Table of Contents

July 2014; 24 (7)

Research

  • Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencing

    • Elena Helman,
    • Michael S. Lawrence,
    • Chip Stewart,
    • Carrie Sougnez,
    • Gad Getz,
    • and Matthew Meyerson
    Genome Res. July 2014 24: 1053-1063; Published in Advance May 13, 2014, doi:10.1101/gr.163659.113

  • The effect of genotype and in utero environment on interindividual variation in neonate DNA methylomes

    • Ai Ling Teh,
    • Hong Pan,
    • Li Chen,
    • Mei-Lyn Ong,
    • Shaillay Dogra,
    • Johnny Wong,
    • Julia L. MacIsaac,
    • Sarah M. Mah,
    • Lisa M. McEwen,
    • Seang-Mei Saw,
    • Keith M. Godfrey,
    • Yap-Seng Chong,
    • Kenneth Kwek,
    • Chee-Keong Kwoh,
    • Shu-E. Soh,
    • Mary F.F. Chong,
    • Sheila Barton,
    • Neerja Karnani,
    • Clara Y. Cheong,
    • Jan Paul Buschdorf,
    • Walter Stünkel,
    • Michael S. Kobor,
    • Michael J. Meaney,
    • Peter D. Gluckman,
    • and Joanna D. Holbrook
    Genome Res. July 2014 24: 1064-1074; Published in Advance April 7, 2014, doi:10.1101/gr.171439.113
    OPEN ACCESS ARTICLE

  • Comparative epigenomics in distantly related teleost species identifies conserved cis-regulatory nodes active during the vertebrate phylotypic period

    • Juan J. Tena,
    • Cristina González-Aguilera,
    • Ana Fernández-Miñán,
    • Javier Vázquez-Marín,
    • Helena Parra-Acero,
    • Joe W. Cross,
    • Peter W.J. Rigby,
    • Jaime J. Carvajal,
    • Joachim Wittbrodt,
    • José L. Gómez-Skarmeta,
    • and Juan R. Martínez-Morales
    Genome Res. July 2014 24: 1075-1085; Published in Advance April 7, 2014, doi:10.1101/gr.163915.113

  • Comparison of D. melanogaster and C. elegans developmental stages, tissues, and cells by modENCODE RNA-seq data

    • Jingyi Jessica Li,
    • Haiyan Huang,
    • Peter J. Bickel,
    • and Steven E. Brenner
    Genome Res. July 2014 24: 1086-1101; Published in Advance July 1, 2014, doi:10.1101/gr.170100.113
    OPEN ACCESS ARTICLE

  • DNA replication and transcription programs respond to the same chromatin cues

    • Yoav Lubelsky,
    • Joseph A. Prinz,
    • Leyna DeNapoli,
    • Yulong Li,
    • Jason A. Belsky,
    • and David M. MacAlpine
    Genome Res. July 2014 24: 1102-1114; Published in Advance July 1, 2014, doi:10.1101/gr.160010.113
    OPEN ACCESS ARTICLE

  • Evolution of H3K27me3-marked chromatin is linked to gene expression evolution and to patterns of gene duplication and diversification

    • Robert K. Arthur,
    • Lijia Ma,
    • Matthew Slattery,
    • Rebecca F. Spokony,
    • Alexander Ostapenko,
    • Nicolas Nègre,
    • and Kevin P. White
    Genome Res. July 2014 24: 1115-1124; Published in Advance July 1, 2014, doi:10.1101/gr.162008.113
    OPEN ACCESS ARTICLE

  • The chromatin landscape of Drosophila: comparisons between species, sexes, and chromosomes

    • Emily J. Brown and
    • Doris Bachtrog
    Genome Res. July 2014 24: 1125-1137; Published in Advance May 19, 2014, doi:10.1101/gr.172155.114

  • Extreme HOT regions are CpG-dense promoters in C. elegans and humans

    • Ron A.-J. Chen,
    • Przemyslaw Stempor,
    • Thomas A. Down,
    • Eva Zeiser,
    • Sky K. Feuer,
    • and Julie Ahringer
    Genome Res. July 2014 24: 1138-1146; Published in Advance March 20, 2014, doi:10.1101/gr.161992.113
    OPEN ACCESS ARTICLE

