Table of Contents

December 2014; 24 (12)

Research

  • Genome-wide map of regulatory interactions in the human genome

    • Nastaran Heidari,
    • Douglas H. Phanstiel,
    • Chao He,
    • Fabian Grubert,
    • Fereshteh Jahanbani,
    • Maya Kasowski,
    • Michael Q. Zhang,
    • and Michael P. Snyder
    Genome Res. December 2014 24: 1905-1917; Published in Advance September 16, 2014, doi:10.1101/gr.176586.114
    OPEN ACCESS ARTICLE

  • Population and single-cell genomics reveal the Aire dependency, relief from Polycomb silencing, and distribution of self-antigen expression in thymic epithelia

    • Stephen N. Sansom,
    • Noriko Shikama-Dorn,
    • Saule Zhanybekova,
    • Gretel Nusspaumer,
    • Iain C. Macaulay,
    • Mary E. Deadman,
    • Andreas Heger,
    • Chris P. Ponting,
    • and Georg A. Holländer
    Genome Res. December 2014 24: 1918-1931; Published in Advance September 15, 2014, doi:10.1101/gr.171645.113
    OPEN ACCESS ARTICLE

  • Divergent functions of hematopoietic transcription factors in lineage priming and differentiation during erythro-megakaryopoiesis

    • Maxim Pimkin,
    • Andrew V. Kossenkov,
    • Tejaswini Mishra,
    • Christapher S. Morrissey,
    • Weisheng Wu,
    • Cheryl A. Keller,
    • Gerd A. Blobel,
    • Dongwon Lee,
    • Michael A. Beer,
    • Ross C. Hardison,
    • and Mitchell J. Weiss
    Genome Res. December 2014 24: 1932-1944; Published in Advance October 15, 2014, doi:10.1101/gr.164178.113
    OPEN ACCESS ARTICLE

  • Dynamic shifts in occupancy by TAL1 are guided by GATA factors and drive large-scale reprogramming of gene expression during hematopoiesis

    • Weisheng Wu,
    • Christapher S. Morrissey,
    • Cheryl A. Keller,
    • Tejaswini Mishra,
    • Maxim Pimkin,
    • Gerd A. Blobel,
    • Mitchell J. Weiss,
    • and Ross C. Hardison
    Genome Res. December 2014 24: 1945-1962; Published in Advance October 15, 2014, doi:10.1101/gr.164830.113
    OPEN ACCESS ARTICLE

  • Widespread contribution of transposable elements to the innovation of gene regulatory networks

    • Vasavi Sundaram,
    • Yong Cheng,
    • Zhihai Ma,
    • Daofeng Li,
    • Xiaoyun Xing,
    • Peter Edge,
    • Michael P. Snyder,
    • and Ting Wang
    Genome Res. December 2014 24: 1963-1976; Published in Advance October 15, 2014, doi:10.1101/gr.168872.113

  • Transposable element dynamics and PIWI regulation impacts lncRNA and gene expression diversity in Drosophila ovarian cell cultures

    • Yuliya A. Sytnikova,
    • Reazur Rahman,
    • Gung-wei Chirn,
    • Josef P. Clark,
    • and Nelson C. Lau
    Genome Res. December 2014 24: 1977-1990; Published in Advance September 29, 2014, doi:10.1101/gr.178129.114

  • Molecular dissection of the genetic mechanisms that underlie expression conservation in orthologous yeast ribosomal promoters

    • Danny Zeevi,
    • Shai Lubliner,
    • Maya Lotan-Pompan,
    • Eran Hodis,
    • Rita Vesterman,
    • Adina Weinberger,
    • and Eran Segal
    Genome Res. December 2014 24: 1991-1999; Published in Advance October 7, 2014, doi:10.1101/gr.179259.114

  • Heritable variation of mRNA decay rates in yeast

    • Jennifer M. Andrie,
    • Jon Wakefield,
    • and Joshua M. Akey
    Genome Res. December 2014 24: 2000-2010; Published in Advance September 25, 2014, doi:10.1101/gr.175802.114

  • Accounting for biases in riboprofiling data indicates a major role for proline in stalling translation

    • Carlo G. Artieri and
    • Hunter B. Fraser
    Genome Res. December 2014 24: 2011-2021; Published in Advance October 7, 2014, doi:10.1101/gr.175893.114

