Volume 18, Issue 9 | September 2008

PERSPECTIVE
- - Genome-wide analyses of alternative splicing in plants: Opportunities and challenges
    W. Brad Barbazuk
    Yan Fu
    Karen M. McGinnis
    First Published July 30, 2008
LETTERS
- - Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes
    Romain A. Studer
    Simon Penel
    Laurent Duret
    Marc Robinson-Rechavi
    First Published June 18, 2008
  - CpG dinucleotides and the mutation rate of non-CpG DNA
    Jean-Claude Walser
    Loïc Ponger
    Anthony V. Furano
    First Published June 11, 2008
  - A deletion in nephronophthisis 4 (NPHP4) is associated with recessive cone-rod dystrophy in standard wire-haired dachshund
    Anne Caroline Wiik
    Claire Wade
    Tara Biagi
    Ernst-Otto Ropstad
    Ellen Bjerkås
    First Published August 7, 2008
  - A novel mode of enhancer evolution: The Tal1 stem cell enhancer recruited a MIR element to specifically boost its activity
    Aileen M. Smith
    Maria-Jose Sanchez
    George A. Follows
    Sarah Kinston
    Ian J. Donaldson
    First Published August 7, 2008
  - Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation
    Marcel E. Dinger
    Paulo P. Amaral
    Tim R. Mercer
    Ken C. Pang
    Stephen J. Bruce
    Brooke B. Gardiner Marjan E. Askarian-Amiri Kelin Ru Giulia Soldà Cas Simons Susan M. Sunkin
    ...[+6 authors]...,
    Mark L. Crowe
    Sean M. Grimmond
    Andrew C. Perkins
    John S. Mattick
    First Published June 18, 2008
  - On the origin of new genes in Drosophila
    Qi Zhou
    Guojie Zhang
    Yue Zhang
    Shiyu Xu
    Ruoping Zhao
    Zubing Zhan
    ...[+1 authors]...,
    Xin Li
    Yun Ding
    Shuang Yang
    Wen Wang
    First Published June 11, 2008
  - A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains
    Qian-Hao Zhu
    Andrew Spriggs
    Louisa Matthew
    Longjiang Fan
    Gavin Kennedy
    First Published August 7, 2008
  - Relaxation of yeast mitochondrial functions after whole-genome duplication
    Huifeng Jiang
    Wenjun Guan
    David Pinney
    Wen Wang
    Zhenglong Gu
    First Published July 30, 2008
  - Genome sequence of the β-rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia
    Claire Amadou
    Géraldine Pascal
    Sophie Mangenot
    Michelle Glew
    Cyril Bontemps
    Delphine Capela Sébastien Carrère Stéphane Cruveiller Carole Dossat Aurélie Lajus Marta Marchetti Véréna Poinsot Zoé Rouy Bertrand Servin Maged Saad Chantal Schenowitz
    ...[+11 authors]...,
    Valérie Barbe
    Jacques Batut
    Claudine Médigue
    Catherine Masson-Boivin
    First Published May 19, 2008
  - Very small mobile repeated elements in cyanobacterial genomes
    Jeff Elhai
    Michiko Kato
    Sarah Cousins
    Peter Lindblad
    José Luis Costa
    First Published July 3, 2008
  - Impacts of protein–protein interaction domains on organism and network complexity
    Kai Xia
    Zheng Fu
    Lei Hou
    Jing-Dong J. Han
    First Published August 7, 2008
Methods
- - RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays
    John C. Marioni
    Christopher E. Mason
    Shrikant M. Mane
    Matthew Stephens
    Yoav Gilad
    First Published June 11, 2008
RESOURCES
- - An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)
    Vardhman K. Rakyan
    Thomas A. Down
    Natalie P. Thorne
    Paul Flicek
    Eugene Kulesha
    Stefan Gräf Eleni M. Tomazou Liselotte Bäckdahl Nathan Johnson Marlis Herberth Kevin L. Howe David K. Jackson Marcos M. Miretti Heike Fiegler John C. Marioni Ewan Birney
    ...[+11 authors]...,
    Tim J.P. Hubbard
    Nigel P. Carter
    Simon Tavaré
    Stephan Beck
    First Published June 24, 2008
  - Tracking the complex flow of chromosome rearrangements from the Hominoidea Ancestor to extant Hylobates and Nomascus Gibbons by high-resolution synteny mapping
    Doriana Misceo
    Oronzo Capozzi
    Roberta Roberto
    Maria P. Dell’Oglio
    Mariano Rocchi
    First Published June 13, 2008
  - EagleView: A genome assembly viewer for next-generation sequencing technologies
    Weichun Huang
    Gabor Marth
    First Published June 11, 2008
ERRATUM
- - Erratum
    First Published August 28, 2008

Table of Contents

Volume 18, Issue 9 | September 2008

PERSPECTIVE

Genome-wide analyses of alternative splicing in plants: Opportunities and challenges

LETTERS

Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes

CpG dinucleotides and the mutation rate of non-CpG DNA

A deletion in nephronophthisis 4 (NPHP4) is associated with recessive cone-rod dystrophy in standard wire-haired dachshund

A novel mode of enhancer evolution: The Tal1 stem cell enhancer recruited a MIR element to specifically boost its activity

Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation

On the origin of new genes in Drosophila

A diverse set of microRNAs and microRNA-like small RNAs in developing rice grains

Relaxation of yeast mitochondrial functions after whole-genome duplication

Genome sequence of the β-rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia

Very small mobile repeated elements in cyanobacterial genomes

Impacts of protein–protein interaction domains on organism and network complexity

Methods

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

RESOURCES

An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs)

Tracking the complex flow of chromosome rearrangements from the Hominoidea Ancestor to extant Hylobates and Nomascus Gibbons by high-resolution synteny mapping

EagleView: A genome assembly viewer for next-generation sequencing technologies

ERRATUM

Erratum

Table of Contents

Volume 18, Issue 9 | September 2008

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PERSPECTIVE

LETTERS

Methods

RESOURCES

ERRATUM