Volume 19, Issue 7 | July 2009

Next-Generation DNA Sequencing/Review
- - Microbial community profiling for human microbiome projects: Tools, techniques, and challenges
    Micah Hamady
    Rob Knight
    First Published April 21, 2009
Letter
- - Ride the wavelet: A multiscale analysis of genomic contexts flanking small insertions and deletions
    Erika M. Kvikstad
    Francesca Chiaromonte
    Kateryna D. Makova
    First Published June 5, 2009
  - Lineage-specific DNA methylation in T cells correlates with histone methylation and enhancer activity
    Christian Schmidl
    Maja Klug
    Tina J. Boeld
    Reinhard Andreesen
    Petra Hoffmann
    First Published June 3, 2009
  - New class of microRNA targets containing simultaneous 5′-UTR and 3′-UTR interaction sites
    Inhan Lee
    Subramanian S. Ajay
    Jong In Yook
    Hyun Sil Kim
    Su Hyung Hong
    First Published March 31, 2009
  - Lack of bystander activation shows that localization exterior to chromosome territories is not sufficient to up-regulate gene expression
    Céline Morey
    Clémence Kress
    Wendy A. Bickmore
    First Published April 23, 2009
  - Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines
    Peter D. Keightley
    Urmi Trivedi
    Marian Thomson
    Fiona Oliver
    Sujai Kumar
    First Published May 13, 2009
  - The origins of apicomplexan sequence innovation
    James Wasmuth
    Jennifer Daub
    José Manuel Peregrín-Alvarez
    Constance A.M. Finney
    John Parkinson
    First Published April 10, 2009
  - Genome sequencing of linezolid-resistant Streptococcus pneumoniae mutants reveals novel mechanisms of resistance
    Jie Feng
    Andréanne Lupien
    Hélène Gingras
    Jessica Wasserscheid
    Ken Dewar
    First Published April 6, 2009
  - Pervasive, genome-wide positive selection leading to functional divergence in the bacterial genus Campylobacter
    Tristan Lefébure
    Michael J. Stanhope
    First Published March 20, 2009
  - The polyadenylation site of Mimivirus transcripts obeys a stringent ‘hairpin rule’
    Deborah Byrne
    Renata Grzela
    Audrey Lartigue
    Stéphane Audic
    Sabine Chenivesse
    First Published April 29, 2009
Methods
- - DNA Sudoku—harnessing high-throughput sequencing for multiplexed specimen analysis
    Yaniv Erlich
    Kenneth Chang
    Assaf Gordon
    Roy Ronen
    Oron Navon
    First Published May 15, 2009
  - Overlapping pools for high-throughput targeted resequencing
    Snehit Prabhu
    Itsik Pe'er
    First Published May 15, 2009
  - Shifted Transversal Design smart-pooling for high coverage interactome mapping
    Xiaofeng Xin
    Jean-François Rual
    Tomoko Hirozane-Kishikawa
    David E. Hill
    Marc Vidal
    First Published May 15, 2009
  - Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes
    Fereydoun Hormozdiari
    Can Alkan
    Evan E. Eichler
    S. Cenk Sahinalp
    First Published May 15, 2009
  - Targeted genome editing in human cells with zinc finger nucleases constructed via modular assembly
    Hye Joo Kim
    Hyung Joo Lee
    Hyojin Kim
    Seung Woo Cho
    Jin-Soo Kim
    First Published May 21, 2009
  - Conserved introns reveal novel transcripts in Drosophila melanogaster
    Michael Hiller
    Sven Findeiß
    Sandro Lein
    Manja Marz
    Claudia Nickel
    Dominic Rose Christine Schulz
    ...[+2 authors]...,
    Rolf Backofen
    Sonja J. Prohaska
    Gunter Reuter
    Peter F. Stadler
    First Published May 20, 2009
  - Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system
    Manman Guo
    Hui Feng
    Jun Zhang
    Wenqin Wang
    Yi Wang
    Yuqing Li
    ...[+1 authors]...,
    Chunhui Gao
    Huanchun Chen
    Ying Feng
    Zheng-Guo He
    First Published February 18, 2009
Resource
- - Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing
    Wei Qu
    Shin-ichi Hashimoto
    Shinichi Morishita
    First Published May 13, 2009
  - The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes
    Kim D. Pruitt
    Jennifer Harrow
    Rachel A. Harte
    Craig Wallin
    Mark Diekhans
    Donna R. Maglott Steve Searle Catherine M. Farrell Jane E. Loveland Barbara J. Ruef Elizabeth Hart Marie-Marthe Suner Melissa J. Landrum Bronwen Aken Sarah Ayling Robert Baertsch Julio Fernandez-Banet Joshua L. Cherry Val Curwen Michael DiCuccio Manolis Kellis Jennifer Lee Michael F. Lin Michael Schuster Andrew Shkeda Clara Amid Garth Brown Oksana Dukhanina Adam Frankish Jennifer Hart Bonnie L. Maidak Jonathan Mudge Michael R. Murphy Terence Murphy Jeena Rajan Bhanu Rajput Lillian D. Riddick Catherine Snow Charles Steward David Webb Janet A. Weber Laurens Wilming Wenyu Wu Ewan Birney David Haussler
    ...[+40 authors]...,
    Tim Hubbard
    James Ostell
    Richard Durbin
    David Lipman
    First Published June 4, 2009

Table of Contents

Volume 19, Issue 7 | July 2009

Next-Generation DNA Sequencing/Review

Microbial community profiling for human microbiome projects: Tools, techniques, and challenges

Letter

Ride the wavelet: A multiscale analysis of genomic contexts flanking small insertions and deletions

Lineage-specific DNA methylation in T cells correlates with histone methylation and enhancer activity

New class of microRNA targets containing simultaneous 5′-UTR and 3′-UTR interaction sites

Lack of bystander activation shows that localization exterior to chromosome territories is not sufficient to up-regulate gene expression

Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines

The origins of apicomplexan sequence innovation

Genome sequencing of linezolid-resistant Streptococcus pneumoniae mutants reveals novel mechanisms of resistance

Pervasive, genome-wide positive selection leading to functional divergence in the bacterial genus Campylobacter

The polyadenylation site of Mimivirus transcripts obeys a stringent ‘hairpin rule’

Methods

DNA Sudoku—harnessing high-throughput sequencing for multiplexed specimen analysis

Overlapping pools for high-throughput targeted resequencing

Shifted Transversal Design smart-pooling for high coverage interactome mapping

Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes

Targeted genome editing in human cells with zinc finger nucleases constructed via modular assembly

Conserved introns reveal novel transcripts in Drosophila melanogaster

Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system

Resource

Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing

The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes

Table of Contents

Volume 19, Issue 7 | July 2009

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Next-Generation DNA Sequencing/Review

Letter

Methods

Resource