Volume 18, Issue 10 | October 2008

LETTERS
- - Abundance and length of simple repeats in vertebrate genomes are determined by their structural properties
    Albino Bacolla
    Jacquelynn E. Larson
    Jack R. Collins
    Jian Li
    Aleksandar Milosavljevic
    First Published August 7, 2008
  - Nucleosome positioning in human HOX gene clusters
    Peter V. Kharchenko
    Caroline J. Woo
    Michael Y. Tolstorukov
    Robert E. Kingston
    Peter J. Park
    First Published August 22, 2008
  - Global organization of replication time zones of the mouse genome
    Shlomit Farkash-Amar
    Doron Lipson
    Andreas Polten
    Alon Goren
    Charles Helmstetter
    First Published July 30, 2008
  - Mouse let-7 miRNA populations exhibit RNA editing that is constrained in the 5′-seed/ cleavage/anchor regions and stabilize predicted mmu-let-7a:mRNA duplexes
    Jeffrey G. Reid
    Ankur K. Nagaraja
    Francis C. Lynn
    Rafal B. Drabek
    Donna M. Muzny
    Chad A. Shaw Michelle K. Weiss Arash O. Naghavi Mahjabeen Khan Huifeng Zhu Jayantha Tennakoon Gemunu H. Gunaratne David B. Corry Jonathan Miller Michael T. McManus
    ...[+10 authors]...,
    Michael S. German
    Richard A. Gibbs
    Martin M. Matzuk
    Preethi H. Gunaratne
    First Published July 9, 2008
  - Early vertebrate whole genome duplications were predated by a period of intense genome rearrangement
    Andrew L. Hufton
    Detlef Groth
    Martin Vingron
    Hans Lehrach
    Albert J. Poustka
    First Published July 14, 2008
  - Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster
    Alisha K. Holloway
    David J. Begun
    Adam Siepel
    Katherine S. Pollard
    First Published June 26, 2008
  - Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening
    Simon Moxon
    Runchun Jing
    Gyorgy Szittya
    Frank Schwach
    Rachel L. Rusholme Pilcher
    First Published July 24, 2008
  - Reconstruction of the genome origins and evolution of the hybrid lager yeast Saccharomyces pastorianus
    Barbara Dunn
    Gavin Sherlock
    First Published September 11, 2008
  - Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways
    Nicholas R. Thomson
    Debra J. Clayton
    Daniel Windhorst
    Georgios Vernikos
    Susanne Davidson
    Carol Churcher Michael A. Quail Mark Stevens Michael A. Jones Michael Watson Andy Barron Abigail Layton Derek Pickard Robert A. Kingsley Alex Bignell Louise Clark Barbara Harris Doug Ormond Zahra Abdellah Karen Brooks Inna Cherevach Tracey Chillingworth John Woodward Halina Norberczak Angela Lord Claire Arrowsmith Kay Jagels Sharon Moule Karen Mungall Mandy Sanders Sally Whitehead Jose A. Chabalgoity Duncan Maskell Tom Humphrey
    ...[+29 authors]...,
    Mark Roberts
    Paul A. Barrow
    Gordon Dougan
    Julian Parkhill
    First Published June 26, 2008
Methods
- - Rapid whole-genome mutational profiling using next-generation sequencing technologies
    Douglas R. Smith
    Aaron R. Quinlan
    Heather E. Peckham
    Kathryn Makowsky
    Wei Tao
    Betty Woolf Lei Shen William F. Donahue Nadeem Tusneem Michael P. Stromberg Donald A. Stewart Lu Zhang Swati S. Ranade Jason B. Warner Clarence C. Lee Brittney E. Coleman Zheng Zhang Stephen F. McLaughlin Joel A. Malek Jon M. Sorenson Alan P. Blanchard Jarrod Chapman David Hillman Feng Chen Daniel S. Rokhsar
    ...[+20 authors]...,
    Kevin J. McKernan
    Thomas W. Jeffries
    Gabor T. Marth
    Paul M. Richardson
    First Published September 4, 2008
  - Ab initio identification of functionally interacting pairs of cis-regulatory elements
    Brad A. Friedman
    Michael B. Stadler
    Noam Shomron
    Ye Ding
    Christopher B. Burge
    First Published September 17, 2008
  - MEDME: An experimental and analytical methodology for the estimation of DNA methylation levels based on microarray derived MeDIP-enrichment
    Mattia Pelizzola
    Yasuo Koga
    Alexander Eckehart Urban
    Michael Krauthammer
    Sherman Weissman
    First Published September 2, 2008
  - Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations
    Gennifer E. Merrihew
    Colleen Davis
    Brent Ewing
    Gary Williams
    Lukas Käll
    Barbara E. Frewen
    ...[+1 authors]...,
    William Stafford Noble
    Phil Green
    James H. Thomas
    Michael J. MacCoss
    First Published July 24, 2008
RESOURCE
- - Large-scale gene trapping in C57BL/6N mouse embryonic stem cells
    Gwenn M. Hansen
    Diane C. Markesich
    Michael B. Burnett
    Qichao Zhu
    Karen M. Dionne
    Lizabeth J. Richter
    ...[+1 authors]...,
    Richard H. Finnell
    Arthur T. Sands
    Brian P. Zambrowicz
    Alejandro Abuin
    First Published September 17, 2008
ERRATUM
- - Errata
    First Published October 1, 2008

Table of Contents

Volume 18, Issue 10 | October 2008

LETTERS

Abundance and length of simple repeats in vertebrate genomes are determined by their structural properties

Nucleosome positioning in human HOX gene clusters

Global organization of replication time zones of the mouse genome

Mouse let-7 miRNA populations exhibit RNA editing that is constrained in the 5′-seed/ cleavage/anchor regions and stabilize predicted mmu-let-7a:mRNA duplexes

Early vertebrate whole genome duplications were predated by a period of intense genome rearrangement

Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster

Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening

Reconstruction of the genome origins and evolution of the hybrid lager yeast Saccharomyces pastorianus

Comparative genome analysis of Salmonella Enteritidis PT4 and Salmonella Gallinarum 287/91 provides insights into evolutionary and host adaptation pathways

Methods

Rapid whole-genome mutational profiling using next-generation sequencing technologies

Ab initio identification of functionally interacting pairs of cis-regulatory elements

MEDME: An experimental and analytical methodology for the estimation of DNA methylation levels based on microarray derived MeDIP-enrichment

Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations

RESOURCE

Large-scale gene trapping in C57BL/6N mouse embryonic stem cells

ERRATUM

Errata

Table of Contents

Volume 18, Issue 10 | October 2008

Share this issue

LETTERS

Methods

RESOURCE

ERRATUM