Volume 22, Issue 10 | October 2012

Research
- - Abnormal developmental control of replication-timing domains in pediatric acute lymphoblastic leukemia
    Tyrone Ryba
    Dana Battaglia
    Bill H. Chang
    James W. Shirley
    Quinton Buckley
    First Published May 24, 2012
  - Copy number variation leads to considerable diversity for B but not A haplotypes of the human KIR genes encoding NK cell receptors
    Wei Jiang
    Chris Johnson
    Jyothi Jayaraman
    Nikol Simecek
    Janelle Noble
    First Published September 4, 2012
  - Random X inactivation in the mule and horse placenta
    Xu Wang
    Donald C. Miller
    Andrew G. Clark
    Douglas F. Antczak
    First Published May 29, 2012
  - Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations
    Stefan F. Pinter
    Ruslan I. Sadreyev
    Eda Yildirim
    Yesu Jeon
    Toshiro K. Ohsumi
    First Published September 4, 2012
  - piRNA-mediated transgenerational inheritance of an acquired trait
    Thomas Grentzinger
    Claudia Armenise
    Christine Brun
    Bruno Mugat
    Vincent Serrano
    First Published May 3, 2012
  - Exploring the DNA-recognition potential of homeodomains
    Stephanie W. Chu
    Marcus B. Noyes
    Ryan G. Christensen
    Brian G. Pierce
    Lihua J. Zhu
    First Published April 26, 2012
  - Dynamic landscape of tandem 3′ UTRs during zebrafish development
    Yuxin Li
    Yu Sun
    Yonggui Fu
    Mengzhen Li
    Guangrui Huang
    Chenxu Zhang Jiahui Liang Shengfeng Huang Gaoyang Shen
    ...[+4 authors]...,
    Shaochun Yuan
    Liangfu Chen
    Shangwu Chen
    Anlong Xu
    First Published September 5, 2012
  - Transcription factor redundancy and tissue-specific regulation: Evidence from functional and physical network connectivity
    Steven G. Kuntz
    Brian A. Williams
    Paul W. Sternberg
    Barbara J. Wold
    First Published June 22, 2012
  - Nutritional control of mRNA isoform expression during developmental arrest and recovery in C. elegans
    Colin S. Maxwell
    Igor Antoshechkin
    Nicole Kurhanewicz
    Jason A. Belsky
    L. Ryan Baugh
    First Published April 26, 2012
  - Polygenic cis-regulatory adaptation in the evolution of yeast pathogenicity
    Hunter B. Fraser
    Sasha Levy
    Arun Chavan
    Hiral B. Shah
    J. Christian Perez
    First Published May 29, 2012
  - Maintaining replication origins in the face of genomic change
    Sara C. Di Rienzi
    Kimberly C. Lindstrom
    Tobias Mann
    William S. Noble
    M.K. Raghuraman
    First Published June 4, 2012
  - Conservation of replication timing reveals global and local regulation of replication origin activity
    Carolin A. Müller
    Conrad A. Nieduszynski
    First Published July 5, 2012
  - Natural genetic variation in yeast longevity
    Stefan W. Stumpferl
    Sue E. Brand
    James C. Jiang
    Boguslawa Korona
    Anurag Tiwari
    First Published September 5, 2012
  - Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts
    Catherine Lozupone
    Karoline Faust
    Jeroen Raes
    Jeremiah J. Faith
    Daniel N. Frank
    First Published June 4, 2012
  - CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome
    Adi Stern
    Eran Mick
    Itay Tirosh
    Or Sagy
    Rotem Sorek
    First Published June 25, 2012
Methods
- - Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer
    Gavin Ha
    Andrew Roth
    Daniel Lai
    Ali Bashashati
    Jiarui Ding
    Rodrigo Goya Ryan Giuliany Jamie Rosner Arusha Oloumi Karey Shumansky Suet-Feung Chin Gulisa Turashvili Martin Hirst
    ...[+8 authors]...,
    Carlos Caldas
    Marco A. Marra
    Samuel Aparicio
    Sohrab P. Shah
    First Published May 25, 2012
  - Detecting differential usage of exons from RNA-seq data
    Simon Anders
    Alejandro Reyes
    Wolfgang Huber
    First Published June 21, 2012
  - Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding
    J. Omar Yáñez-Cuna
    Huy Q. Dinh
    Evgeny Z. Kvon
    Daria Shlyueva
    Alexander Stark
    First Published April 25, 2012
  - Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution
    Lukas Windhager
    Thomas Bonfert
    Kaspar Burger
    Zsolt Ruzsics
    Stefan Krebs
    Stefanie Kaufmann Georg Malterer Anne L'Hernault Markus Schilhabel Stefan Schreiber Philip Rosenstiel
    ...[+6 authors]...,
    Ralf Zimmer
    Dirk Eick
    Caroline C. Friedel
    Lars Dölken
    First Published April 26, 2012
Resources
- - Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis
    Ozren Bogdanović
    Ana Fernandez-Miñán
    Juan J. Tena
    Elisa de la Calle-Mustienes
    Carmen Hidalgo
    First Published May 16, 2012
  - Extensive alternative polyadenylation during zebrafish development
    Igor Ulitsky
    Alena Shkumatava
    Calvin H. Jan
    Alexander O. Subtelny
    David Koppstein
    First Published June 21, 2012
  - Incorporating RNA-seq data into the zebrafish Ensembl genebuild
    John E. Collins
    Simon White
    Stephen M.J. Searle
    Derek L. Stemple
    First Published July 12, 2012
  - Gene structure in the sea urchin Strongylocentrotus purpuratus based on transcriptome analysis
    Qiang Tu
    R. Andrew Cameron
    Kim C. Worley
    Richard A. Gibbs
    Eric H. Davidson
    First Published June 18, 2012
Erratum
- - Erratum
    First Published October 1, 2012

