Volume 23, Issue 2 | February 2013

Research
- - Functional genomic analysis of chromosomal aberrations in a compendium of 8000 cancer genomes
    Tae-Min Kim
    Ruibin Xi
    Lovelace J. Luquette
    Richard W. Park
    Mark D. Johnson
    First Published November 6, 2012
  - Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability
    Yotam Drier
    Michael S. Lawrence
    Scott L. Carter
    Chip Stewart
    Stacey B. Gabriel
    First Published November 2, 2012
  - Autozygome-guided exome sequencing in retinal dystrophy patients reveals pathogenetic mutations and novel candidate disease genes
    Leen Abu-Safieh
    May Alrashed
    Shamsa Anazi
    Hisham Alkuraya
    Arif O. Khan
    Mohammed Al-Owain Jawahir Al-Zahrani Lama Al-Abdi Mais Hashem Salwa Al-Tarimi Mohammed-Adeeb Sebai Ahmed Shamia Mohamed D. Ray-zack Malik Nassan Zuhair N. Al-Hassnan Zuhair Rahbeeni Saad Waheeb
    ...[+12 authors]...,
    Abdullah Alkharashi
    Emad Abboud
    Selwa A.F. Al-Hazzaa
    Fowzan S. Alkuraya
    First Published October 26, 2012
  - Pluripotent stem cells escape from senescence-associated DNA methylation changes
    Carmen M. Koch
    Kristina Reck
    Kaifeng Shao
    Qiong Lin
    Sylvia Joussen
    Patrick Ziegler Gudrun Walenda Wolf Drescher Bertram Opalka Tobias May
    ...[+5 authors]...,
    Tim Brümmendorf
    Martin Zenke
    Tomo Šarić
    Wolfgang Wagner
    First Published October 18, 2012
  - Correlated alterations in genome organization, histone methylation, and DNA–lamin A/C interactions in Hutchinson-Gilford progeria syndrome
    Rachel Patton McCord
    Ashley Nazario-Toole
    Haoyue Zhang
    Peter S. Chines
    Ye Zhan
    First Published November 14, 2012
  - Constitutive nuclear lamina–genome interactions are highly conserved and associated with A/T-rich sequence
    Wouter Meuleman
    Daan Peric-Hupkes
    Jop Kind
    Jean-Bernard Beaudry
    Ludo Pagie
    First Published November 2, 2012
  - Differentially expressed, variant U1 snRNAs regulate gene expression in human cells
    Dawn O'Reilly
    Martin Dienstbier
    Sally A. Cowley
    Pilar Vazquez
    Marek Drożdż
    First Published October 15, 2012
  - Targeted gene silencing in mouse germ cells by insertion of a homologous DNA into a piRNA generating locus
    Yasuhiro Yamamoto
    Toshiaki Watanabe
    Yuko Hoki
    Kenjiro Shirane
    Yufeng Li
    Kenji Ichiiyanagi Satomi Kuramochi-Miyagawa Atsushi Toyoda Asao Fujiyama Masayuki Oginuma
    ...[+5 authors]...,
    Hitomi Suzuki
    Takashi Sado
    Toru Nakano
    Hiroyuki Sasaki
    First Published November 6, 2012
  - Identification of dosage-sensitive genes in Saccharomyces cerevisiae using the genetic tug-of-war method
    Koji Makanae
    Reiko Kintaka
    Takashi Makino
    Hiroaki Kitano
    Hisao Moriya
    First Published December 28, 2012
  - Stabilization of the promoter nucleosomes in nucleosome-free regions by the yeast Cyc8–Tup1 corepressor
    Kaifu Chen
    Marenda A. Wilson
    Calley Hirsch
    Anjanette Watson
    Shoudan Liang
    First Published November 2, 2012
Methods
- - Genome-scale coestimation of species and gene trees
    Bastien Boussau
    Gergely J. Szöllősi
    Laurent Duret
    Manolo Gouy
    Eric Tannier
    First Published November 6, 2012
  - PUB-NChIP—“in vivo biotinylation” approach to study chromatin in proximity to a protein of interest
    Muhammad Shoaib
    Arman Kulyyassov
    Chloé Robin
    Kinga Winczura
    Pavel Tarlykov
    Emmanuelle Despas
    ...[+1 authors]...,
    Patricia Kannouche
    Erlan Ramanculov
    Marc Lipinski
    Vasily Ogryzko
    First Published October 4, 2012
  - DANPOS: Dynamic analysis of nucleosome position and occupancy by sequencing
    Kaifu Chen
    Yuanxin Xi
    Xuewen Pan
    Zhaoyu Li
    Klaus Kaestner
    First Published November 28, 2012
  - Spatiotemporal clustering of the epigenome reveals rules of dynamic gene regulation
    Pengfei Yu
    Shu Xiao
    Xiaoyun Xin
    Chun-Xiao Song
    Wei Huang
    Darina McDee
    ...[+1 authors]...,
    Tetsuya Tanaka
    Ting Wang
    Chuan He
    Sheng Zhong
    First Published October 2, 2012
  - Linking the signaling cascades and dynamic regulatory networks controlling stress responses
    Anthony Gitter
    Miri Carmi
    Naama Barkai
    Ziv Bar-Joseph
    First Published October 11, 2012
  - SeqFold: Genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data
    Zhengqing Ouyang
    Michael P. Snyder
    Howard Y. Chang
    First Published October 11, 2012
Resources
- - A calibrated human Y-chromosomal phylogeny based on resequencing
    Wei Wei
    Qasim Ayub
    Yuan Chen
    Shane McCarthy
    Yiping Hou
    First Published October 4, 2012
  - The genome of the pear (Pyrus bretschneideri Rehd.)
    Jun Wu
    Zhiwen Wang
    Zebin Shi
    Shu Zhang
    Ray Ming
    Shilin Zhu M. Awais Khan Shutian Tao Schuyler S. Korban Hao Wang Nancy J. Chen Takeshi Nishio Xun Xu Lin Cong Kaijie Qi Xiaosan Huang Yingtao Wang Xiang Zhao Juyou Wu Cao Deng Caiyun Gou Weili Zhou Hao Yin Gaihua Qin Yuhui Sha Ye Tao Hui Chen Yanan Yang Yue Song Dongliang Zhan Juan Wang Leiting Li Meisong Dai Chao Gu Yuezhi Wang Daihu Shi Xiaowei Wang Huping Zhang Liang Zeng Danman Zheng Chunlei Wang Maoshan Chen Guangbiao Wang Lin Xie Valpuri Sovero Shoufeng Sha Wenjiang Huang Shujun Zhang Mingyue Zhang Jiangmei Sun Linlin Xu Yuan Li Xing Liu Qingsong Li Jiahui Shen Junyi Wang
    ...[+51 authors]...,
    Robert E. Paull
    Jeffrey L. Bennetzen
    Jun Wang
    Shaoling Zhang
    First Published November 13, 2012
Erratum
- - Erratum
    First Published February 1, 2013

