Table of Contents

January 2013; 23 (1)

Research

  • Genome-wide mapping of human DNA-replication origins: Levels of transcription at ORC1 sites regulate origin selection and replication timing

    • Gaetano Ivan Dellino,
    • Davide Cittaro,
    • Rossana Piccioni,
    • Lucilla Luzi,
    • Stefania Banfi,
    • Simona Segalla,
    • Matteo Cesaroni,
    • Ramiro Mendoza-Maldonado,
    • Mauro Giacca,
    • and Pier Giuseppe Pelicci
    Genome Res. January 2013 23: 1-11; Published in Advance November 27, 2012, doi:10.1101/gr.142331.112

  • GATA3 acts upstream of FOXA1 in mediating ESR1 binding by shaping enhancer accessibility

    • Vasiliki Theodorou,
    • Rory Stark,
    • Suraj Menon,
    • and Jason S. Carroll
    Genome Res. January 2013 23: 12-22; Published in Advance November 21, 2012, doi:10.1101/gr.139469.112

  • Small noncoding differentially methylated copy-number variants, including lncRNA genes, cause a lethal lung developmental disorder

    • Przemyslaw Szafranski,
    • Avinash V. Dharmadhikari,
    • Erwin Brosens,
    • Priyatansh Gurha,
    • Katarzyna E. Kołodziejska,
    • Ou Zhishuo,
    • Piotr Dittwald,
    • Tadeusz Majewski,
    • K. Naga Mohan,
    • Bo Chen,
    • Richard E. Person,
    • Dick Tibboel,
    • Annelies de Klein,
    • Jason Pinner,
    • Maya Chopra,
    • Girvan Malcolm,
    • Gregory Peters,
    • Susan Arbuckle,
    • Sixto F. Guiang III,
    • Virginia A. Hustead,
    • Jose Jessurun,
    • Russel Hirsch,
    • David P. Witte,
    • Isabelle Maystadt,
    • Neil Sebire,
    • Richard Fisher,
    • Claire Langston,
    • Partha Sen,
    • and Paweł Stankiewicz
    Genome Res. January 2013 23: 23-33; Published in Advance October 3, 2012, doi:10.1101/gr.141887.112

  • Birth and expression evolution of mammalian microRNA genes

    • Julien Meunier,
    • Frédéric Lemoine,
    • Magali Soumillon,
    • Angélica Liechti,
    • Manuela Weier,
    • Katerina Guschanski,
    • Haiyang Hu,
    • Philipp Khaitovich,
    • and Henrik Kaessmann
    Genome Res. January 2013 23: 34-45; Published in Advance October 3, 2012, doi:10.1101/gr.140269.112
    OPEN ACCESS ARTICLE

  • Evolutionary dynamism of the primate LRRC37 gene family

    • Giuliana Giannuzzi,
    • Priscillia Siswara,
    • Maika Malig,
    • Tomas Marques-Bonet,
    • NISC Comparative Sequencing Program,
    • James C. Mullikin,
    • Mario Ventura,
    • and Evan E. Eichler
    Genome Res. January 2013 23: 46-59; Published in Advance October 11, 2012, doi:10.1101/gr.138842.112

  • Modeling of epigenome dynamics identifies transcription factors that mediate Polycomb targeting

    • Phil Arnold,
    • Anne Schöler,
    • Mikhail Pachkov,
    • Piotr J. Balwierz,
    • Helle Jørgensen,
    • Michael B. Stadler,
    • Erik van Nimwegen,
    • and Dirk Schübeler
    Genome Res. January 2013 23: 60-73; Published in Advance September 10, 2012, doi:10.1101/gr.142661.112
    OPEN ACCESS ARTICLE

  • Comparative motif discovery combined with comparative transcriptomics yields accurate targetome and enhancer predictions

    • Marina Naval-Sánchez,
    • Delphine Potier,
    • Lotte Haagen,
    • Máximo Sánchez,
    • Sebastian Munck,
    • Bram Van de Sande,
    • Fernando Casares,
    • Valerie Christiaens,
    • and Stein Aerts
    Genome Res. January 2013 23: 74-88; Published in Advance October 15, 2012, doi:10.1101/gr.140426.112

  • A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence

    • Tina T. Hu,
    • Michael B. Eisen,
    • Kevin R. Thornton,
    • and Peter Andolfatto
    Genome Res. January 2013 23: 89-98; Published in Advance August 30, 2012, doi:10.1101/gr.141689.112
    OPEN ACCESS ARTICLE

  • Genome-wide patterns of natural variation reveal strong selective sweeps and ongoing genomic conflict in Drosophila mauritiana

