Volume 22, Issue 8 | August 2012

Perspective
- - Human genomic disease variants: A neutral evolutionary explanation
    Joel T. Dudley
    Yuseob Kim
    Li Liu
    Glenn J. Markov
    Kristyn Gerold
    First Published June 4, 2012
Research
- - Neonatal DNA methylation profile in human twins is specified by a complex interplay between intrauterine environmental and genetic factors, subject to tissue-specific influence
    Lavinia Gordon
    Jihoon E. Joo
    Joseph E. Powell
    Miina Ollikainen
    Boris Novakovic
    Xin Li Roberta Andronikos Mark N. Cruickshank Karen N. Conneely Alicia K. Smith Reid S. Alisch
    ...[+6 authors]...,
    Ruth Morley
    Peter M. Visscher
    Jeffrey M. Craig
    Richard Saffery
    First Published July 16, 2012
  - Genome-wide DNA methylation profiles in hematopoietic stem and progenitor cells reveal overrepresentation of ETS transcription factor binding sites
    Amber Hogart
    Jens Lichtenberg
    Subramanian S. Ajay
    Stacie Anderson
    Elliott H. Margulies
    First Published June 8, 2012
  - Genome-wide genetic variations are highly correlated with proximal DNA methylation patterns
    Wei Qu
    Shin-ichi Hashimoto
    Atsuko Shimada
    Yoichiro Nakatani
    Kazuki Ichikawa
    Taro L. Saito Katsumi Ogoshi Kouji Matsushima
    ...[+3 authors]...,
    Yutaka Suzuki
    Sumio Sugano
    Hiroyuki Takeda
    Shinichi Morishita
    First Published June 11, 2012
  - CBX3 regulates efficient RNA processing genome-wide
    Andrea Smallwood
    Gary C. Hon
    Fulai Jin
    Ryan E. Henry
    Joaquín M. Espinosa
    First Published June 8, 2012
  - Integrative functional genomics identifies an enhancer looping to the SOX9 gene disrupted by the 17q24.3 prostate cancer risk locus
    Xiaoyang Zhang
    Richard Cowper-Sal·lari
    Swneke D. Bailey
    Jason H. Moore
    Mathieu Lupien
    First Published June 4, 2012
  - Dynamic transitions in RNA polymerase II density profiles during transcription termination
    Ana Rita Grosso
    Sérgio Fernandes de Almeida
    José Braga
    Maria Carmo-Fonseca
    First Published June 8, 2012
  - Global analysis reveals multiple pathways for unique regulation of mRNA decay in induced pluripotent stem cells
    Ashley T. Neff
    Ju Youn Lee
    Jeffrey Wilusz
    Bin Tian
    Carol J. Wilusz
    First Published April 25, 2012
  - Adenosine deaminases that act on RNA induce reproducible changes in abundance and sequence of embryonic miRNAs
    Cornelia Vesely
    Stefanie Tauber
    Fritz J. Sedlazeck
    Arndt von Haeseler
    Michael F. Jantsch
    First Published February 6, 2012
  - A-to-I editing of microRNAs in the mammalian brain increases during development
    Ylva Ekdahl
    Hossein Shahrabi Farahani
    Mikaela Behm
    Jens Lagergren
    Marie Öhman
    First Published May 29, 2012
  - Effects of ADARs on small RNA processing pathways in C. elegans
    M. Bryan Warf
    Brent A. Shepherd
    W. Evan Johnson
    Brenda L. Bass
    First Published June 6, 2012
  - Genome sequencing reveals complex speciation in the Drosophila simulans clade
    Daniel Garrigan
    Sarah B. Kingan
    Anthony J. Geneva
    Peter Andolfatto
    Andrew G. Clark
    First Published April 13, 2012
  - Genomic characterization of the Bacillus cereus sensu lato species: Backdrop to the evolution of Bacillus anthracis
    Michael E. Zwick
    Sandeep J. Joseph
    Xavier Didelot
    Peter E. Chen
    Kimberly A. Bishop-Lilly
    Andrew C. Stewart Kristin Willner Nichole Nolan Shannon Lentz Maureen K. Thomason
    ...[+5 authors]...,
    Shanmuga Sozhamannan
    Alfred J. Mateczun
    Lei Du
    Timothy D. Read
    First Published May 29, 2012
Methods
- - Copy number variation detection and genotyping from exome sequence data
    Niklas Krumm
    Peter H. Sudmant
    Arthur Ko
    Brian J. O'Roak
    Maika Malig
    First Published May 14, 2012
  - Systematic identification of edited microRNAs in the human brain
    Shahar Alon
    Eyal Mor
    Francois Vigneault
    George M. Church
    Franco Locatelli
    First Published April 12, 2012
  - Mutation mapping and identification by whole-genome sequencing
    Ignaty Leshchiner
    Kristen Alexa
    Peter Kelsey
    Ivan Adzhubei
    Christina A. Austin-Tse
    Jeffrey D. Cooney Heidi Anderson Matthew J. King Rolf W. Stottmann Maija K. Garnaas Seungshin Ha Iain A. Drummond Barry H. Paw
    ...[+8 authors]...,
    Trista E. North
    David R. Beier
    Wolfram Goessling
    Shamil R. Sunyaev
    First Published May 3, 2012
  - Dissection of complex adult traits in a mouse synthetic population
    David T. Burke
    Kenneth M. Kozloff
    Shu Chen
    Joshua L. West
    Jodi M. Wilkowski
    First Published May 15, 2012
Resources
- - Genetic dissection of a model complex trait using the Drosophila Synthetic Population Resource
    Elizabeth G. King
    Chris M. Merkes
    Casey L. McNeil
    Steven R. Hoofer
    Saunak Sen
    First Published April 10, 2012
  - RNA-seq analysis of the C. briggsae transcriptome
    Bora Uyar
    Jeffrey S.C. Chu
    Ismael A. Vergara
    Shu Yi Chua
    Martin R. Jones
    First Published July 6, 2012
  - HaploMerger: Reconstructing allelic relationships for polymorphic diploid genome assemblies
    Shengfeng Huang
    Zelin Chen
    Guangrui Huang
    Ting Yu
    Ping Yang
    Jie Li
    ...[+1 authors]...,
    Yonggui Fu
    Shaochun Yuan
    Shangwu Chen
    Anlong Xu
    First Published May 3, 2012
  - MuSiC: Identifying mutational significance in cancer genomes
    Nathan D. Dees
    Qunyuan Zhang
    Cyriac Kandoth
    Michael C. Wendl
    William Schierding
    Daniel C. Koboldt Thomas B. Mooney Matthew B. Callaway
    ...[+3 authors]...,
    David Dooling
    Elaine R. Mardis
    Richard K. Wilson
    Li Ding
    First Published July 3, 2012

