Table of Contents

November 2013; 23 (11)

Research

  • Hominoid fission of chromosome 14/15 and the role of segmental duplications

    • Giuliana Giannuzzi,
    • Michele Pazienza,
    • John Huddleston,
    • Francesca Antonacci,
    • Maika Malig,
    • Laura Vives,
    • Evan E. Eichler,
    • and Mario Ventura
    Genome Res. November 2013 23: 1763-1773; Published in Advance September 27, 2013, doi:10.1101/gr.156240.113

  • Bubble-seq analysis of the human genome reveals distinct chromatin-mediated mechanisms for regulating early- and late-firing origins

    • Larry D. Mesner,
    • Veena Valsakumar,
    • Marcin Cieślik,
    • Rebecca Pickin,
    • Joyce L. Hamlin,
    • and Stefan Bekiranov
    Genome Res. November 2013 23: 1774-1788; Published in Advance July 16, 2013, doi:10.1101/gr.155218.113

  • RNA–DNA differences in human mitochondria restore ancestral form of 16S ribosomal RNA

    • Dan Bar-Yaacov,
    • Gal Avital,
    • Liron Levin,
    • Allison L. Richards,
    • Naomi Hachen,
    • Boris Rebolledo Jaramillo,
    • Anton Nekrutenko,
    • Raz Zarivach,
    • and Dan Mishmar
    Genome Res. November 2013 23: 1789-1796; Published in Advance August 2, 2013, doi:10.1101/gr.161265.113

  • Oncogenic ETS fusions deregulate E2F3 target genes in Ewing sarcoma and prostate cancer

    • Sven Bilke,
    • Raphaela Schwentner,
    • Fan Yang,
    • Maximilian Kauer,
    • Gunhild Jug,
    • Robert L. Walker,
    • Sean Davis,
    • Yuelin J. Zhu,
    • Marbin Pineda,
    • Paul S. Meltzer,
    • and Heinrich Kovar
    Genome Res. November 2013 23: 1797-1809; Published in Advance August 12, 2013, doi:10.1101/gr.151340.112
    OPEN ACCESS ARTICLE

  • The evolution of evolvability in microRNA target sites in vertebrates

    • Jin Xu,
    • Rui Zhang,
    • Yang Shen,
    • Guojing Liu,
    • Xuemei Lu,
    • and Chung-I Wu
    Genome Res. November 2013 23: 1810-1816; Published in Advance September 27, 2013, doi:10.1101/gr.148916.112

  • Genome-wide evidence for speciation with gene flow in Heliconius butterflies

    • Simon H. Martin,
    • Kanchon K. Dasmahapatra,
    • Nicola J. Nadeau,
    • Camilo Salazar,
    • James R. Walters,
    • Fraser Simpson,
    • Mark Blaxter,
    • Andrea Manica,
    • James Mallet,
    • and Chris D. Jiggins
    Genome Res. November 2013 23: 1817-1828; Published in Advance September 17, 2013, doi:10.1101/gr.159426.113

  • High-throughput chromatin motion tracking in living yeast reveals the flexibility of the fiber throughout the genome

    • Houssam Hajjoul,
    • Julien Mathon,
    • Hubert Ranchon,
    • Isabelle Goiffon,
    • Julien Mozziconacci,
    • Benjamin Albert,
    • Pascal Carrivain,
    • Jean-Marc Victor,
    • Olivier Gadal,
    • Kerstin Bystricky,
    • and Aurélien Bancaud
    Genome Res. November 2013 23: 1829-1838; Published in Advance September 27, 2013, doi:10.1101/gr.157008.113

  • A systems level predictive model for global gene regulation of methanogenesis in a hydrogenotrophic methanogen

    • Sung Ho Yoon,
    • Serdar Turkarslan,
    • David J. Reiss,
    • Min Pan,
    • June A. Burn,
    • Kyle C. Costa,
    • Thomas J. Lie,
    • Joseph Slagel,
    • Robert L. Moritz,
    • Murray Hackett,
    • John A. Leigh,
    • and Nitin S. Baliga
    Genome Res. November 2013 23: 1839-1851; Published in Advance October 2, 2013, doi:10.1101/gr.153916.112
    OPEN ACCESS ARTICLE

Methods

  • Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation

    • Filipe G. Vieira,
    • Matteo Fumagalli,
    • Anders Albrechtsen,
    • and Rasmus Nielsen
    Genome Res. November 2013 23: 1852-1861; Published in Advance August 15, 2013, doi:10.1101/gr.157388.113

