Volume 22, Issue 4 | April 2012

Research
- - The effects of hepatitis B virus integration into the genomes of hepatocellular carcinoma patients
    Zhaoshi Jiang
    Suchit Jhunjhunwala
    Jinfeng Liu
    Peter M. Haverty
    Michael I. Kennemer
    Yinghui Guan William Lee Paolo Carnevali Jeremy Stinson Stephanie Johnson Jingyu Diao Stacy Yeung Adrian Jubb Weilan Ye Thomas D. Wu Sharookh B. Kapadia Frederic J. de Sauvage Robert C. Gentleman Howard M. Stern Somasekar Seshagiri
    ...[+15 authors]...,
    Krishna P. Pant
    Zora Modrusan
    Dennis G. Ballinger
    Zemin Zhang
    First Published January 20, 2012
  - Comparative RNA sequencing reveals substantial genetic variation in endangered primates
    George H. Perry
    Páll Melsted
    John C. Marioni
    Ying Wang
    Russell Bainer
    Joseph K. Pickrell Katelyn Michelini Sarah Zehr
    ...[+3 authors]...,
    Anne D. Yoder
    Matthew Stephens
    Jonathan K. Pritchard
    Yoav Gilad
    First Published December 29, 2011
  - Extension of cortical synaptic development distinguishes humans from chimpanzees and macaques
    Xiling Liu
    Mehmet Somel
    Lin Tang
    Zheng Yan
    Xi Jiang
    Song Guo Yuan Yuan Liu He Anna Oleksiak Yan Zhang Na Li Yuhui Hu
    ...[+7 authors]...,
    Wei Chen
    Zilong Qiu
    Svante Pääbo
    Philipp Khaitovich
    First Published February 2, 2012
  - Age-associated DNA methylation in pediatric populations
    Reid S. Alisch
    Benjamin G. Barwick
    Pankaj Chopra
    Leila K. Myrick
    Glen A. Satten
    First Published February 1, 2012
  - Global profiling of DNA methylation erasure in mouse primordial germ cells
    Sylvain Guibert
    Thierry Forné
    Michael Weber
    First Published February 22, 2012
  - An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement
    Ignacio Maeso
    Manuel Irimia
    Juan J. Tena
    Esther González-Pérez
    David Tran
    Vydianathan Ravi
    ...[+1 authors]...,
    Byrappa Venkatesh
    Sonsoles Campuzano
    José Luis Gómez-Skarmeta
    Jordi Garcia-Fernàndez
    First Published January 10, 2012
  - The TAGteam motif facilitates binding of 21 sequence-specific transcription factors in the Drosophila embryo
    Rahul Satija
    Robert K. Bradley
    First Published January 13, 2012
  - A multiplicity of factors contributes to selective RNA polymerase III occupancy of a subset of RNA polymerase III genes in mouse liver
    Donatella Canella
    David Bernasconi
    Federica Gilardi
    Gwendal LeMartelot
    Eugenia Migliavacca
    Viviane Praz Pascal Cousin Mauro Delorenzi Nouria Hernandez Nouria Hernandez Mauro Delorenzi Bart Deplancke Béatrice Desvergne Nicolas Guex Winship Herr Felix Naef Jacques Rougemont Ueli Schibler Bart Deplancke Nicolas Guex Winship Herr Nicolas Guex Teemu Andersin Pascal Cousin Federica Gilardi Pascal Gos Gwendal Le Martelot Fabienne Lammers Donatella Canella Federica Gilardi Sunil Raghav Roberto Fabbretti Arnaud Fortier Li Long Volker Vlegel Ioannis Xenarios Eugenia Migliavacca Viviane Praz Nicolas Guex Felix Naef Jacques Rougemont Fabrice David Yohan Jarosz Dmitry Kuznetsov Robin Liechti Olivier Martin Frederick Ross Lucas Sinclair Julia Cajan Irina Krier Marion Leleu Eugenia Migliavacca Nacho Molina Aurélien Naldi Guillaume Rey Laura Symul Nicolas Guex Felix Naef Jacques Rougemont David Bernasconi Mauro Delorenzi Teemu Andersin Donatella Canella
    ...[+58 authors]...,
    Federica Gilardi
    Gwendal Le Martelot
    Fabienne Lammers
    Sunil Raghav
    First Published January 27, 2012
  - Retrotransposon profiling of RNA polymerase III initiation sites
    Xiaojie Qi
    Kenneth Daily
    Kim Nguyen
    Haoyi Wang
    David Mayhew
    Paul Rigor Sholeh Forouzan
    ...[+2 authors]...,
    Mark Johnston
    Robi David Mitra
    Pierre Baldi
    Suzanne Sandmeyer
    First Published January 27, 2012
  - Retrotransposon Ty1 integration targets specifically positioned asymmetric nucleosomal DNA segments in tRNA hotspots
    Loris Mularoni
    Yulian Zhou
    Tyson Bowen
    Sunil Gangadharan
    Sarah J. Wheelan
    First Published January 4, 2012
  - A nucleosomal surface defines an integration hotspot for the Saccharomyces cerevisiae Ty1 retrotransposon
    Joshua A. Baller
    Jiquan Gao
    Radostina Stamenova
    M. Joan Curcio
    Daniel F. Voytas
    First Published January 4, 2012
  - Evolutionary rate covariation reveals shared functionality and coexpression of genes
    Nathan L. Clark
    Eric Alani
    Charles F. Aquadro
    First Published January 27, 2012
  - After the bottleneck: Genome-wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection
    Amine Namouchi
    Xavier Didelot
    Ulrike Schöck
    Brigitte Gicquel
    Eduardo P.C. Rocha
    First Published February 29, 2012
  - Microevolution of extensively drug-resistant tuberculosis in Russia
    Nicola Casali
    Vladyslav Nikolayevskyy
    Yanina Balabanova
    Olga Ignatyeva
    Irina Kontsevaya
    Simon R. Harris Stephen D. Bentley Julian Parkhill Sergey Nejentsev
    ...[+4 authors]...,
    Sven E. Hoffner
    Rolf D. Horstmann
    Timothy Brown
    Francis Drobniewski
    First Published January 31, 2012
Methods
- - Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis
    John E. McCormack
    Brant C. Faircloth
    Nicholas G. Crawford
    Patricia Adair Gowaty
    Robb T. Brumfield
    First Published December 29, 2011
  - Unified modeling of gene duplication, loss, and coalescence using a locus tree
    Matthew D. Rasmussen
    Manolis Kellis
    First Published January 23, 2012
  - Cell-type-specific nuclei purification from whole animals for genome-wide expression and chromatin profiling
    Florian A. Steiner
    Paul B. Talbert
    Sivakanthan Kasinathan
    Roger B. Deal
    Steven Henikoff
    First Published January 4, 2012
Resources
- - Copy number variation of individual cattle genomes using next-generation sequencing
    Derek M. Bickhart
    Yali Hou
    Steven G. Schroeder
    Can Alkan
    Maria Francesca Cardone
    Lakshmi K. Matukumalli Jiuzhou Song Robert D. Schnabel Mario Ventura Jeremy F. Taylor Jose Fernando Garcia
    ...[+6 authors]...,
    Curtis P. Van Tassell
    Tad S. Sonstegard
    Evan E. Eichler
    George E. Liu
    First Published February 2, 2012
  - Functional wiring of the yeast kinome revealed by global analysis of genetic network motifs
    Sara Sharifpoor
    Dewald van Dyk
    Michael Costanzo
    Anastasia Baryshnikova
    Helena Friesen
    Alison C. Douglas Ji-Young Youn Benjamin VanderSluis
    ...[+3 authors]...,
    Chad L. Myers
    Balázs Papp
    Charles Boone
    Brenda J. Andrews
    First Published January 26, 2012
  - A vast collection of microbial genes that are toxic to bacteria
    Aya Kimelman
    Asaf Levy
    Hila Sberro
    Shahar Kidron
    Azita Leavitt
    Gil Amitai Deborah R. Yoder-Himes
    ...[+2 authors]...,
    Omri Wurtzel
    Yiwen Zhu
    Edward M. Rubin
    Rotem Sorek
    First Published February 1, 2012
Erratum
- - Errata
    First Published April 2, 2012

