Volume 21, Issue 10 | October 2011

Research
- - Loss of exon identity is a common mechanism of human inherited disease
    Timothy Sterne-Weiler
    Jonathan Howard
    Matthew Mort
    David N. Cooper
    Jeremy R. Sanford
    First Published July 12, 2011
  - Analysis of alternative splicing associated with aging and neurodegeneration in the human brain
    James R. Tollervey
    Zhen Wang
    Tibor Hortobágyi
    Joshua T. Witten
    Kathi Zarnack
    Melis Kayikci Tyson A. Clark Anthony C. Schweitzer Gregor Rot Tomaž Curk
    ...[+5 authors]...,
    Blaž Zupan
    Boris Rogelj
    Christopher E. Shaw
    Jernej Ule
    First Published August 16, 2011
  - Large-scale methylation domains mark a functional subset of neuronally expressed genes
    Diane I. Schroeder
    Paul Lott
    Ian Korf
    Janine M. LaSalle
    First Published July 22, 2011
  - DNA methylation profiles of human active and inactive X chromosomes
    Andrew J. Sharp
    Elisavet Stathaki
    Eugenia Migliavacca
    Manisha Brahmachary
    Stephen B. Montgomery
    First Published August 23, 2011
  - Genome-wide analysis distinguishes hyperglycemia regulated epigenetic signatures of primary vascular cells
    Luciano Pirola
    Aneta Balcerczyk
    Richard W. Tothill
    Izhak Haviv
    Antony Kaspi
    Sebastian Lunke Mark Ziemann Tom Karagiannis Stephen Tonna Adam Kowalczyk Bryan Beresford-Smith Geoff Macintyre
    ...[+7 authors]...,
    Ma Kelong
    Zhang Hongyu
    Jingde Zhu
    Assam El-Osta
    First Published September 2, 2011
  - The human gut virome: Inter-individual variation and dynamic response to diet
    Samuel Minot
    Rohini Sinha
    Jun Chen
    Hongzhe Li
    Sue A. Keilbaugh
    First Published August 31, 2011
  - Copy number variation analysis in the great apes reveals species-specific patterns of structural variation
    Elodie Gazave
    Fleur Darré
    Carlos Morcillo-Suarez
    Natalia Petit-Marty
    Angel Carreño
    Urko M. Marigorta Oliver A. Ryder Antoine Blancher Mariano Rocchi Elena Bosch
    ...[+5 authors]...,
    Carl Baker
    Tomàs Marquès-Bonet
    Evan E. Eichler
    Arcadi Navarro
    First Published August 8, 2011
  - Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee
    Mario Ventura
    Claudia R. Catacchio
    Can Alkan
    Tomas Marques-Bonet
    Saba Sajjadian
    Tina A. Graves Fereydoun Hormozdiari Arcadi Navarro Maika Malig Carl Baker Choli Lee Emily H. Turner Lin Chen Jeffrey M. Kidd
    ...[+9 authors]...,
    Nicoletta Archidiacono
    Jay Shendure
    Richard K. Wilson
    Evan E. Eichler
    First Published June 17, 2011
  - Regulation of nucleosome landscape and transcription factor targeting at tissue-specific enhancers by BRG1
    Gangqing Hu
    Dustin E. Schones
    Kairong Cui
    River Ybarra
    Daniel Northrup
    Qingsong Tang
    ...[+1 authors]...,
    Luca Gattinoni
    Nicholas P. Restifo
    Suming Huang
    Keji Zhao
    First Published July 27, 2011
  - Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration
    Weisheng Wu
    Yong Cheng
    Cheryl A. Keller
    Jason Ernst
    Swathi Ashok Kumar
    Tejaswini Mishra Christapher Morrissey Christine M. Dorman Kuan-Bei Chen Daniela Drautz Belinda Giardine Yoichiro Shibata Lingyun Song Max Pimkin Gregory E. Crawford Terrence S. Furey Manolis Kellis Webb Miller James Taylor Stephan C. Schuster Yu Zhang
    ...[+16 authors]...,
    Francesca Chiaromonte
    Gerd A. Blobel
    Mitchell J. Weiss
    Ross C. Hardison
    First Published July 27, 2011
Methods
- - A comprehensively molecular haplotype-resolved genome of a European individual
    Eun-Kyung Suk
    Gayle K. McEwen
    Jorge Duitama
    Katja Nowick
    Sabrina Schulz
    Stefanie Palczewski Stefan Schreiber Dustin T. Holloway Stephen McLaughlin
    ...[+4 authors]...,
    Heather Peckham
    Clarence Lee
    Thomas Huebsch
    Margret R. Hoehe
    First Published August 3, 2011
  - Trans genomic capture and sequencing of primate exomes reveals new targets of positive selection
    Renee D. George
    Graham McVicker
    Rachel Diederich
    Sarah B. Ng
    Alexandra P. MacKenzie
    First Published July 27, 2011
  - Efficient cross-species capture hybridization and next-generation sequencing of mitochondrial genomes from noninvasively sampled museum specimens
    Victor C. Mason
    Gang Li
    Kristofer M. Helgen
    William J. Murphy
    First Published August 31, 2011
  - True single-molecule DNA sequencing of a pleistocene horse bone
    Ludovic Orlando
    Aurelien Ginolhac
    Maanasa Raghavan
    Julia Vilstrup
    Morten Rasmussen
    Kim Magnussen Kathleen E. Steinmann Philipp Kapranov John F. Thompson Grant Zazula Duane Froese Ida Moltke Beth Shapiro
    ...[+8 authors]...,
    Michael Hofreiter
    Khaled A.S. Al-Rasheid
    M. Thomas P. Gilbert
    Eske Willerslev
    First Published July 29, 2011
  - Characterization of complex chromosomal rearrangements by targeted capture and next-generation sequencing
    Nara L.M. Sobreira
    Veena Gnanakkan
    Michael Walsh
    Beth Marosy
    Elizabeth Wohler
    George Thomas
    ...[+1 authors]...,
    Julie E. Hoover-Fong
    Ada Hamosh
    Sarah J. Wheelan
    David Valle
    First Published September 2, 2011
  - A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data
    Daniel A. Skelly
    Marnie Johansson
    Jennifer Madeoy
    Jon Wakefield
    Joshua M. Akey
    First Published August 26, 2011
  - Application of microdroplet PCR for large-scale targeted bisulfite sequencing
    H. Kiyomi Komori
    Sarah A. LaMere
    Ali Torkamani
    G. Traver Hart
    Steve Kotsopoulos
    Jason Warner Michael L. Samuels Jeff Olson Steven R. Head
    ...[+4 authors]...,
    Phillip Ordoukhanian
    Pauline L. Lee
    Darren R. Link
    Daniel R. Salomon
    First Published July 14, 2011
Resources
- - Genome-based analysis of the nonhuman primate Macaca fascicularis as a model for drug safety assessment
    Martin Ebeling
    Erich Küng
    Angela See
    Clemens Broger
    Guido Steiner
    Marco Berrera Tobias Heckel Leonardo Iniguez Thomas Albert
    ...[+4 authors]...,
    Roland Schmucki
    Hermann Biller
    Thomas Singer
    Ulrich Certa
    First Published August 23, 2011
  - Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity
    Lingyun Song
    Zhancheng Zhang
    Linda L. Grasfeder
    Alan P. Boyle
    Paul G. Giresi
    Bum-Kyu Lee Nathan C. Sheffield Stefan Gräf Mikael Huss Damian Keefe Zheng Liu Darin London Ryan M. McDaniell Yoichiro Shibata Kimberly A. Showers Jeremy M. Simon Teresa Vales Tianyuan Wang Deborah Winter Zhuzhu Zhang Neil D. Clarke Ewan Birney
    ...[+17 authors]...,
    Vishwanath R. Iyer
    Gregory E. Crawford
    Jason D. Lieb
    Terrence S. Furey
    First Published July 12, 2011