  • Defining cell-type specificity at the transcriptional level in human disease

    • Wenjun Ju,
    • Casey S. Greene,
    • Felix Eichinger,
    • Viji Nair,
    • Jeffrey B. Hodgin,
    • Markus Bitzer,
    • Young-suk Lee,
    • Qian Zhu,
    • Masami Kehata,
    • Min Li,
    • Song Jiang,
    • Maria Pia Rastaldi,
    • Clemens D. Cohen,
    • Olga G. Troyanskaya,
    • and Matthias Kretzler
    Genome Res. November 2013 23: 1862-1873; Published in Advance August 15, 2013, doi:10.1101/gr.155697.113

  • Network properties derived from deep sequencing of human B-cell receptor repertoires delineate B-cell populations

    • Rachael J.M. Bashford-Rogers,
    • Anne L. Palser,
    • Brian J. Huntly,
    • Richard Rance,
    • George S. Vassiliou,
    • George A. Follows,
    • and Paul Kellam
    Genome Res. November 2013 23: 1874-1884; Published in Advance June 6, 2013, doi:10.1101/gr.154815.113
    OPEN ACCESS ARTICLE

  • Analysis and correction of crosstalk effects in pathway analysis

    • Michele Donato,
    • Zhonghui Xu,
    • Alin Tomoiaga,
    • James G. Granneman,
    • Robert G. MacKenzie,
    • Riyue Bao,
    • Nandor Gabor Than,
    • Peter H. Westfall,
    • Roberto Romero,
    • and Sorin Draghici
    Genome Res. November 2013 23: 1885-1893; Published in Advance August 9, 2013, doi:10.1101/gr.153551.112

  • Efficient identification of Y chromosome sequences in the human and Drosophila genomes

    • Antonio Bernardo Carvalho and
    • Andrew G. Clark
    Genome Res. November 2013 23: 1894-1907; Published in Advance August 6, 2013, doi:10.1101/gr.156034.113

  • Massively parallel synthetic promoter assays reveal the in vivo effects of binding site variants

    • Ilaria Mogno,
    • Jamie C. Kwasnieski,
    • and Barak A. Cohen
    Genome Res. November 2013 23: 1908-1915; Published in Advance August 6, 2013, doi:10.1101/gr.157891.113

  • Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome

    • Ulrich Omasits,
    • Maxime Quebatte,
    • Daniel J. Stekhoven,
    • Claudia Fortes,
    • Bernd Roschitzki,
    • Mark D. Robinson,
    • Christoph Dehio,
    • and Christian H. Ahrens
    Genome Res. November 2013 23: 1916-1927; Published in Advance July 22, 2013, doi:10.1101/gr.151035.112

Resources

  • Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach

    • Pablo Meyer,
    • Geoffrey Siwo,
    • Danny Zeevi,
    • Eilon Sharon,
    • Raquel Norel,
    • DREAM6 Promoter Prediction Consortium,
    • Eran Segal,
    • and Gustavo Stolovitzky
    Genome Res. November 2013 23: 1928-1937; Published in Advance August 15, 2013, doi:10.1101/gr.157420.113

  • Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis

    • Chirag Nepal,
    • Yavor Hadzhiev,
    • Christopher Previti,
    • Vanja Haberle,
    • Nan Li,
    • Hazuki Takahashi,
    • Ana Maria M. Suzuki,
    • Ying Sheng,
    • Rehab F. Abdelhamid,
    • Santosh Anand,
    • Jochen Gehrig,
    • Altuna Akalin,
    • Christel E.M. Kockx,
    • Antoine A.J. van der Sloot,
    • Wilfred F.J. van IJcken,
    • Olivier Armant,
    • Sepand Rastegar,
    • Craig Watson,
    • Uwe Strähle,
    • Elia Stupka,
    • Piero Carninci,
    • Boris Lenhard,
    • and Ferenc Müller
    Genome Res. November 2013 23: 1938-1950; Published in Advance September 3, 2013, doi:10.1101/gr.153692.112

  • Honey bee protein atlas at organ-level resolution

    • Queenie W.T. Chan,
    • Man Yi Chan,
    • Michelle Logan,
    • Yuan Fang,
    • Heather Higo,
    • and Leonard J. Foster
    Genome Res. November 2013 23: 1951-1960; Published in Advance July 22, 2013, doi:10.1101/gr.155994.113
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This Issue

November 2013; 23 (11)
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