Table of Contents

Volume 22, Issue 10 | October 2012

Research

Abnormal developmental control of replication-timing domains in pediatric acute lymphoblastic leukemia

Copy number variation leads to considerable diversity for B but not A haplotypes of the human KIR genes encoding NK cell receptors

Random X inactivation in the mule and horse placenta

Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations

piRNA-mediated transgenerational inheritance of an acquired trait

Exploring the DNA-recognition potential of homeodomains

Dynamic landscape of tandem 3′ UTRs during zebrafish development

Transcription factor redundancy and tissue-specific regulation: Evidence from functional and physical network connectivity

Nutritional control of mRNA isoform expression during developmental arrest and recovery in C. elegans

Polygenic cis-regulatory adaptation in the evolution of yeast pathogenicity

Maintaining replication origins in the face of genomic change

Conservation of replication timing reveals global and local regulation of replication origin activity

Natural genetic variation in yeast longevity

Identifying genomic and metabolic features that can underlie early successional and opportunistic lifestyles of human gut symbionts

CRISPR targeting reveals a reservoir of common phages associated with the human gut microbiome

Methods

Integrative analysis of genome-wide loss of heterozygosity and monoallelic expression at nucleotide resolution reveals disrupted pathways in triple-negative breast cancer

Detecting differential usage of exons from RNA-seq data

Uncovering cis-regulatory sequence requirements for context-specific transcription factor binding

Ultrashort and progressive 4sU-tagging reveals key characteristics of RNA processing at nucleotide resolution

Resources

Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis

Extensive alternative polyadenylation during zebrafish development

Incorporating RNA-seq data into the zebrafish Ensembl genebuild

Gene structure in the sea urchin Strongylocentrotus purpuratus based on transcriptome analysis

Erratum

Erratum

Table of Contents

Volume 22, Issue 10 | October 2012

Share this issue

Research

Methods

Resources

Erratum