  • Dissection of thousands of cell type-specific enhancers identifies dinucleotide repeat motifs as general enhancer features

    • J. Omar Yáñez-Cuna,
    • Cosmas D. Arnold,
    • Gerald Stampfel,
    • Łukasz M. Boryń,
    • Daniel Gerlach,
    • Martina Rath,
    • and Alexander Stark
    Genome Res. July 2014 24: 1147-1156; Published in Advance April 8, 2014, doi:10.1101/gr.169243.113
    OPEN ACCESS ARTICLE

Methods

  • Quantifying ChIP-seq data: a spiking method providing an internal reference for sample-to-sample normalization

    • Nicolas Bonhoure,
    • Gergana Bounova,
    • David Bernasconi,
    • Viviane Praz,
    • Fabienne Lammers,
    • Donatella Canella,
    • Ian M. Willis,
    • Winship Herr,
    • Nouria Hernandez,
    • Mauro Delorenzi,
    • and The CycliX Consortium
    Genome Res. July 2014 24: 1157-1168; Published in Advance April 7, 2014, doi:10.1101/gr.168260.113
    OPEN ACCESS ARTICLE

  • LaSSO, a strategy for genome-wide mapping of intronic lariats and branch points using RNA-seq

    • Danny A. Bitton,
    • Charalampos Rallis,
    • Daniel C. Jeffares,
    • Graeme C. Smith,
    • Yuan Y.C. Chen,
    • Sandra Codlin,
    • Samuel Marguerat,
    • and Jürg Bähler
    Genome Res. July 2014 24: 1169-1179; Published in Advance April 7, 2014, doi:10.1101/gr.166819.113
    OPEN ACCESS ARTICLE

Resources

  • A cloud-compatible bioinformatics pipeline for ultrarapid pathogen identification from next-generation sequencing of clinical samples

    • Samia N. Naccache,
    • Scot Federman,
    • Narayanan Veeraraghavan,
    • Matei Zaharia,
    • Deanna Lee,
    • Erik Samayoa,
    • Jerome Bouquet,
    • Alexander L. Greninger,
    • Ka-Cheung Luk,
    • Barryett Enge,
    • Debra A. Wadford,
    • Sharon L. Messenger,
    • Gillian L. Genrich,
    • Kristen Pellegrino,
    • Gilda Grard,
    • Eric Leroy,
    • Bradley S. Schneider,
    • Joseph N. Fair,
    • Miguel A. Martínez,
    • Pavel Isa,
    • John A. Crump,
    • Joseph L. DeRisi,
    • Taylor Sittler,
    • John Hackett, Jr.,
    • Steve Miller,
    • and Charles Y. Chiu
    Genome Res. July 2014 24: 1180-1192; Published in Advance June 4, 2014, doi:10.1101/gr.171934.113
    OPEN ACCESS ARTICLE

  • Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines

    • Wen Huang,
    • Andreas Massouras,
    • Yutaka Inoue,
    • Jason Peiffer,
    • Miquel Ràmia,
    • Aaron M. Tarone,
    • Lavanya Turlapati,
    • Thomas Zichner,
    • Dianhui Zhu,
    • Richard F. Lyman,
    • Michael M. Magwire,
    • Kerstin Blankenburg,
    • Mary Anna Carbone,
    • Kyle Chang,
    • Lisa L. Ellis,
    • Sonia Fernandez,
    • Yi Han,
    • Gareth Highnam,
    • Carl E. Hjelmen,
    • John R. Jack,
    • Mehwish Javaid,
    • Joy Jayaseelan,
    • Divya Kalra,
    • Sandy Lee,
    • Lora Lewis,
    • Mala Munidasa,
    • Fiona Ongeri,
    • Shohba Patel,
    • Lora Perales,
    • Agapito Perez,
    • LingLing Pu,
    • Stephanie M. Rollmann,
    • Robert Ruth,
    • Nehad Saada,
    • Crystal Warner,
    • Aneisa Williams,
    • Yuan-Qing Wu,
    • Akihiko Yamamoto,
    • Yiqing Zhang,
    • Yiming Zhu,
    • Robert R.H. Anholt,
    • Jan O. Korbel,
    • David Mittelman,
    • Donna M. Muzny,
    • Richard A. Gibbs,
    • Antonio Barbadilla,
    • J. Spencer Johnston,
    • Eric A. Stone,
    • Stephen Richards,
    • Bart Deplancke,
    • and Trudy F.C. Mackay
    Genome Res. July 2014 24: 1193-1208; Published in Advance April 8, 2014, doi:10.1101/gr.171546.113
    OPEN ACCESS ARTICLE

