Table of Contents

Forum

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Don’t throw the baby out with the bathwater: Enabling a bottom-up approach in genome-wide association studies
- Sean E. McGuire and
- Amy L. McGuire
Genome Res. November 2008 18: 1683-1685; doi:10.1101/gr.083584.108

REVIEW

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Defensins and the dynamic genome: What we can learn from structural variation at human chromosome band 8p23.1
- Edward J. Hollox,
- John C.K. Barber,
- Anthony J. Brookes,
- and John A.L. Armour
Genome Res. November 2008 18: 1686-1697; doi:10.1101/gr.080945.108

ARTICLE

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Copy number variation and evolution in humans and chimpanzees
- George H. Perry,
- Fengtang Yang,
- Tomas Marques-Bonet,
- Carly Murphy,
- Tomas Fitzgerald,
- Arthur S. Lee,
- Courtney Hyland,
- Anne C. Stone,
- Matthew E. Hurles,
- Chris Tyler-Smith,
- Evan E. Eichler,
- Nigel P. Carter,
- Charles Lee,
- and Richard Redon
Genome Res. November 2008 18: 1698-1710; Published in Advance September 4, 2008, doi:10.1101/gr.082016.108

LETTERS

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Reduced purifying selection prevails over positive selection in human copy number variant evolution
- Duc-Quang Nguyen,
- Caleb Webber,
- Jayne Hehir-Kwa,
- Rolph Pfundt,
- Joris Veltman,
- and Chris P. Ponting
Genome Res. November 2008 18: 1711-1723; Published in Advance August 7, 2008, doi:10.1101/gr.077289.108
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Copy number variation at the breakpoint region of isochromosome 17q
- Claudia M.B. Carvalho and
- James R. Lupski
Genome Res. November 2008 18: 1724-1732; Published in Advance August 19, 2008, doi:10.1101/gr.080697.108
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Unexpected complexity at breakpoint junctions in phenotypically normal individuals and mechanisms involved in generating balanced translocations t(1;22)(p36;q13)
- Marzena Gajecka,
- Andrew J. Gentles,
- Albert Tsai,
- David Chitayat,
- Katherine L. Mackay,
- Caron D. Glotzbach,
- Michael R. Lieber,
- and Lisa G. Shaffer
Genome Res. November 2008 18: 1733-1742; Published in Advance September 2, 2008, doi:10.1101/gr.077453.108
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Dispensability of mammalian DNA
- Cory McLean and
- Gill Bejerano
Genome Res. November 2008 18: 1743-1751; Published in Advance October 2, 2008, doi:10.1101/gr.080184.108
OPEN ACCESS ARTICLE
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Evolution of the mammalian transcription factor binding repertoire via transposable elements
- Guillaume Bourque,
- Bernard Leong,
- Vinsensius B. Vega,
- Xi Chen,
- Yen Ling Lee,
- Kandhadayar G. Srinivasan,
- Joon-Lin Chew,
- Yijun Ruan,
- Chia-Lin Wei,
- Huck Hui Ng,
- and Edison T. Liu
Genome Res. November 2008 18: 1752-1762; Published in Advance August 5, 2008, doi:10.1101/gr.080663.108
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E2F in vivo binding specificity: Comparison of consensus versus nonconsensus binding sites
- Alina Rabinovich,
- Victor X. Jin,
- Roman Rabinovich,
- Xiaoqin Xu,
- and Peggy J. Farnham
Genome Res. November 2008 18: 1763-1777; Published in Advance October 3, 2008, doi:10.1101/gr.080622.108
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Reconfiguration of genomic anchors upon transcriptional activation of the human major histocompatibility complex
- Diego Ottaviani,
- Elliott Lever,
- Richard Mitter,
- Tania Jones,
- Tim Forshew,
- Rossitza Christova,
- Eleni M. Tomazou,
- Vardhman K. Rakyan,
- Stephen A. Krawetz,
- Adrian E. Platts,
- Badmavady Segarane,
- Stephan Beck,
- and Denise Sheer
Genome Res. November 2008 18: 1778-1786; Published in Advance October 10, 2008, doi:10.1101/gr.082313.108
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In-depth characterization of the microRNA transcriptome in a leukemia progression model
- Florian Kuchenbauer,
- Ryan D. Morin,
- Bob Argiropoulos,
- Oleh I. Petriv,
- Malachi Griffith,
- Michael Heuser,
- Eric Yung,
- Jessica Piper,
- Allen Delaney,
- Anna-Liisa Prabhu,
- Yongjun Zhao,
- Helen McDonald,
- Thomas Zeng,
- Martin Hirst,
- Carl L. Hansen,
- Marco A. Marra,
- and R. Keith Humphries
Genome Res. November 2008 18: 1787-1797; Published in Advance October 10, 2008, doi:10.1101/gr.077578.108
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Transcription of foreign DNA in Escherichia coli
- René L. Warren,
- John D. Freeman,
- Roger C. Levesque,
- Duane E. Smailus,
- Stephane Flibotte,
- and Robert A. Holt
Genome Res. November 2008 18: 1798-1805; Published in Advance August 13, 2008, doi:10.1101/gr.080358.108