Methods

  • DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly

    • Ilari Scheinin,
    • Daoud Sie,
    • Henrik Bengtsson,
    • Mark A. van de Wiel,
    • Adam B. Olshen,
    • Hinke F. van Thuijl,
    • Hendrik F. van Essen,
    • Paul P. Eijk,
    • François Rustenburg,
    • Gerrit A. Meijer,
    • Jaap C. Reijneveld,
    • Pieter Wesseling,
    • Daniel Pinkel,
    • Donna G. Albertson,
    • and Bauke Ylstra
    Genome Res. December 2014 24: 2022-2032; Published in Advance September 18, 2014, doi:10.1101/gr.175141.114
    OPEN ACCESS ARTICLE

  • Tn5 transposase and tagmentation procedures for massively scaled sequencing projects

    • Simone Picelli,
    • Åsa K. Björklund,
    • Björn Reinius,
    • Sven Sagasser,
    • Gösta Winberg,
    • and Rickard Sandberg
    Genome Res. December 2014 24: 2033-2040; Published in Advance July 30, 2014, doi:10.1101/gr.177881.114
    OPEN ACCESS ARTICLE

  • In vitro, long-range sequence information for de novo genome assembly via transposase contiguity

    • Andrew Adey,
    • Jacob O. Kitzman,
    • Joshua N. Burton,
    • Riza Daza,
    • Akash Kumar,
    • Lena Christiansen,
    • Mostafa Ronaghi,
    • Sasan Amini,
    • Kevin L. Gunderson,
    • Frank J. Steemers,
    • and Jay Shendure
    Genome Res. December 2014 24: 2041-2049; Published in Advance October 19, 2014, doi:10.1101/gr.178319.114

  • A formal perturbation equation between genotype and phenotype determines the Evolutionary Action of protein-coding variations on fitness

    • Panagiotis Katsonis and
    • Olivier Lichtarge
    Genome Res. December 2014 24: 2050-2058; Published in Advance September 12, 2014, doi:10.1101/gr.176214.114
    OPEN ACCESS ARTICLE

  • Megabase-scale deletion using CRISPR/Cas9 to generate a fully haploid human cell line

    • Patrick Essletzbichler,
    • Tomasz Konopka,
    • Federica Santoro,
    • Doris Chen,
    • Bianca V. Gapp,
    • Robert Kralovics,
    • Thijn R. Brummelkamp,
    • Sebastian M.B. Nijman,
    • and Tilmann Bürckstümmer
    Genome Res. December 2014 24: 2059-2065; Published in Advance November 4, 2014, doi:10.1101/gr.177220.114

Resources

  • Single haplotype assembly of the human genome from a hydatidiform mole

    • Karyn Meltz Steinberg,
    • Valerie A. Schneider,
    • Tina A. Graves-Lindsay,
    • Robert S. Fulton,
    • Richa Agarwala,
    • John Huddleston,
    • Sergey A. Shiryev,
    • Aleksandr Morgulis,
    • Urvashi Surti,
    • Wesley C. Warren,
    • Deanna M. Church,
    • Evan E. Eichler,
    • and Richard K. Wilson
    Genome Res. December 2014 24: 2066-2076; Published in Advance November 4, 2014, doi:10.1101/gr.180893.114

  • Alignathon: a competitive assessment of whole-genome alignment methods

    • Dent Earl,
    • Ngan Nguyen,
    • Glenn Hickey,
    • Robert S. Harris,
    • Stephen Fitzgerald,
    • Kathryn Beal,
    • Igor Seledtsov,
    • Vladimir Molodtsov,
    • Brian J. Raney,
    • Hiram Clawson,
    • Jaebum Kim,
    • Carsten Kemena,
    • Jia-Ming Chang,
    • Ionas Erb,
    • Alexander Poliakov,
    • Minmei Hou,
    • Javier Herrero,
    • William James Kent,
    • Victor Solovyev,
    • Aaron E. Darling,
    • Jian Ma,
    • Cedric Notredame,
    • Michael Brudno,
    • Inna Dubchak,
    • David Haussler,
    • and Benedict Paten
    Genome Res. December 2014 24: 2077-2089; Published in Advance October 1, 2014, doi:10.1101/gr.174920.114
    OPEN ACCESS ARTICLE

Author Index

Reviewer Index

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This Issue

December 2014; 24 (12)
Cover
  1. Research
  2. Methods
  3. Resources
  4. Author Index
  5. Reviewer Index

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