  • Comparative validation of the D. melanogaster modENCODE transcriptome annotation

    • Zhen-Xia Chen,
    • David Sturgill,
    • Jiaxin Qu,
    • Huaiyang Jiang,
    • Soo Park,
    • Nathan Boley,
    • Ana Maria Suzuki,
    • Anthony R. Fletcher,
    • David C. Plachetzki,
    • Peter C. FitzGerald,
    • Carlo G. Artieri,
    • Joel Atallah,
    • Olga Barmina,
    • James B. Brown,
    • Kerstin P. Blankenburg,
    • Emily Clough,
    • Abhijit Dasgupta,
    • Sai Gubbala,
    • Yi Han,
    • Joy C. Jayaseelan,
    • Divya Kalra,
    • Yoo-Ah Kim,
    • Christie L. Kovar,
    • Sandra L. Lee,
    • Mingmei Li,
    • James D. Malley,
    • John H. Malone,
    • Tittu Mathew,
    • Nicolas R. Mattiuzzo,
    • Mala Munidasa,
    • Donna M. Muzny,
    • Fiona Ongeri,
    • Lora Perales,
    • Teresa M. Przytycka,
    • Ling-Ling Pu,
    • Garrett Robinson,
    • Rebecca L. Thornton,
    • Nehad Saada,
    • Steven E. Scherer,
    • Harold E. Smith,
    • Charles Vinson,
    • Crystal B. Warner,
    • Kim C. Worley,
    • Yuan-Qing Wu,
    • Xiaoyan Zou,
    • Peter Cherbas,
    • Manolis Kellis,
    • Michael B. Eisen,
    • Fabio Piano,
    • Karin Kionte,
    • David H. Fitch,
    • Paul W. Sternberg,
    • Asher D. Cutter,
    • Michael O. Duff,
    • Roger A. Hoskins,
    • Brenton R. Graveley,
    • Richard A. Gibbs,
    • Peter J. Bickel,
    • Artyom Kopp,
    • Piero Carninci,
    • Susan E. Celniker,
    • Brian Oliver,
    • and Stephen Richards
    Genome Res. July 2014 24: 1209-1223; Published in Advance July 1, 2014, doi:10.1101/gr.159384.113
    OPEN ACCESS ARTICLE

  • Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster

    • Matthew Slattery,
    • Lijia Ma,
    • Rebecca F. Spokony,
    • Robert K. Arthur,
    • Pouya Kheradpour,
    • Anshul Kundaje,
    • Nicolas Nègre,
    • Alex Crofts,
    • Ryan Ptashkin,
    • Jennifer Zieba,
    • Alexander Ostapenko,
    • Sarah Suchy,
    • Alec Victorsen,
    • Nader Jameel,
    • A. Jason Grundstad,
    • Wenxuan Gao,
    • Jennifer R. Moran,
    • E. Jay Rehm,
    • Robert L. Grossman,
    • Manolis Kellis,
    • and Kevin P. White
    Genome Res. July 2014 24: 1224-1235; Published in Advance July 1, 2014, doi:10.1101/gr.168807.113
    OPEN ACCESS ARTICLE

  • Diversity of miRNAs, siRNAs, and piRNAs across 25 Drosophila cell lines

    • Jiayu Wen,
    • Jaaved Mohammed,
    • Diane Bortolamiol-Becet,
    • Harrison Tsai,
    • Nicolas Robine,
    • Jakub O. Westholm,
    • Erik Ladewig,
    • Qi Dai,
    • Katsutomo Okamura,
    • Alex S. Flynt,
    • Dayu Zhang,
    • Justen Andrews,
    • Lucy Cherbas,
    • Thomas C. Kaufman,
    • Peter Cherbas,
    • Adam Siepel,
    • and Eric C. Lai
    Genome Res. July 2014 24: 1236-1250; Published in Advance July 1, 2014, doi:10.1101/gr.161554.113
    OPEN ACCESS ARTICLE
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This Issue

July 2014; 24 (7)
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