Volume 24, Issue 11 | November 2014

Research
- - Genetic and environmental exposures constrain epigenetic drift over the human life course
    Shah Sonia
    McRae Allan F.
    Marioni Riccardo E.
    Harris Sarah E.
    Gibson Jude
    Henders Anjali K. Redmond Paul Cox Simon R. Pattie Alison Corley Janie Murphy Lee Martin Nicholas G. Montgomery Grant W.
    ...[+8 authors]...,
    Starr John M.
    Wray Naomi R.
    Deary Ian J.
    Visscher Peter M.
    First Published September 23, 2014
  - Estimating genotype error rates from high-coverage next-generation sequence data
    Jeffrey D. Wall
    Ling Fung Tang
    Brandon Zerbe
    Mark N. Kvale
    Pui-Yan Kwok
    Catherine Schaefer
    Neil Risch
    First Published October 10, 2014
  - Exonuclease mutations in DNA polymerase epsilon reveal replication strand specific mutation patterns and human origins of replication
    Eve Shinbrot
    Erin E. Henninger
    Nils Weinhold
    Kyle R. Covington
    A. Yasemin Göksenin
    Nikolaus Schultz Hsu Chao HarshaVardhan Doddapaneni Donna M. Muzny
    ...[+4 authors]...,
    Richard A. Gibbs
    Chris Sander
    Zachary F. Pursell
    David A. Wheeler
    First Published September 16, 2014
  - Heterogeneous polymerase fidelity and mismatch repair bias genome variation and composition
    Lujan Scott A.
    Clausen Anders R.
    Clark Alan B.
    MacAlpine Heather K.
    MacAlpine David M.
    Malc Ewa P. Mieczkowski Piotr A.
    ...[+2 authors]...,
    Burkholder Adam B.
    Fargo David C.
    Gordenin Dmitry A.
    Kunkel Thomas A.
    First Published September 12, 2014
  - RNA-seq of 272 gliomas revealed a novel, recurrent PTPRZ1-MET fusion transcript in secondary glioblastomas
    Zhao-Shi Bao
    Hui-Min Chen
    Ming-Yu Yang
    Chuan-Bao Zhang
    Kai Yu
    Wan-Lu Ye Bo-Qiang Hu Wei Yan Wei Zhang Johnny Akers Valya Ramakrishnan Jie Li Bob Carter Yan-Wei Liu Hui-Min Hu Zheng Wang Ming-Yang Li Kun Yao Xiao-Guang Qiu Chun-Sheng Kang Yong-Ping You Xiao-Long Fan Wei Sonya Song
    ...[+18 authors]...,
    Rui-Qiang Li
    Xiao-Dong Su
    Clark C. Chen
    Tao Jiang
    First Published August 18, 2014
  - Widespread intron retention in mammals functionally tunes transcriptomes
    Ulrich Braunschweig
    Nuno L. Barbosa-Morais
    Qun Pan
    Emil N. Nachman
    Babak Alipanahi
    Thomas Gonatopoulos-Pournatzis
    Brendan Frey
    Manuel Irimia
    Benjamin J. Blencowe
    First Published September 25, 2014
  - Cell fate inclination within 2-cell and 4-cell mouse embryos revealed by single-cell RNA sequencing
    Fernando H. Biase
    Xiaoyi Cao
    Sheng Zhong
    First Published August 5, 2014
  - High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA–tRNA interface
    Bianca M. Schmitt
    Konrad L.M. Rudolph
    Panagiota Karagianni
    Nuno A. Fonseca
    Robert J. White
    Iannis Talianidis
    Duncan T. Odom
    John C. Marioni
    Claudia Kutter
    First Published August 13, 2014
  - H3S28 phosphorylation is a hallmark of the transcriptional response to cellular stress
    Anna Sawicka
    Dominik Hartl
    Malgorzata Goiser
    Oliver Pusch
    Roman R. Stocsits
    Ido M. Tamir
    Karl Mechtler
    Christian Seiser
    First Published August 18, 2014
  - Environmentally responsive genome-wide accumulation of de novo Arabidopsis thaliana mutations and epimutations
    Caifu Jiang
    Aziz Mithani
    Eric J. Belfield
    Richard Mott
    Laurence D. Hurst
    Nicholas P. Harberd
    First Published October 14, 2014
  - Preservation of genetic and regulatory robustness in ancient gene duplicates of Saccharomyces cerevisiae
    Orla M. Keane
    Christina Toft
    Lorenzo Carretero-Paulet
    Gary W. Jones
    Mario A. Fares
    First Published August 22, 2014
Methods
- - Application of histone modification-specific interaction domains as an alternative to antibodies
    Goran Kungulovski
    Ina Kycia
    Raluca Tamas
    Renata Z. Jurkowska
    Srikanth Kudithipudi
    Chisato Henry
    Richard Reinhardt
    Paul Labhart
    Albert Jeltsch
    First Published October 9, 2014
  - Unbiased analysis of potential targets of breast cancer susceptibility loci by Capture Hi-C
    Nicola H. Dryden
    Laura R. Broome
    Frank Dudbridge
    Nichola Johnson
    Nick Orr
    Stefan Schoenfelder Takashi Nagano Simon Andrews Steven Wingett Iwanka Kozarewa Ioannis Assiotis Kerry Fenwick Sarah L. Maguire James Campbell Rachael Natrajan Maryou Lambros
    ...[+11 authors]...,
    Eleni Perrakis
    Alan Ashworth
    Peter Fraser
    Olivia Fletcher
    First Published August 13, 2014
  - Linking signaling pathways to transcriptional programs in breast cancer
    Hatice U. Osmanbeyoglu
    Raphael Pelossof
    Jacqueline F. Bromberg
    Christina S. Leslie
    First Published September 2, 2014
  - TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data
    Gavin Ha
    Andrew Roth
    Jaswinder Khattra
    Julie Ho
    Damian Yap
    Leah M. Prentice Nataliya Melnyk Andrew McPherson Ali Bashashati Emma Laks Justina Biele Jiarui Ding Alan Le Jamie Rosner Karey Shumansky Marco A. Marra C. Blake Gilks
    ...[+12 authors]...,
    David G. Huntsman
    Jessica N. McAlpine
    Samuel Aparicio
    Sohrab P. Shah
    First Published July 24, 2014
Resource
- - The landscape of human STR variation
    Thomas Willems
    Melissa Gymrek
    Gareth Highnam
    David Mittelman
    Yaniv Erlich
    First Published August 18, 2014

