Volume 21, Issue 12 | December 2011

Research
- - Homozygosity mapping and targeted genomic sequencing reveal the gene responsible for cerebellar hypoplasia and quadrupedal locomotion in a consanguineous kindred
    Suleyman Gulsuner
    Ayse Begum Tekinay
    Katja Doerschner
    Huseyin Boyaci
    Kaya Bilguvar
    Hilal Unal Aslihan Ors O. Emre Onat Ergin Atalar A. Nazli Basak Haluk Topaloglu Tulay Kansu
    ...[+7 authors]...,
    Meliha Tan
    Uner Tan
    Murat Gunel
    Tayfun Ozcelik
    First Published September 1, 2011
  - Relating CNVs to transcriptome data at fine resolution: Assessment of the effect of variant size, type, and overlap with functional regions
    Andreas Schlattl
    Simon Anders
    Sebastian M. Waszak
    Wolfgang Huber
    Jan O. Korbel
    First Published August 23, 2011
  - Deep-transcriptome and ribonome sequencing redefines the molecular networks of pluripotency and the extracellular space in human embryonic stem cells
    Gabriel Kolle
    Jill L. Shepherd
    Brooke Gardiner
    Karin S. Kassahn
    Nicole Cloonan
    David L.A. Wood Ehsan Nourbakhsh Darrin F. Taylor Shivangi Wani Hun S. Chy Qi Zhou
    ...[+6 authors]...,
    Kevin McKernan
    Scott Kuersten
    Andrew L. Laslett
    Sean M. Grimmond
    First Published October 31, 2011
  - Epigenetic regulation of normal human mammary cell type–specific miRNAs
    Lukas Vrba
    James C. Garbe
    Martha R. Stampfer
    Bernard W. Futscher
    First Published August 26, 2011
  - A matter of life or death: How microsatellites emerge in and vanish from the human genome
    Yogeshwar D. Kelkar
    Kristin A. Eckert
    Francesca Chiaromonte
    Kateryna D. Makova
    First Published October 12, 2011
  - Phyloepigenomic comparison of great apes reveals a correlation between somatic and germline methylation states
    David I.K. Martin
    Meromit Singer
    Joseph Dhahbi
    Guanxiong Mao
    Lu Zhang
    First Published September 9, 2011
  - Locus- and domain-dependent control of DNA methylation at mouse B1 retrotransposons during male germ cell development
    Kenji Ichiyanagi
    Yungfeng Li
    Toshiaki Watanabe
    Tomoko Ichiyanagi
    Kei Fukuda
    Junko Kitayama Yasuhiro Yamamoto Satomi Kuramochi-Miyagawa Toru Nakano
    ...[+4 authors]...,
    Yukihiro Yabuta
    Yoshiyuki Seki
    Mitinori Saitou
    Hiroyuki Sasaki
    First Published October 31, 2011
  - Delineation of key regulatory elements identifies points of vulnerability in the mitogen-activated signaling network
    Noor Jailkhani
    Srikanth Ravichandran
    Shubhada R. Hegde
    Zaved Siddiqui
    Shekhar C. Mande
    First Published August 24, 2011
  - Emergence of male-biased genes on the chicken Z-chromosome: Sex-chromosome contrasts between male and female heterogametic systems
    Hans Ellegren
    First Published August 25, 2011
  - Genome-wide analysis of retrogene polymorphisms in Drosophila melanogaster
    Daniel R. Schrider
    Kristian Stevens
    Charis M. Cardeño
    Charles H. Langley
    Matthew W. Hahn
    First Published December 1, 2011
  - Evidence of abundant stop codon readthrough in Drosophila and other metazoa
    Irwin Jungreis
    Michael F. Lin
    Rebecca Spokony
    Clara S. Chan
    Nicolas Negre
    First Published October 12, 2011
  - Compensation for differences in gene copy number among yeast ribosomal proteins is encoded within their promoters
    Danny Zeevi
    Eilon Sharon
    Maya Lotan-Pompan
    Yaniv Lubling
    Zohar Shipony
    Tali Raveh-Sadka
    ...[+1 authors]...,
    Leeat Keren
    Michal Levo
    Adina Weinberger
    Eran Segal
    First Published October 18, 2011
  - Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania
    Matthew B. Rogers
    James D. Hilley
    Nicholas J. Dickens
    Jon Wilkes
    Paul A. Bates
    Daniel P. Depledge David Harris Yerim Her Pawel Herzyk Hideo Imamura Thomas D. Otto Mandy Sanders Kathy Seeger Jean-Claude Dujardin
    ...[+9 authors]...,
    Matthew Berriman
    Deborah F. Smith
    Christiane Hertz-Fowler
    Jeremy C. Mottram
    First Published October 28, 2011
  - Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance
    Tim Downing
    Hideo Imamura
    Saskia Decuypere
    Taane G. Clark
    Graham H. Coombs
    James A. Cotton James D. Hilley Simonne de Doncker Ilse Maes Jeremy C. Mottram Mike A. Quail Suman Rijal Mandy Sanders Gabriele Schönian Olivia Stark Shyam Sundar
    ...[+11 authors]...,
    Manu Vanaerschot
    Christiane Hertz-Fowler
    Jean-Claude Dujardin
    Matthew Berriman
    First Published October 28, 2011
  - The making of a new pathogen: Insights from comparative population genomics of the domesticated wheat pathogen Mycosphaerella graminicola and its wild sister species
    Eva H. Stukenbrock
    Thomas Bataillon
    Julien Y. Dutheil
    Troels T. Hansen
    Ruiqiang Li
    First Published October 12, 2011
Methods
- - Discriminative prediction of mammalian enhancers from DNA sequence
    Dongwon Lee
    Rachel Karchin
    Michael A. Beer
    First Published August 29, 2011
  - High-throughput semiquantitative analysis of insertional mutations in heterogeneous tumors
    Marco J. Koudijs
    Christiaan Klijn
    Louise van der Weyden
    Jaap Kool
    Jelle ten Hoeve
    Daoud Sie Pramudita R. Prasetyanti Eva Schut Sjors Kas Theodore Whipp
    ...[+5 authors]...,
    Edwin Cuppen
    Lodewyk Wessels
    David J. Adams
    Jos Jonkers
    First Published August 18, 2011
  - A metabolomic and systems biology perspective on the brain of the Fragile X syndrome mouse model
    Laetitia Davidovic
    Vincent Navratil
    Carmela M. Bonaccorso
    Maria Vincenza Catania
    Barbara Bardoni
    First Published September 7, 2011
Resources
- - Simultaneous structural variation discovery among multiple paired-end sequenced genomes
    Fereydoun Hormozdiari
    Iman Hajirasouliha
    Andrew McPherson
    Evan E. Eichler
    S. Cenk Sahinalp
    First Published November 2, 2011
  - Differential expression in RNA-seq: A matter of depth
    Sonia Tarazona
    Fernando García-Alcalde
    Joaquín Dopazo
    Alberto Ferrer
    Ana Conesa
    First Published September 8, 2011
  - Assemblathon 1: A competitive assessment of de novo short read assembly methods
    Dent Earl
    Keith Bradnam
    John St. John
    Aaron Darling
    Dawei Lin
    Joseph Fass Hung On Ken Yu Vince Buffalo Daniel R. Zerbino Mark Diekhans Ngan Nguyen Pramila Nuwantha Ariyaratne Wing-Kin Sung Zemin Ning Matthias Haimel Jared T. Simpson Nuno A. Fonseca İnanç Birol T. Roderick Docking Isaac Y. Ho Daniel S. Rokhsar Rayan Chikhi Dominique Lavenier Guillaume Chapuis Delphine Naquin Nicolas Maillet Michael C. Schatz David R. Kelley Adam M. Phillippy Sergey Koren Shiaw-Pyng Yang Wei Wu Wen-Chi Chou Anuj Srivastava Timothy I. Shaw J. Graham Ruby Peter Skewes-Cox Miguel Betegon Michelle T. Dimon Victor Solovyev Igor Seledtsov Petr Kosarev Denis Vorobyev Ricardo Ramirez-Gonzalez Richard Leggett Dan MacLean Fangfang Xia Ruibang Luo Zhenyu Li Yinlong Xie Binghang Liu Sante Gnerre Iain MacCallum Dariusz Przybylski Filipe J. Ribeiro Shuangye Yin Ted Sharpe Giles Hall Paul J. Kersey Richard Durbin Shaun D. Jackman Jarrod A. Chapman Xiaoqiu Huang Joseph L. DeRisi Mario Caccamo Yingrui Li David B. Jaffe
    ...[+62 authors]...,
    Richard E. Green
    David Haussler
    Ian Korf
    Benedict Paten
    First Published September 16, 2011
Author Index
- - Author Index, Volume 21, 2011
    First Published December 1, 2011
Reviewer Index
- - Reviewer Index, Volume 21, 2011
    First Published December 1, 2011

