Table of Contents

Next-Generation DNA Sequencing/Review

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The new paradigm of flow cell sequencing
- Robert A. Holt and
- Steven J.M. Jones
Genome Res. June 2008 18: 839-846; doi:10.1101/gr.073262.107

LETTERS

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Nonrecurrent MECP2 duplications mediated by genomic architecture-driven DNA breaks and break-induced replication repair
- Marijke Bauters,
- Hilde Van Esch,
- Michael J. Friez,
- Odile Boespflug-Tanguy,
- Martin Zenker,
- Angela M. Vianna-Morgante,
- Carla Rosenberg,
- Jaakko Ignatius,
- Martine Raynaud,
- Karen Hollanders,
- Karen Govaerts,
- Kris Vandenreijt,
- Florence Niel,
- Pierre Blanc,
- Roger E. Stevenson,
- Jean-Pierre Fryns,
- Peter Marynen,
- Charles E. Schwartz,
- and Guy Froyen
Genome Res. June 2008 18: 847-858; Published in Advance April 2, 2008, doi:10.1101/gr.075903.107
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Translation from nonautonomous type IAP retrotransposon is a critical determinant of transposition activity: Implication for retrotransposon-mediated genome evolution
- Ei-suke Saito,
- Vincent W. Keng,
- Junji Takeda,
- and Kyoji Horie
Genome Res. June 2008 18: 859-868; Published in Advance May 2, 2008, doi:10.1101/gr.069310.107
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Extensive variation between inbred mouse strains due to endogenous L1 retrotransposition
- Keiko Akagi,
- Jingfeng Li,
- Robert M. Stephens,
- Natalia Volfovsky,
- and David E. Symer
Genome Res. June 2008 18: 869-880; Published in Advance April 1, 2008, doi:10.1101/gr.075770.107
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Genome-wide analysis of microsatellite polymorphism in chicken circumventing the ascertainment bias
- Mikael Brandström and
- Hans Ellegren
Genome Res. June 2008 18: 881-887; Published in Advance March 20, 2008, doi:10.1101/gr.075242.107
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De novo search for non-coding RNA genes in the AT-rich genome of Dictyostelium discoideum: Performance of Markov-dependent genome feature scoring
- Pontus Larsson,
- Andrea Hinas,
- David H. Ardell,
- Leif A. Kirsebom,
- Anders Virtanen,
- and Fredrik Söderbom
Genome Res. June 2008 18: 888-899; Published in Advance March 17, 2008, doi:10.1101/gr.069104.107
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Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts
- Byung-Kwan Cho,
- Eric M. Knight,
- Christian L. Barrett,
- and Bernhard Ø. Palsson
Genome Res. June 2008 18: 900-910; Published in Advance March 13, 2008, doi:10.1101/gr.070276.107

Methods

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Power and SNP tagging in whole mitochondrial genome association studies
- Allan F. McRae,
- Enda M. Byrne,
- Zhen Zhen Zhao,
- Grant W. Montgomery,
- and Peter M. Visscher
Genome Res. June 2008 18: 911-917; Published in Advance March 20, 2008, doi:10.1101/gr.074872.107
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Detecting polymorphic regions in Arabidopsis thaliana with resequencing microarrays
- Georg Zeller,
- Richard M. Clark,
- Korbinian Schneeberger,
- Anja Bohlen,
- Detlef Weigel,
- and Gunnar Rätsch
Genome Res. June 2008 18: 918-929; Published in Advance March 6, 2008, doi:10.1101/gr.070169.107
OPEN ACCESS ARTICLE
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Identification of active transcriptional regulatory modules by the functional assay of DNA from nucleosome-free regions
- Mahesh Yaragatti,
- Claudio Basilico,
- and Lisa Dailey
Genome Res. June 2008 18: 930-938; Published in Advance April 25, 2008, doi:10.1101/gr.073460.107
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Direct targets of the TRP63 transcription factor revealed by a combination of gene expression profiling and reverse engineering
- Giusy Della Gatta,
- Mukesh Bansal,
- Alberto Ambesi-Impiombato,
- Dario Antonini,
- Caterina Missero,
- and Diego di Bernardo
Genome Res. June 2008 18: 939-948; Published in Advance April 25, 2008, doi:10.1101/gr.073601.107
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Large-scale analysis of gene clustering in bacteria
- Qingwu Yang and
- Sing-Hoi Sze
Genome Res. June 2008 18: 949-956; Published in Advance April 4, 2008, doi:10.1101/gr.072322.107

