Table of Contents

Next-Generation DNA Sequencing/Review

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Microbial community profiling for human microbiome projects: Tools, techniques, and challenges
- Micah Hamady and
- Rob Knight
Genome Res. July 2009 19: 1141-1152; Published in Advance April 21, 2009, doi:10.1101/gr.085464.108

Letter

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Ride the wavelet: A multiscale analysis of genomic contexts flanking small insertions and deletions
- Erika M. Kvikstad,
- Francesca Chiaromonte,
- and Kateryna D. Makova
Genome Res. July 2009 19: 1153-1164; Published in Advance June 5, 2009, doi:10.1101/gr.088922.108
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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,
- Matthias Edinger,
- and Michael Rehli
Genome Res. July 2009 19: 1165-1174; Published in Advance June 3, 2009, doi:10.1101/gr.091470.109
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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,
- Nam Hee Kim,
- Saravana M. Dhanasekaran,
- Arul M. Chinnaiyan,
- and Brian D. Athey
Genome Res. July 2009 19: 1175-1183; Published in Advance March 31, 2009, doi:10.1101/gr.089367.108
OPEN ACCESS ARTICLE
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Lack of bystander activation shows that localization exterior to chromosome territories is not sufficient to up-regulate gene expression
- Céline Morey,
- Clémence Kress,
- and Wendy A. Bickmore
Genome Res. July 2009 19: 1184-1194; Published in Advance April 23, 2009, doi:10.1101/gr.089045.108
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Analysis of the genome sequences of three Drosophila melanogaster spontaneous mutation accumulation lines
- Peter D. Keightley,
- Urmi Trivedi,
- Marian Thomson,
- Fiona Oliver,
- Sujai Kumar,
- and Mark L. Blaxter
Genome Res. July 2009 19: 1195-1201; Published in Advance May 13, 2009, doi:10.1101/gr.091231.109
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The origins of apicomplexan sequence innovation
- James Wasmuth,
- Jennifer Daub,
- José Manuel Peregrín-Alvarez,
- Constance A.M. Finney,
- and John Parkinson
Genome Res. July 2009 19: 1202-1213; Published in Advance April 10, 2009, doi:10.1101/gr.083386.108
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Genome sequencing of linezolid-resistant Streptococcus pneumoniae mutants reveals novel mechanisms of resistance
- Jie Feng,
- Andréanne Lupien,
- Hélène Gingras,
- Jessica Wasserscheid,
- Ken Dewar,
- Danielle Légaré,
- and Marc Ouellette
Genome Res. July 2009 19: 1214-1223; Published in Advance April 6, 2009, doi:10.1101/gr.089342.108
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Pervasive, genome-wide positive selection leading to functional divergence in the bacterial genus Campylobacter
- Tristan Lefébure and
- Michael J. Stanhope
Genome Res. July 2009 19: 1224-1232; Published in Advance March 20, 2009, doi:10.1101/gr.089250.108
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The polyadenylation site of Mimivirus transcripts obeys a stringent ‘hairpin rule’
- Deborah Byrne,
- Renata Grzela,
- Audrey Lartigue,
- Stéphane Audic,
- Sabine Chenivesse,
- Stéphanie Encinas,
- Jean-Michel Claverie,
- and Chantal Abergel
Genome Res. July 2009 19: 1233-1242; Published in Advance April 29, 2009, doi:10.1101/gr.091561.109

Methods

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DNA Sudoku—harnessing high-throughput sequencing for multiplexed specimen analysis
- Yaniv Erlich,
- Kenneth Chang,
- Assaf Gordon,
- Roy Ronen,
- Oron Navon,
- Michelle Rooks,
- and Gregory J. Hannon
Genome Res. July 2009 19: 1243-1253; Published in Advance May 15, 2009, doi:10.1101/gr.092957.109
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Overlapping pools for high-throughput targeted resequencing
- Snehit Prabhu and
- Itsik Pe'er
Genome Res. July 2009 19: 1254-1261; Published in Advance May 15, 2009, doi:10.1101/gr.088559.108
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Shifted Transversal Design smart-pooling for high coverage interactome mapping
- Xiaofeng Xin,
- Jean-François Rual,
- Tomoko Hirozane-Kishikawa,
- David E. Hill,
- Marc Vidal,
- Charles Boone,
- and Nicolas Thierry-Mieg
Genome Res. July 2009 19: 1262-1269; Published in Advance May 15, 2009, doi:10.1101/gr.090019.108
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Combinatorial algorithms for structural variation detection in high-throughput sequenced genomes
- Fereydoun Hormozdiari,
- Can Alkan,
- Evan E. Eichler,
- and S. Cenk Sahinalp
Genome Res. July 2009 19: 1270-1278; Published in Advance May 15, 2009, doi:10.1101/gr.088633.108
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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,
- and Jin-Soo Kim
Genome Res. July 2009 19: 1279-1288; Published in Advance May 21, 2009, doi:10.1101/gr.089417.108
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Conserved introns reveal novel transcripts in Drosophila melanogaster
- Michael Hiller,
- Sven Findeiß,
- Sandro Lein,
- Manja Marz,
- Claudia Nickel,
- Dominic Rose,
- Christine Schulz,
- Rolf Backofen,
- Sonja J. Prohaska,
- Gunter Reuter,
- and Peter F. Stadler
Genome Res. July 2009 19: 1289-1300; Published in Advance May 20, 2009, doi:10.1101/gr.090050.108
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Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system
- Manman Guo,
- Hui Feng,
- Jun Zhang,
- Wenqin Wang,
- Yi Wang,
- Yuqing Li,
- Chunhui Gao,
- Huanchun Chen,
- Ying Feng,
- and Zheng-Guo He
Genome Res. July 2009 19: 1301-1308; Published in Advance February 18, 2009, doi:10.1101/gr.086595.108

Resource

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Efficient frequency-based de novo short-read clustering for error trimming in next-generation sequencing
- Wei Qu,
- Shin-ichi Hashimoto,
- and Shinichi Morishita
Genome Res. July 2009 19: 1309-1315; Published in Advance May 13, 2009, doi:10.1101/gr.089151.108
OPEN ACCESS ARTICLE
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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,
- Tim Hubbard,
- James Ostell,
- Richard Durbin,
- and David Lipman
Genome Res. July 2009 19: 1316-1323; Published in Advance June 4, 2009, doi:10.1101/gr.080531.108

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

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