Volume 19, Issue 6 | June 2009

Next-Generation DNA Sequencing/Review
- - Finding the fifth base: Genome-wide sequencing of cytosine methylation
    Ryan Lister
    Joseph R. Ecker
    First Published March 9, 2009
Letter
- - Comparative analysis of H2A.Z nucleosome organization in the human and yeast genomes
    Michael Y. Tolstorukov
    Peter V. Kharchenko
    Joseph A. Goldman
    Robert E. Kingston
    Peter J. Park
    First Published February 26, 2009
  - Large-scale mRNA sequencing determines global regulation of RNA editing during brain development
    Helene Wahlstedt
    Chammiran Daniel
    Mats Ensterö
    Marie Öhman
    First Published May 6, 2009
  - The colorectal cancer risk at 18q21 is caused by a novel variant altering SMAD7 expression
    Alan M. Pittman
    Silvia Naranjo
    Emily Webb
    Peter Broderick
    Esther H. Lips
    Tom van Wezel Hans Morreau Kate Sullivan Sarah Fielding Philip Twiss Jayaram Vijayakrishnan
    ...[+6 authors]...,
    Fernando Casares
    Mobshra Qureshi
    José Luis Gómez-Skarmeta
    Richard S. Houlston
    First Published April 24, 2009
  - Functional diversity for REST (NRSF) is defined by in vivo binding affinity hierarchies at the DNA sequence level
    Alexander W. Bruce
    Andrés J. López-Contreras
    Paul Flicek
    Thomas A. Down
    Pawandeep Dhami
    Shane C. Dillon Christoph M. Koch
    ...[+2 authors]...,
    Cordelia F. Langford
    Ian Dunham
    Robert M. Andrews
    David Vetrie
    First Published April 28, 2009
  - Genomic mapping of binding regions for the Ecdysone receptor protein complex
    Zareen Gauhar
    Ling V. Sun
    Sujun Hua
    Christopher E. Mason
    Florian Fuchs
    First Published February 23, 2009
  - Dynamic reprogramming of transcription factors to and from the subtelomere
    H. Craig Mak
    Lorraine Pillus
    Trey Ideker
    First Published April 16, 2009
  - Comparative inference of illegitimate recombination between rice and sorghum duplicated genes produced by polyploidization
    Xiyin Wang
    Haibao Tang
    John E. Bowers
    Andrew H. Paterson
    First Published April 16, 2009
  - Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations
    Ravi D. Barabote
    Gary Xie
    David H. Leu
    Philippe Normand
    Anamaria Necsulea
    Vincent Daubin Claudine Médigue William S. Adney Xin Clare Xu Alla Lapidus Rebecca E. Parales Chris Detter Petar Pujic David Bruce
    ...[+9 authors]...,
    Celine Lavire
    Jean F. Challacombe
    Thomas S. Brettin
    Alison M. Berry
    First Published March 6, 2009
Methods
- - Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver
    Alayne L. Brunner
    David S. Johnson
    Si Wan Kim
    Anton Valouev
    Timothy E. Reddy
    Norma F. Neff Elizabeth Anton Catherine Medina Loan Nguyen Eric Chiao Chuba B. Oyolu
    ...[+6 authors]...,
    Gary P. Schroth
    Devin M. Absher
    Julie C. Baker
    Richard M. Myers
    First Published March 9, 2009
  - Integrating siRNA and protein–protein interaction data to identify an expanded insulin signaling network
    Zhidong Tu
    Carmen Argmann
    Kenny K. Wong
    Lyndon J. Mitnaul
    Stephen Edwards
    First Published March 4, 2009
  - High-throughput genotyping by whole-genome resequencing
    Xuehui Huang
    Qi Feng
    Qian Qian
    Qiang Zhao
    Lu Wang
    Ahong Wang Jianping Guan Danlin Fan Qijun Weng
    ...[+4 authors]...,
    Tao Huang
    Guojun Dong
    Tao Sang
    Bin Han
    First Published May 6, 2009
  - Mapping epigenetic mutations in fission yeast using whole-genome next-generation sequencing
    Danielle V. Irvine
    Derek B. Goto
    Matthew W. Vaughn
    Yukinobu Nakaseko
    W. Richard McCombie
    First Published May 7, 2009
  - Single-pass classification of all noncoding sequences in a bacterial genome using phylogenetic profiles
    Antonin Marchais
    Magali Naville
    Chantal Bohn
    Philippe Bouloc
    Daniel Gautheret
    First Published February 23, 2009
Resource
- - Exploring the human genome with functional maps
    Curtis Huttenhower
    Erin M. Haley
    Matthew A. Hibbs
    Vanessa Dumeaux
    Daniel R. Barrett
    First Published February 26, 2009
  - Global networks of functional coupling in eukaryotes from comprehensive data integration
    Andrey Alexeyenko
    Erik L.L. Sonnhammer
    First Published February 25, 2009
  - ABySS: A parallel assembler for short read sequence data
    Jared T. Simpson
    Kim Wong
    Shaun D. Jackman
    Jacqueline E. Schein
    Steven J.M. Jones
    First Published February 27, 2009
  - SNP detection for massively parallel whole-genome resequencing
    Ruiqiang Li
    Yingrui Li
    Xiaodong Fang
    Huanming Yang
    Jian Wang
    First Published May 6, 2009
  - High resolution mapping of expression QTLs in heterogeneous stock mice in multiple tissues
    Guo-Jen Huang
    Sagiv Shifman
    William Valdar
    Martina Johannesson
    Binnaz Yalcin
    First Published April 17, 2009

Table of Contents

Volume 19, Issue 6 | June 2009

Next-Generation DNA Sequencing/Review

Finding the fifth base: Genome-wide sequencing of cytosine methylation

Letter

Comparative analysis of H2A.Z nucleosome organization in the human and yeast genomes

Large-scale mRNA sequencing determines global regulation of RNA editing during brain development

The colorectal cancer risk at 18q21 is caused by a novel variant altering SMAD7 expression

Functional diversity for REST (NRSF) is defined by in vivo binding affinity hierarchies at the DNA sequence level

Genomic mapping of binding regions for the Ecdysone receptor protein complex

Dynamic reprogramming of transcription factors to and from the subtelomere

Comparative inference of illegitimate recombination between rice and sorghum duplicated genes produced by polyploidization

Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations

Methods

Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver

Integrating siRNA and protein–protein interaction data to identify an expanded insulin signaling network

High-throughput genotyping by whole-genome resequencing

Mapping epigenetic mutations in fission yeast using whole-genome next-generation sequencing

Single-pass classification of all noncoding sequences in a bacterial genome using phylogenetic profiles

Resource

Exploring the human genome with functional maps

Global networks of functional coupling in eukaryotes from comprehensive data integration

ABySS: A parallel assembler for short read sequence data

SNP detection for massively parallel whole-genome resequencing

High resolution mapping of expression QTLs in heterogeneous stock mice in multiple tissues

Table of Contents

Volume 19, Issue 6 | June 2009

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Next-Generation DNA Sequencing/Review

Letter

Methods

Resource