Volume 25, Issue 8 | August 2015

Research
- - The sea lamprey meiotic map improves resolution of ancient vertebrate genome duplications
    Jeramiah J. Smith
    Melissa C. Keinath
    First Published June 5, 2015
  - Dynamic changes in replication timing and gene expression during lineage specification of human pluripotent stem cells
    Juan Carlos Rivera-Mulia
    Quinton Buckley
    Takayo Sasaki
    Jared Zimmerman
    Ruth A. Didier
    Kristopher Nazor Jeanne F. Loring Zheng Lian Sherman Weissman Allan J. Robins Thomas C. Schulz Laura Menendez Michael J. Kulik
    ...[+8 authors]...,
    Stephen Dalton
    Haitham Gabr
    Tamer Kahveci
    David M. Gilbert
    First Published June 8, 2015
  - Topologically associating domains and their long-range contacts are established during early G1 coincident with the establishment of the replication-timing program
    Vishnu Dileep
    Ferhat Ay
    Jiao Sima
    Daniel L. Vera
    William S. Noble
    First Published May 20, 2015
  - Divergence patterns of genic copy number variation in natural populations of the house mouse (Mus musculus domesticus) reveal three conserved genes with major population-specific expansions
    Željka Pezer
    Bettina Harr
    Meike Teschke
    Hiba Babiker
    Diethard Tautz
    First Published July 6, 2015
  - Germline mutation rates and the long-term phenotypic effects of mutation accumulation in wild-type laboratory mice and mutator mice
    Arikuni Uchimura
    Mayumi Higuchi
    Yohei Minakuchi
    Mizuki Ohno
    Atsushi Toyoda
    Asao Fujiyama
    ...[+1 authors]...,
    Ikuo Miura
    Shigeharu Wakana
    Jo Nishino
    Takeshi Yagi
    First Published June 30, 2015
  - Retrotransposition creates sloping shores: a graded influence of hypomethylated CpG islands on flanking CpG sites
    Fiorella C. Grandi
    James M. Rosser
    Simon J. Newkirk
    Jun Yin
    Xiaoling Jiang
    Zhuo Xing Leanne Whitmore Sanum Bashir Zoltán Ivics
    ...[+4 authors]...,
    Zsuzsanna Izsvák
    Ping Ye
    Y. Eugene Yu
    Wenfeng An
    First Published May 20, 2015
  - Sequence determinants of improved CRISPR sgRNA design
    Han Xu
    Tengfei Xiao
    Chen-Hao Chen
    Wei Li
    Clifford A. Meyer
    Qiu Wu Di Wu Le Cong
    ...[+3 authors]...,
    Feng Zhang
    Jun S. Liu
    Myles Brown
    X. Shirley Liu
    First Published June 10, 2015
  - Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators
    Lauren R. Polstein
    Pablo Perez-Pinera
    D. Dewran Kocak
    Christopher M. Vockley
    Peggy Bledsoe
    Lingyun Song
    ...[+1 authors]...,
    Alexias Safi
    Gregory E. Crawford
    Timothy E. Reddy
    Charles A. Gersbach
    First Published May 29, 2015
  - Genome-wide activities of Polycomb complexes control pervasive transcription
    Hun-Goo Lee
    Tatyana G. Kahn
    Amanda Simcox
    Yuri B. Schwartz
    Vincenzo Pirrotta
    First Published May 18, 2015
  - Determinants of nucleosome positioning and their influence on plant gene expression
    Ming-Jung Liu
    Alexander E. Seddon
    Zing Tsung-Yeh Tsai
    Ian T. Major
    Monique Floer
    First Published June 10, 2015
  - Genome-wide analysis of translational efficiency reveals distinct but overlapping functions of yeast DEAD-box RNA helicases Ded1 and eIF4A
    Neelam Dabas Sen
    Fujun Zhou
    Nicholas T. Ingolia
    Alan G. Hinnebusch
    First Published June 29, 2015
Methods
- - Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort
    Christopher M. Vockley
    Cong Guo
    William H. Majoros
    Michael Nodzenski
    Denise M. Scholtens
    First Published June 17, 2015
  - Quantification of GC-biased gene conversion in the human genome
    Sylvain Glémin
    Peter F. Arndt
    Philipp W. Messer
    Dmitri Petrov
    Nicolas Galtier
    First Published May 20, 2015
Resource
- - Analysis of dynamic changes in retinoid-induced transcription and epigenetic profiles of murine Hox clusters in ES cells
    Bony De Kumar
    Mark E. Parrish
    Brian D. Slaughter
    Jay R. Unruh
    Madelaine Gogol
    Christopher Seidel Ariel Paulson Hua Li Karin Gaudenz Allison Peak William McDowell Brian Fleharty Youngwook Ahn
    ...[+8 authors]...,
    Chengqi Lin
    Edwin Smith
    Ali Shilatifard
    Robb Krumlauf
    First Published May 29, 2015
Corrigendum
- - Corrigendum: MIPSTR: a method for multiplex genotyping of germline and somatic STR variation across many individuals
    Keisha D. Carlson
    Peter H. Sudmant
    Maximilian O. Press
    Evan E. Eichler
    Jay Shendure
    First Published August 3, 2015

Table of Contents

Volume 25, Issue 8 | August 2015

Research

The sea lamprey meiotic map improves resolution of ancient vertebrate genome duplications

Dynamic changes in replication timing and gene expression during lineage specification of human pluripotent stem cells

Topologically associating domains and their long-range contacts are established during early G1 coincident with the establishment of the replication-timing program

Divergence patterns of genic copy number variation in natural populations of the house mouse (Mus musculus domesticus) reveal three conserved genes with major population-specific expansions

Germline mutation rates and the long-term phenotypic effects of mutation accumulation in wild-type laboratory mice and mutator mice

Retrotransposition creates sloping shores: a graded influence of hypomethylated CpG islands on flanking CpG sites

Sequence determinants of improved CRISPR sgRNA design

Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators

Genome-wide activities of Polycomb complexes control pervasive transcription

Determinants of nucleosome positioning and their influence on plant gene expression

Genome-wide analysis of translational efficiency reveals distinct but overlapping functions of yeast DEAD-box RNA helicases Ded1 and eIF4A

Methods

Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort

Quantification of GC-biased gene conversion in the human genome

Resource

Analysis of dynamic changes in retinoid-induced transcription and epigenetic profiles of murine Hox clusters in ES cells

Corrigendum

Corrigendum: MIPSTR: a method for multiplex genotyping of germline and somatic STR variation across many individuals

Table of Contents

Volume 25, Issue 8 | August 2015

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Research

Methods

Resource

Corrigendum