Table of Contents

Volume 21, Issue 12 | December 2011

Research

Homozygosity mapping and targeted genomic sequencing reveal the gene responsible for cerebellar hypoplasia and quadrupedal locomotion in a consanguineous kindred

Relating CNVs to transcriptome data at fine resolution: Assessment of the effect of variant size, type, and overlap with functional regions

Deep-transcriptome and ribonome sequencing redefines the molecular networks of pluripotency and the extracellular space in human embryonic stem cells

Epigenetic regulation of normal human mammary cell type–specific miRNAs

A matter of life or death: How microsatellites emerge in and vanish from the human genome

Phyloepigenomic comparison of great apes reveals a correlation between somatic and germline methylation states

Locus- and domain-dependent control of DNA methylation at mouse B1 retrotransposons during male germ cell development

Delineation of key regulatory elements identifies points of vulnerability in the mitogen-activated signaling network

Emergence of male-biased genes on the chicken Z-chromosome: Sex-chromosome contrasts between male and female heterogametic systems

Genome-wide analysis of retrogene polymorphisms in Drosophila melanogaster

Evidence of abundant stop codon readthrough in Drosophila and other metazoa

Compensation for differences in gene copy number among yeast ribosomal proteins is encoded within their promoters

Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania

Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance

The making of a new pathogen: Insights from comparative population genomics of the domesticated wheat pathogen Mycosphaerella graminicola and its wild sister species

Methods

Discriminative prediction of mammalian enhancers from DNA sequence

High-throughput semiquantitative analysis of insertional mutations in heterogeneous tumors

A metabolomic and systems biology perspective on the brain of the Fragile X syndrome mouse model

Resources

Simultaneous structural variation discovery among multiple paired-end sequenced genomes

Differential expression in RNA-seq: A matter of depth

Assemblathon 1: A competitive assessment of de novo short read assembly methods

Author Index

Author Index, Volume 21, 2011

Reviewer Index

Reviewer Index, Volume 21, 2011

Table of Contents

Volume 21, Issue 12 | December 2011

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Research

Methods

Resources

Author Index

Reviewer Index