Table of Contents

Volume 21, Issue 10 | October 2011

Research

Loss of exon identity is a common mechanism of human inherited disease

Analysis of alternative splicing associated with aging and neurodegeneration in the human brain

Large-scale methylation domains mark a functional subset of neuronally expressed genes

DNA methylation profiles of human active and inactive X chromosomes

Genome-wide analysis distinguishes hyperglycemia regulated epigenetic signatures of primary vascular cells

The human gut virome: Inter-individual variation and dynamic response to diet

Copy number variation analysis in the great apes reveals species-specific patterns of structural variation

Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee

Regulation of nucleosome landscape and transcription factor targeting at tissue-specific enhancers by BRG1

Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration

Methods

A comprehensively molecular haplotype-resolved genome of a European individual

Trans genomic capture and sequencing of primate exomes reveals new targets of positive selection

Efficient cross-species capture hybridization and next-generation sequencing of mitochondrial genomes from noninvasively sampled museum specimens

True single-molecule DNA sequencing of a pleistocene horse bone

Characterization of complex chromosomal rearrangements by targeted capture and next-generation sequencing

A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data

Application of microdroplet PCR for large-scale targeted bisulfite sequencing

Resources

Genome-based analysis of the nonhuman primate Macaca fascicularis as a model for drug safety assessment

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity

Table of Contents

Volume 21, Issue 10 | October 2011

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Research

Methods

Resources