    • Viola Nolte,
    • Ram Vinay Pandey,
    • Robert Kofler,
    • and Christian Schlötterer
    Genome Res. January 2013 23: 99-110; Published in Advance October 10, 2012, doi:10.1101/gr.139873.112
    OPEN ACCESS ARTICLE

  • Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization

    • Itai Sharon,
    • Michael J. Morowitz,
    • Brian C. Thomas,
    • Elizabeth K. Costello,
    • David A. Relman,
    • and Jillian F. Banfield
    Genome Res. January 2013 23: 111-120; Published in Advance August 30, 2012, doi:10.1101/gr.142315.112

Methods

  • Sequencing the unsequenceable: Expanded CGG-repeat alleles of the fragile X gene

    • Erick W. Loomis,
    • John S. Eid,
    • Paul Peluso,
    • Jun Yin,
    • Luke Hickey,
    • David Rank,
    • Sarah McCalmon,
    • Randi J. Hagerman,
    • Flora Tassone,
    • and Paul J. Hagerman
    Genome Res. January 2013 23: 121-128; Published in Advance October 11, 2012, doi:10.1101/gr.141705.112

  • Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases

    • Eric E. Schadt,
    • Onureena Banerjee,
    • Gang Fang,
    • Zhixing Feng,
    • Wing H. Wong,
    • Xuegong Zhang,
    • Andrey Kislyuk,
    • Tyson A. Clark,
    • Khai Luong,
    • Alona Keren-Paz,
    • Andrew Chess,
    • Vipin Kumar,
    • Alice Chen-Plotkin,
    • Neal Sondheimer,
    • Jonas Korlach,
    • and Andrew Kasarskis
    Genome Res. January 2013 23: 129-141; Published in Advance October 23, 2012, doi:10.1101/gr.136739.111
    OPEN ACCESS ARTICLE

  • Genotype calling and haplotyping in parent-offspring trios

    • Wei Chen,
    • Bingshan Li,
    • Zhen Zeng,
    • Serena Sanna,
    • Carlo Sidore,
    • Fabio Busonero,
    • Hyun Min Kang,
    • Yun Li,
    • and Gonçalo R. Abecasis
    Genome Res. January 2013 23: 142-151; Published in Advance October 11, 2012, doi:10.1101/gr.142455.112
    OPEN ACCESS ARTICLE

  • Haplotype-based profiling of subtle allelic imbalance with SNP arrays

    • Selina Vattathil and
    • Paul Scheet
    Genome Res. January 2013 23: 152-158; Published in Advance October 1, 2012, doi:10.1101/gr.141374.112

  • Efficient targeted mutagenesis in the monarch butterfly using zinc-finger nucleases

    • Christine Merlin,
    • Lauren E. Beaver,
    • Orley R. Taylor,
    • Scot A. Wolfe,
    • and Steven M. Reppert
    Genome Res. January 2013 23: 159-168; Published in Advance September 25, 2012, doi:10.1101/gr.145599.112
    OPEN ACCESS ARTICLE

  • High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression

    • Philippe Batut,
    • Alexander Dobin,
    • Charles Plessy,
    • Piero Carninci,
    • and Thomas R. Gingeras
    Genome Res. January 2013 23: 169-180; Published in Advance August 30, 2012, doi:10.1101/gr.139618.112

  • P-value-based regulatory motif discovery using positional weight matrices

    • Holger Hartmann,
    • Eckhart W. Guthöhrlein,
    • Matthias Siebert,
    • Sebastian Luehr,
    • and Johannes Söding
    Genome Res. January 2013 23: 181-194; Published in Advance September 18, 2012, doi:10.1101/gr.139881.112

Resources

  • SOAPindel: Efficient identification of indels from short paired reads

    • Shengting Li,
    • Ruiqiang Li,
    • Heng Li,
    • Jianliang Lu,
    • Yingrui Li,
    • Lars Bolund,
    • Mikkel H. Schierup,
    • and Jun Wang
    Genome Res. January 2013 23: 195-200; Published in Advance September 12, 2012, doi:10.1101/gr.132480.111

  • RNA sequencing reveals a diverse and dynamic repertoire of the Xenopus tropicalis transcriptome over development

    • Meng How Tan,
    • Kin Fai Au,
    • Arielle L. Yablonovitch,
    • Andrea E. Wills,
    • Jason Chuang,
    • Julie C. Baker,
    • Wing Hung Wong,
    • and Jin Billy Li
    Genome Res. January 2013 23: 201-216; Published in Advance September 7, 2012, doi:10.1101/gr.141424.112
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This Issue

January 2013; 23 (1)
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  2. Methods
  3. Resources

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