Volume 22, Issue 7 | July 2012

Research
- - Genome-scale analysis of DNA methylation in lung adenocarcinoma and integration with mRNA expression
    Suhaida A. Selamat
    Brian S. Chung
    Luc Girard
    Wei Zhang
    Ying Zhang
    Mihaela Campan Kimberly D. Siegmund Michael N. Koss Jeffrey A. Hagen
    ...[+4 authors]...,
    Wan L. Lam
    Stephen Lam
    Adi F. Gazdar
    Ite A. Laird-Offringa
    First Published May 21, 2012
  - Reorganization of the host epigenome by a viral oncogene
    Roberto Ferrari
    Trent Su
    Bing Li
    Giancarlo Bonora
    Amit Oberai
    Yvonne Chan
    ...[+1 authors]...,
    Rajkumar Sasidharan
    Arnold J. Berk
    Matteo Pellegrini
    Siavash K. Kurdistani
    First Published April 12, 2012
  - The human phosphotyrosine signaling network: Evolution and hotspots of hijacking in cancer
    Lei Li
    Chabane Tibiche
    Cong Fu
    Tomonori Kaneko
    Michael F. Moran
    First Published December 22, 2011
  - Chimeras taking shape: Potential functions of proteins encoded by chimeric RNA transcripts
    Milana Frenkel-Morgenstern
    Vincent Lacroix
    Iakes Ezkurdia
    Yishai Levin
    Alexandra Gabashvili
    Jaime Prilusky Angela del Pozo
    ...[+2 authors]...,
    Michael Tress
    Rory Johnson
    Roderic Guigo
    Alfonso Valencia
    First Published May 15, 2012
  - Impact of microRNA regulation on variation in human gene expression
    Jian Lu
    Andrew G. Clark
    First Published March 28, 2012
  - Disentangling the relationship between sex-biased gene expression and X-linkage
    Richard P. Meisel
    John H. Malone
    Andrew G. Clark
    First Published April 12, 2012
  - Deep sequencing the circadian and diurnal transcriptome of Drosophila brain
    Michael E. Hughes
    Gregory R. Grant
    Christina Paquin
    Jack Qian
    Michael N. Nitabach
    First Published April 3, 2012
  - Multidimensional regulation of gene expression in the C. elegans embryo
    John Isaac Murray
    Thomas J. Boyle
    Elicia Preston
    Dionne Vafeados
    Barbara Mericle
    Peter Weisdepp
    ...[+1 authors]...,
    Zhongying Zhao
    Zhirong Bao
    Max Boeck
    Robert H. Waterston
    First Published April 16, 2012
  - Physical tethering and volume exclusion determine higher-order genome organization in budding yeast
    Harianto Tjong
    Ke Gong
    Lin Chen
    Frank Alber
    First Published May 22, 2012
  - Genome-wide analysis of mutations in mutant lineages selected following fast-neutron irradiation mutagenesis of Arabidopsis thaliana
    Eric J. Belfield
    Xiangchao Gan
    Aziz Mithani
    Carly Brown
    Caifu Jiang
    Keara Franklin Elizabeth Alvey Anjar Wibowo Marko Jung Kit Bailey
    ...[+5 authors]...,
    Sharan Kalwani
    Jiannis Ragoussis
    Richard Mott
    Nicholas P. Harberd
    First Published April 12, 2012
Methods
- - Targeted gene addition to a predetermined site in the human genome using a ZFN-based nicking enzyme
    Jianbin Wang
    Geoffrey Friedman
    Yannick Doyon
    Nathaniel S. Wang
    Carrie Jiaxin Li
    Jeffrey C. Miller Kevin L. Hua
    ...[+2 authors]...,
    Jenny Jiacheng Yan
    Joshua E. Babiarz
    Philip D. Gregory
    Michael C. Holmes
    First Published March 20, 2012
  - Precision genome engineering with programmable DNA-nicking enzymes
    Eunji Kim
    Sojung Kim
    Duk Hyoung Kim
    Beom-Soon Choi
    Ik-Young Choi
    First Published April 20, 2012
  - Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks
    Daniel Marbach
    Sushmita Roy
    Ferhat Ay
    Patrick E. Meyer
    Rogerio Candeias
    First Published March 28, 2012
  - Comparative dynamic transcriptome analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation
    Mai Sun
    Björn Schwalb
    Daniel Schulz
    Nicole Pirkl
    Stefanie Etzold
    Laurent Larivière
    ...[+1 authors]...,
    Kerstin C. Maier
    Martin Seizl
    Achim Tresch
    Patrick Cramer
    First Published March 30, 2012
  - RIP-chip-SRM—a new combinatorial large-scale approach identifies a set of translationally regulated bantam/miR-58 targets in C. elegans
    Marko Jovanovic
    Lukas Reiter
    Alejandra Clark
    Manuel Weiss
    Paola Picotti
    Hubert Rehrauer Andreas Frei Lukas J. Neukomm Ethan Kaufman Bernd Wollscheid Martin J. Simard
    ...[+6 authors]...,
    Eric A. Miska
    Ruedi Aebersold
    André P. Gerber
    Michael O. Hengartner
    First Published March 27, 2012
Resource
- - Triplexator: Detecting nucleic acid triple helices in genomic and transcriptomic data
    Fabian A. Buske
    Denis C. Bauer
    John S. Mattick
    Timothy L. Bailey
    First Published May 1, 2012
Erratum
- - Errata
    First Published July 2, 2012

Table of Contents

Volume 22, Issue 7 | July 2012

Research

Genome-scale analysis of DNA methylation in lung adenocarcinoma and integration with mRNA expression

Reorganization of the host epigenome by a viral oncogene

The human phosphotyrosine signaling network: Evolution and hotspots of hijacking in cancer

Chimeras taking shape: Potential functions of proteins encoded by chimeric RNA transcripts

Impact of microRNA regulation on variation in human gene expression

Disentangling the relationship between sex-biased gene expression and X-linkage

Deep sequencing the circadian and diurnal transcriptome of Drosophila brain

Multidimensional regulation of gene expression in the C. elegans embryo

Physical tethering and volume exclusion determine higher-order genome organization in budding yeast

Genome-wide analysis of mutations in mutant lineages selected following fast-neutron irradiation mutagenesis of Arabidopsis thaliana

Methods

Targeted gene addition to a predetermined site in the human genome using a ZFN-based nicking enzyme

Precision genome engineering with programmable DNA-nicking enzymes

Predictive regulatory models in Drosophila melanogaster by integrative inference of transcriptional networks

Comparative dynamic transcriptome analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation

RIP-chip-SRM—a new combinatorial large-scale approach identifies a set of translationally regulated bantam/miR-58 targets in C. elegans

Resource

Triplexator: Detecting nucleic acid triple helices in genomic and transcriptomic data

Erratum

Errata

Table of Contents

Volume 22, Issue 7 | July 2012

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Research

Methods

Resource

Erratum