RESOURCE

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A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach
- Evgeny A. Glazov,
- Pauline A. Cottee,
- Wesley C. Barris,
- Robert J. Moore,
- Brian P. Dalrymple,
- and Mark L. Tizard
Genome Res. June 2008 18: 957-964; Published in Advance May 9, 2008, doi:10.1101/gr.074740.107

Platypus Special/Letter

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Bird-like sex chromosomes of platypus imply recent origin of mammal sex chromosomes
- Frédéric Veyrunes,
- Paul D. Waters,
- Pat Miethke,
- Willem Rens,
- Daniel McMillan,
- Amber E. Alsop,
- Frank Grützner,
- Janine E. Deakin,
- Camilla M. Whittington,
- Kyriena Schatzkamer,
- Colin L. Kremitzki,
- Tina Graves,
- Malcolm A. Ferguson-Smith,
- Wes Warren,
- and Jennifer A. Marshall Graves
Genome Res. June 2008 18: 965-973; Published in Advance May 7, 2008, doi:10.1101/gr.7101908
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Origin of INSL3-mediated testicular descent in therian mammals
- Jae-Il Park,
- Jenia Semyonov,
- Chia Lin Chang,
- Wei Yi,
- Wesley Warren,
- and Sheau Yu Teddy Hsu
Genome Res. June 2008 18: 974-985; Published in Advance May 7, 2008, doi:10.1101/gr.7119108
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Defensins and the convergent evolution of platypus and reptile venom genes
- Camilla M. Whittington,
- Anthony T. Papenfuss,
- Paramjit Bansal,
- Allan M. Torres,
- Emily S.W. Wong,
- Janine E. Deakin,
- Tina Graves,
- Amber Alsop,
- Kyriena Schatzkamer,
- Colin Kremitzki,
- Chris P. Ponting,
- Peter Temple-Smith,
- Wesley C. Warren,
- Philip W. Kuchel,
- and Katherine Belov
Genome Res. June 2008 18: 986-994; Published in Advance May 7, 2008, doi:10.1101/gr.7149808
OPEN ACCESS ARTICLE
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Conservation of small RNA pathways in platypus
- Elizabeth P. Murchison,
- Pouya Kheradpour,
- Ravi Sachidanandam,
- Carly Smith,
- Emily Hodges,
- Zhenyu Xuan,
- Manolis Kellis,
- Frank Grützner,
- Alexander Stark,
- and Gregory J. Hannon
Genome Res. June 2008 18: 995-1004; Published in Advance May 7, 2008, doi:10.1101/gr.073056.107
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Retroposed SNOfall—A mammalian-wide comparison of platypus snoRNAs
- Jürgen Schmitz,
- Anja Zemann,
- Gennady Churakov,
- Heiner Kuhl,
- Frank Grützner,
- Richard Reinhardt,
- and Jürgen Brosius
Genome Res. June 2008 18: 1005-1010; Published in Advance May 7, 2008, doi:10.1101/gr.7177908

Next-Generation DNA Sequencing/Review

The new paradigm of flow cell sequencing

LETTERS

Nonrecurrent MECP2 duplications mediated by genomic architecture-driven DNA breaks and break-induced replication repair

Translation from nonautonomous type IAP retrotransposon is a critical determinant of transposition activity: Implication for retrotransposon-mediated genome evolution

Extensive variation between inbred mouse strains due to endogenous L1 retrotransposition

Genome-wide analysis of microsatellite polymorphism in chicken circumventing the ascertainment bias

De novo search for non-coding RNA genes in the AT-rich genome of Dictyostelium discoideum: Performance of Markov-dependent genome feature scoring

Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts

Methods

Power and SNP tagging in whole mitochondrial genome association studies

Detecting polymorphic regions in Arabidopsis thaliana with resequencing microarrays

Identification of active transcriptional regulatory modules by the functional assay of DNA from nucleosome-free regions

Direct targets of the TRP63 transcription factor revealed by a combination of gene expression profiling and reverse engineering

Large-scale analysis of gene clustering in bacteria

RESOURCE

A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach

Platypus Special/Letter

Bird-like sex chromosomes of platypus imply recent origin of mammal sex chromosomes

Origin of INSL3-mediated testicular descent in therian mammals

Defensins and the convergent evolution of platypus and reptile venom genes

Conservation of small RNA pathways in platypus

Retroposed SNOfall—A mammalian-wide comparison of platypus snoRNAs

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