Table of Contents

Volume 22, Issue 8 | August 2012

Perspective

Human genomic disease variants: A neutral evolutionary explanation

Research

Neonatal DNA methylation profile in human twins is specified by a complex interplay between intrauterine environmental and genetic factors, subject to tissue-specific influence

Genome-wide DNA methylation profiles in hematopoietic stem and progenitor cells reveal overrepresentation of ETS transcription factor binding sites

Genome-wide genetic variations are highly correlated with proximal DNA methylation patterns

CBX3 regulates efficient RNA processing genome-wide

Integrative functional genomics identifies an enhancer looping to the SOX9 gene disrupted by the 17q24.3 prostate cancer risk locus

Dynamic transitions in RNA polymerase II density profiles during transcription termination

Global analysis reveals multiple pathways for unique regulation of mRNA decay in induced pluripotent stem cells

Adenosine deaminases that act on RNA induce reproducible changes in abundance and sequence of embryonic miRNAs

A-to-I editing of microRNAs in the mammalian brain increases during development

Effects of ADARs on small RNA processing pathways in C. elegans

Genome sequencing reveals complex speciation in the Drosophila simulans clade

Genomic characterization of the Bacillus cereus sensu lato species: Backdrop to the evolution of Bacillus anthracis

Methods

Copy number variation detection and genotyping from exome sequence data

Systematic identification of edited microRNAs in the human brain

Mutation mapping and identification by whole-genome sequencing

Dissection of complex adult traits in a mouse synthetic population

Resources

Genetic dissection of a model complex trait using the Drosophila Synthetic Population Resource

RNA-seq analysis of the C. briggsae transcriptome

HaploMerger: Reconstructing allelic relationships for polymorphic diploid genome assemblies

MuSiC: Identifying mutational significance in cancer genomes

Table of Contents

Volume 22, Issue 8 | August 2012

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Perspective

Research

Methods

Resources