Volume 24, Issue 7 | July 2014

Research
- - Somatic retrotransposition in human cancer revealed by whole-genome and exome sequencing
    Elena Helman
    Michael S. Lawrence
    Chip Stewart
    Carrie Sougnez
    Gad Getz
    First Published May 13, 2014
  - 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
    ...[+16 authors]...,
    Michael S. Kobor
    Michael J. Meaney
    Peter D. Gluckman
    Joanna D. Holbrook
    First Published April 7, 2014
  - 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
    ...[+2 authors]...,
    Jaime J. Carvajal
    Joachim Wittbrodt
    José L. Gómez-Skarmeta
    Juan R. Martínez-Morales
    First Published April 7, 2014
  - 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
    Steven E. Brenner
    First Published July 1, 2014
  - DNA replication and transcription programs respond to the same chromatin cues
    Yoav Lubelsky
    Joseph A. Prinz
    Leyna DeNapoli
    Yulong Li
    Jason A. Belsky
    First Published July 1, 2014
  - 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
    First Published July 1, 2014
  - The chromatin landscape of Drosophila: comparisons between species, sexes, and chromosomes
    Emily J. Brown
    Doris Bachtrog
    First Published May 19, 2014
  - 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
    First Published March 20, 2014
  - 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
    First Published April 8, 2014
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 Nouria Hernandez Mauro Delorenzi Bart Deplancke Béatrice Desvergne Nicolas Guex Winship Herr Felix Naef Jacques Rougemont Ueli Schibler Teemu Andersin Pascal Cousin Federica Gilardi Pascal Gos Fabienne Lammers Sunil Raghav Dominic Villeneuve Roberto Fabbretti Volker Vlegel Ioannis Xenarios Eugenia Migliavacca Viviane Praz Fabrice David Yohan Jarosz Dmitry Kuznetsov Robin Liechti Olivier Martin Julien Delafontaine Julia Cajan Kyle Gustafson Irina Krier Marion Leleu Nacho Molina
    ...[+37 authors]...,
    Aurélien Naldi
    Leonor Rib
    Laura Symul
    Gergana Bounova
    First Published April 7, 2014
  - 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
    First Published April 7, 2014
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
    ...[+17 authors]...,
    Taylor Sittler
    John Hackett
    Steve Miller
    Charles Y. Chiu
    First Published June 4, 2014
  - 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
    ...[+42 authors]...,
    Eric A. Stone
    Stephen Richards
    Bart Deplancke
    Trudy F.C. Mackay
    First Published April 8, 2014
  - 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
    ...[+54 authors]...,
    Piero Carninci
    Susan E. Celniker
    Brian Oliver
    Stephen Richards
    First Published July 1, 2014
  - 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
    ...[+12 authors]...,
    E. Jay Rehm
    Robert L. Grossman
    Manolis Kellis
    Kevin P. White
    First Published July 1, 2014
  - 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
    ...[+8 authors]...,
    Thomas C. Kaufman
    Peter Cherbas
    Adam Siepel
    Eric C. Lai
    First Published July 1, 2014

Table of Contents

Volume 24, Issue 7 | July 2014

Research

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

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

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

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

DNA replication and transcription programs respond to the same chromatin cues

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

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

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

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

Methods

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

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

Resources

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

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

Comparative validation of the D. melanogaster modENCODE transcriptome annotation

Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster

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

Table of Contents

Volume 24, Issue 7 | July 2014

Share this issue

Research

Methods

Resources