Table of Contents

March 2016; 26 (3)

Research

  • Whole-genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection

    • PingHsun Hsieh,
    • Krishna R. Veeramah,
    • Joseph Lachance,
    • Sarah A. Tishkoff,
    • Jeffrey D. Wall,
    • Michael F. Hammer,
    • and Ryan N. Gutenkunst
    Genome Res. March 2016 26: 279-290; Published in Advance February 17, 2016, doi:10.1101/gr.192971.115

  • Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies

    • PingHsun Hsieh,
    • August E. Woerner,
    • Jeffrey D. Wall,
    • Joseph Lachance,
    • Sarah A. Tishkoff,
    • Ryan N. Gutenkunst,
    • and Michael F. Hammer
    Genome Res. March 2016 26: 291-300; Published in Advance February 17, 2016, doi:10.1101/gr.196634.115

  • The life history of retrocopies illuminates the evolution of new mammalian genes

    • Francesco Nicola Carelli,
    • Takashi Hayakawa,
    • Yasuhiro Go,
    • Hiroo Imai,
    • Maria Warnefors,
    • and Henrik Kaessmann
    Genome Res. March 2016 26: 301-314; Published in Advance January 4, 2016, doi:10.1101/gr.198473.115

  • Concerted activities of Mcm4, Sld3, and Dbf4 in control of origin activation and DNA replication fork progression

    • Yi-Jun Sheu,
    • Justin B. Kinney,
    • and Bruce Stillman
    Genome Res. March 2016 26: 315-330; Published in Advance January 5, 2016, doi:10.1101/gr.195248.115

  • TP53 regulates miRNA association with AGO2 to remodel the miRNA–mRNA interaction network

    • Jonathan Krell,
    • Justin Stebbing,
    • Claudia Carissimi,
    • Aleksandra F. Dabrowska,
    • Alexander de Giorgio,
    • Adam E. Frampton,
    • Victoria Harding,
    • Valerio Fulci,
    • Giuseppe Macino,
    • Teresa Colombo,
    • and Leandro Castellano
    Genome Res. March 2016 26: 331-341; Published in Advance December 23, 2015, doi:10.1101/gr.191759.115
    OPEN ACCESS ARTICLE

Methods

  • Chromosome-scale shotgun assembly using an in vitro method for long-range linkage

    • Nicholas H. Putnam,
    • Brendan L. O'Connell,
    • Jonathan C. Stites,
    • Brandon J. Rice,
    • Marco Blanchette,
    • Robert Calef,
    • Christopher J. Troll,
    • Andrew Fields,
    • Paul D. Hartley,
    • Charles W. Sugnet,
    • David Haussler,
    • Daniel S. Rokhsar,
    • and Richard E. Green
    Genome Res. March 2016 26: 342-350; Published in Advance February 4, 2016, doi:10.1101/gr.193474.115
    OPEN ACCESS ARTICLE

  • Mapping nucleosome positions using DNase-seq

    • Jianling Zhong,
    • Kaixuan Luo,
    • Peter S. Winter,
    • Gregory E. Crawford,
    • Edwin S. Iversen,
    • and Alexander J. Hartemink
    Genome Res. March 2016 26: 351-364; Published in Advance January 15, 2016, doi:10.1101/gr.195602.115

  • Quantitative BrdU immunoprecipitation method demonstrates that Fkh1 and Fkh2 are rate-limiting activators of replication origins that reprogram replication timing in G1 phase

    • Jared M. Peace,
    • Sandra K. Villwock,
    • John L. Zeytounian,
    • Yan Gan,
    • and Oscar M. Aparicio
    Genome Res. March 2016 26: 365-375; Published in Advance January 4, 2016, doi:10.1101/gr.196857.115

  • Assessment of megabase-scale somatic copy number variation using single-cell sequencing

    • Kristin A. Knouse,
    • Jie Wu,
    • and Angelika Amon
    Genome Res. March 2016 26: 376-384; Published in Advance January 15, 2016, doi:10.1101/gr.198937.115
    OPEN ACCESS ARTICLE

  • Models of human core transcriptional regulatory circuitries

    • Violaine Saint-André,
    • Alexander J. Federation,
    • Charles Y. Lin,
    • Brian J. Abraham,
    • Jessica Reddy,
    • Tong Ihn Lee,
    • James E. Bradner,
    • and Richard A. Young
    Genome Res. March 2016 26: 385-396; Published in Advance February 3, 2016, doi:10.1101/gr.197590.115

  • A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening

    • Yarui Diao,
    • Bin Li,
    • Zhipeng Meng,
    • Inkyung Jung,
    • Ah Young Lee,
    • Jesse Dixon,
    • Lenka Maliskova,
    • Kun-liang Guan,
    • Yin Shen,
    • and Bing Ren
    Genome Res. March 2016 26: 397-405; Published in Advance January 26, 2016, doi:10.1101/gr.197152.115

  • Genome-wide target specificities of CRISPR-Cas9 nucleases revealed by multiplex Digenome-seq

    • Daesik Kim,
    • Sojung Kim,
    • Sunghyun Kim,
    • Jeongbin Park,
    • and Jin-Soo Kim
    Genome Res. March 2016 26: 406-415; Published in Advance January 19, 2016, doi:10.1101/gr.199588.115
    OPEN ACCESS ARTICLE
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This Issue

March 2016; 26 (3)
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