Table of Contents

Volume 22, Issue 4 | April 2012

Research

The effects of hepatitis B virus integration into the genomes of hepatocellular carcinoma patients

Comparative RNA sequencing reveals substantial genetic variation in endangered primates

Extension of cortical synaptic development distinguishes humans from chimpanzees and macaques

Age-associated DNA methylation in pediatric populations

Global profiling of DNA methylation erasure in mouse primordial germ cells

An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement

The TAGteam motif facilitates binding of 21 sequence-specific transcription factors in the Drosophila embryo

A multiplicity of factors contributes to selective RNA polymerase III occupancy of a subset of RNA polymerase III genes in mouse liver

Retrotransposon profiling of RNA polymerase III initiation sites

Retrotransposon Ty1 integration targets specifically positioned asymmetric nucleosomal DNA segments in tRNA hotspots

A nucleosomal surface defines an integration hotspot for the Saccharomyces cerevisiae Ty1 retrotransposon

Evolutionary rate covariation reveals shared functionality and coexpression of genes

After the bottleneck: Genome-wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection

Microevolution of extensively drug-resistant tuberculosis in Russia

Methods

Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis

Unified modeling of gene duplication, loss, and coalescence using a locus tree

Cell-type-specific nuclei purification from whole animals for genome-wide expression and chromatin profiling

Resources

Copy number variation of individual cattle genomes using next-generation sequencing

Functional wiring of the yeast kinome revealed by global analysis of genetic network motifs

A vast collection of microbial genes that are toxic to bacteria

Erratum

Errata

Table of Contents

Volume 22, Issue 4 | April 2012

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Research

Methods

Resources

Erratum