Table of Contents

Methods

Select this article
Genome-scale coestimation of species and gene trees
- Bastien Boussau,
- Gergely J. Szöllősi,
- Laurent Duret,
- Manolo Gouy,
- Eric Tannier,
- and Vincent Daubin
Genome Res. February 2013 23: 323-330; Published in Advance November 6, 2012, doi:10.1101/gr.141978.112
OPEN ACCESS ARTICLE
Select this article
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,
- Patricia Kannouche,
- Erlan Ramanculov,
- Marc Lipinski,
- and Vasily Ogryzko
Genome Res. February 2013 23: 331-340; Published in Advance October 4, 2012, doi:10.1101/gr.134874.111
Select this article
DANPOS: Dynamic analysis of nucleosome position and occupancy by sequencing
- Kaifu Chen,
- Yuanxin Xi,
- Xuewen Pan,
- Zhaoyu Li,
- Klaus Kaestner,
- Jessica Tyler,
- Sharon Dent,
- Xiangwei He,
- and Wei Li
Genome Res. February 2013 23: 341-351; Published in Advance November 28, 2012, doi:10.1101/gr.142067.112
Select this article
Spatiotemporal clustering of the epigenome reveals rules of dynamic gene regulation
- Pengfei Yu,
- Shu Xiao,
- Xiaoyun Xin,
- Chun-Xiao Song,
- Wei Huang,
- Darina McDee,
- Tetsuya Tanaka,
- Ting Wang,
- Chuan He,
- and Sheng Zhong
Genome Res. February 2013 23: 352-364; Published in Advance October 2, 2012, doi:10.1101/gr.144949.112
Select this article
Linking the signaling cascades and dynamic regulatory networks controlling stress responses
- Anthony Gitter,
- Miri Carmi,
- Naama Barkai,
- and Ziv Bar-Joseph
Genome Res. February 2013 23: 365-376; Published in Advance October 11, 2012, doi:10.1101/gr.138628.112
Select this article
SeqFold: Genome-scale reconstruction of RNA secondary structure integrating high-throughput sequencing data
- Zhengqing Ouyang,
- Michael P. Snyder,
- and Howard Y. Chang
Genome Res. February 2013 23: 377-387; Published in Advance October 11, 2012, doi:10.1101/gr.138545.112
OPEN ACCESS ARTICLE

Resources

Select this article
A calibrated human Y-chromosomal phylogeny based on resequencing
- Wei Wei,
- Qasim Ayub,
- Yuan Chen,
- Shane McCarthy,
- Yiping Hou,
- Ignazio Carbone,
- Yali Xue,
- and Chris Tyler-Smith
Genome Res. February 2013 23: 388-395; Published in Advance October 4, 2012, doi:10.1101/gr.143198.112
OPEN ACCESS ARTICLE
Select this article
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,
- Robert E. Paull,
- Jeffrey L. Bennetzen,
- Jun Wang,
- and Shaoling Zhang
Genome Res. February 2013 23: 396-408; Published in Advance November 13, 2012, doi:10.1101/gr.144311.112
OPEN ACCESS ARTICLE

Erratum

Select this article

Erratum
Genome Res. February 2013 23: 409

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

This Issue

Preprint Server

Current Issue

In This Issue