICLE
  5. Research: Whole-genome sequencing reveals high complexity of copy number variation at insecticide resistance loci in malaria mosquitoes
    • Eric R. Lucas,
    • Alistair Miles,
    • Nicholas J. Harding,
    • Chris S. Clarkson,
    • Mara K.N. Lawniczak,
    • Dominic P. Kwiatkowski,
    • David Weetman,
    • Martin J. Donnelly,
    • and The Anopheles gambiae 1000 Genomes Consortium
    Genome Res. August 2019 29: 1250-1261; Published in Advance July 25, 2019, doi:10.1101/gr.245795.118
    OPEN ACCESS ARTICLE
  6. Research: Determinants of nucleosome positioning and their influence on plant gene expression
    • Ming-Jung Liu,
    • Alexander E. Seddon,
    • Zing Tsung-Yeh Tsai,
    • Ian T. Major,
    • Monique Floer,
    • Gregg A. Howe,
    • and Shin-Han Shiu
    Genome Res. August 2015 25: 1182-1195; Published in Advance June 10, 2015, doi:10.1101/gr.188680.114
  7. Research: Retrotransposition creates sloping shores: a graded influence of hypomethylated CpG islands on flanking CpG sites
    • Fiorella C. Grandi,
    • James M. Rosser,
    • Simon J. Newkirk,
    • Jun Yin,
    • Xiaoling Jiang,
    • Zhuo Xing,
    • Leanne Whitmore,
    • Sanum Bashir,
    • Zoltán Ivics,
    • Zsuzsanna Izsvák,
    • Ping Ye,
    • Y. Eugene Yu,
    • and Wenfeng An
    Genome Res. August 2015 25: 1135-1146; Published in Advance May 20, 2015, doi:10.1101/gr.185132.114
    OPEN ACCESS ARTICLE
  8. Research: Redundant and specific roles of cohesin STAG subunits in chromatin looping and transcriptional control
    • Valentina Casa,
    • Macarena Moronta Gines,
    • Eduardo Gade Gusmao,
    • Johan A. Slotman,
    • Anne Zirkel,
    • Natasa Josipovic,
    • Edwin Oole,
    • Wilfred F.J. van IJcken,
    • Adriaan B. Houtsmuller,
    • Argyris Papantonis,
    • and Kerstin S. Wendt
    Genome Res. April 2020 30: 515-527; Published in Advance April 6, 2020, doi:10.1101/gr.253211.119
    OPEN ACCESS ARTICLE
  9. Resource: Integrated annotations and analyses of small RNA–producing loci from 47 diverse plants
    • Alice Lunardon,
    • Nathan R. Johnson,
    • Emily Hagerott,
    • Tamia Phifer,
    • Seth Polydore,
    • Ceyda Coruh,
    • and Michael J. Axtell
    Genome Res. March 2020 30: 497-513; Published in Advance March 16, 2020, doi:10.1101/gr.256750.119
  10. Research: Thrombopoietin signaling to chromatin elicits rapid and pervasive epigenome remodeling within poised chromatin architectures
    • Federico Comoglio,
    • Hyun Jung Park,
    • Stefan Schoenfelder,
    • Iros Barozzi,
    • Daniel Bode,
    • Peter Fraser,
    • and Anthony R. Green
    Genome Res. March 2018 28: 295-309; Published in Advance February 2, 2018, doi:10.1101/gr.227272.117
    OPEN ACCESS ARTICLE
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