Methods

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Overlapping euchromatin/heterochromatin- associated marks are enriched in imprinted gene regions and predict allele-specific modification
- Bo Wen,
- Hao Wu,
- Hans Bjornsson,
- Roland D. Green,
- Rafael Irizarry,
- and Andrew P. Feinberg
Genome Res. November 2008 18: 1806-1813; Published in Advance September 16, 2008, doi:10.1101/gr.067587.107
OPEN ACCESS ARTICLE
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Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs
- Benedict Paten,
- Javier Herrero,
- Kathryn Beal,
- Stephen Fitzgerald,
- and Ewan Birney
Genome Res. November 2008 18: 1814-1828; Published in Advance October 10, 2008, doi:10.1101/gr.076554.108
OPEN ACCESS ARTICLE
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Genome-wide nucleotide-level mammalian ancestor reconstruction
- Benedict Paten,
- Javier Herrero,
- Stephen Fitzgerald,
- Kathryn Beal,
- Paul Flicek,
- Ian Holmes,
- and Ewan Birney
Genome Res. November 2008 18: 1829-1843; Published in Advance October 10, 2008, doi:10.1101/gr.076521.108
OPEN ACCESS ARTICLE
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Nested Patch PCR enables highly multiplexed mutation discovery in candidate genes
- Katherine Elena Varley and
- Robi David Mitra
Genome Res. November 2008 18: 1844-1850; Published in Advance October 10, 2008, doi:10.1101/gr.078204.108

RESOURCE

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Mapping short DNA sequencing reads and calling variants using mapping quality scores
- Heng Li,
- Jue Ruan,
- and Richard Durbin
Genome Res. November 2008 18: 1851-1858; Published in Advance August 19, 2008, doi:10.1101/gr.078212.108
OPEN ACCESS ARTICLE

ERRATUM

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Erratum
Genome Res. November 2008 18: 1859

Forum

Don’t throw the baby out with the bathwater: Enabling a bottom-up approach in genome-wide association studies

REVIEW

Defensins and the dynamic genome: What we can learn from structural variation at human chromosome band 8p23.1

ARTICLE

Copy number variation and evolution in humans and chimpanzees

LETTERS

Reduced purifying selection prevails over positive selection in human copy number variant evolution

Copy number variation at the breakpoint region of isochromosome 17q

Unexpected complexity at breakpoint junctions in phenotypically normal individuals and mechanisms involved in generating balanced translocations t(1;22)(p36;q13)

Dispensability of mammalian DNA

Evolution of the mammalian transcription factor binding repertoire via transposable elements

E2F in vivo binding specificity: Comparison of consensus versus nonconsensus binding sites

Reconfiguration of genomic anchors upon transcriptional activation of the human major histocompatibility complex

In-depth characterization of the microRNA transcriptome in a leukemia progression model

Transcription of foreign DNA in Escherichia coli

Methods

Overlapping euchromatin/heterochromatin- associated marks are enriched in imprinted gene regions and predict allele-specific modification

Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs

Genome-wide nucleotide-level mammalian ancestor reconstruction

Nested Patch PCR enables highly multiplexed mutation discovery in candidate genes

RESOURCE

Mapping short DNA sequencing reads and calling variants using mapping quality scores

ERRATUM

Erratum

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