Table of Contents

Volume 24, Issue 11 | November 2014

Research

Genetic and environmental exposures constrain epigenetic drift over the human life course

Estimating genotype error rates from high-coverage next-generation sequence data

Exonuclease mutations in DNA polymerase epsilon reveal replication strand specific mutation patterns and human origins of replication

Heterogeneous polymerase fidelity and mismatch repair bias genome variation and composition

RNA-seq of 272 gliomas revealed a novel, recurrent PTPRZ1-MET fusion transcript in secondary glioblastomas

Widespread intron retention in mammals functionally tunes transcriptomes

Cell fate inclination within 2-cell and 4-cell mouse embryos revealed by single-cell RNA sequencing

High-resolution mapping of transcriptional dynamics across tissue development reveals a stable mRNA–tRNA interface

H3S28 phosphorylation is a hallmark of the transcriptional response to cellular stress

Environmentally responsive genome-wide accumulation of de novo Arabidopsis thaliana mutations and epimutations

Preservation of genetic and regulatory robustness in ancient gene duplicates of Saccharomyces cerevisiae

Methods

Application of histone modification-specific interaction domains as an alternative to antibodies

Unbiased analysis of potential targets of breast cancer susceptibility loci by Capture Hi-C

Linking signaling pathways to transcriptional programs in breast cancer

TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data

Resource

The landscape of human STR variation

Table of Contents

Volume 24, Issue 11 | November 2014

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Research

Methods

Resource