Table of Contents

Volume 23, Issue 2 | February 2013

Research

Functional genomic analysis of chromosomal aberrations in a compendium of 8000 cancer genomes

Somatic rearrangements across cancer reveal classes of samples with distinct patterns of DNA breakage and rearrangement-induced hypermutability

Autozygome-guided exome sequencing in retinal dystrophy patients reveals pathogenetic mutations and novel candidate disease genes

Pluripotent stem cells escape from senescence-associated DNA methylation changes

Correlated alterations in genome organization, histone methylation, and DNA–lamin A/C interactions in Hutchinson-Gilford progeria syndrome

Constitutive nuclear lamina–genome interactions are highly conserved and associated with A/T-rich sequence

Differentially expressed, variant U1 snRNAs regulate gene expression in human cells

Targeted gene silencing in mouse germ cells by insertion of a homologous DNA into a piRNA generating locus

Identification of dosage-sensitive genes in Saccharomyces cerevisiae using the genetic tug-of-war method

Stabilization of the promoter nucleosomes in nucleosome-free regions by the yeast Cyc8–Tup1 corepressor

Methods

Genome-scale coestimation of species and gene trees

PUB-NChIP—“in vivo biotinylation” approach to study chromatin in proximity to a protein of interest

DANPOS: Dynamic analysis of nucleosome position and occupancy by sequencing

Spatiotemporal clustering of the epigenome reveals rules of dynamic gene regulation

Linking the signaling cascades and dynamic regulatory networks controlling stress responses

SeqFold: Genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data

Resources

A calibrated human Y-chromosomal phylogeny based on resequencing

The genome of the pear (Pyrus bretschneideri Rehd.)

Erratum

Erratum

Table of Contents

Volume 23, Issue 2 | February 2013

Share this issue

Research

Methods

Resources

Erratum