Table of Contents

COMMENTARY

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2× genomes—Does depth matter?
- Phil Green
Genome Res. November 2007 17: 1547-1549; doi:10.1101/gr.7050807
OPEN ACCESS ARTICLE

ARTICLES

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A comprehensive ChIP–chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members
- Xiaoqin Xu,
- Mark Bieda,
- Victor X. Jin,
- Alina Rabinovich,
- Mathew J. Oberley,
- Roland Green,
- and Peggy J. Farnham
Genome Res. November 2007 17: 1550-1561; Published in Advance October 1, 2007, doi:10.1101/gr.6783507
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Breed relationships facilitate fine-mapping studies: A 7.8-kb deletion cosegregates with Collie eye anomaly across multiple dog breeds
- Heidi G. Parker,
- Anna V. Kukekova,
- Dayna T. Akey,
- Orly Goldstein,
- Ewen F. Kirkness,
- Kathleen C. Baysac,
- Dana S. Mosher,
- Gustavo D. Aguirre,
- Gregory M. Acland,
- and Elaine A. Ostrander
Genome Res. November 2007 17: 1562-1571; Published in Advance October 4, 2007, doi:10.1101/gr.6772807
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Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world
- Minglei Wang,
- Liudmila S. Yafremava,
- Derek Caetano-Anollés,
- Jay E. Mittenthal,
- and Gustavo Caetano-Anollés
Genome Res. November 2007 17: 1572-1585; Published in Advance October 1, 2007, doi:10.1101/gr.6454307

LETTERS

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Altered adenosine-to-inosine RNA editing in human cancer
- Nurit Paz,
- Erez Y. Levanon,
- Ninette Amariglio,
- Amy B. Heimberger,
- Zvi Ram,
- Shlomi Constantini,
- Zohar S. Barbash,
- Konstantin Adamsky,
- Michal Safran,
- Avi Hirschberg,
- Meir Krupsky,
- Issachar Ben-Dov,
- Simona Cazacu,
- Tom Mikkelsen,
- Chaya Brodie,
- Eli Eisenberg,
- and Gideon Rechavi
Genome Res. November 2007 17: 1586-1595; Published in Advance October 1, 2007, doi:10.1101/gr.6493107
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Information capture using SNPs from HapMap and whole-genome chips differs in a sample of inflammatory and cardiovascular gene-centric regions from genome-wide estimates
- Chris Wallace,
- Richard J. Dobson,
- Patricia B. Munroe,
- and Mark J. Caulfield
Genome Res. November 2007 17: 1596-1602; Published in Advance September 25, 2007, doi:10.1101/gr.5996407
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Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions
- Laurie Gordon,
- Shan Yang,
- Mary Tran-Gyamfi,
- Dan Baggott,
- Mari Christensen,
- Aaron Hamilton,
- Richard Crooijmans,
- Martien Groenen,
- Susan Lucas,
- Ivan Ovcharenko,
- and Lisa Stubbs
Genome Res. November 2007 17: 1603-1613; Published in Advance October 5, 2007, doi:10.1101/gr.6775107
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An Arabidopsis gene network based on the graphical Gaussian model
- Shisong Ma,
- Qingqiu Gong,
- and Hans J. Bohnert
Genome Res. November 2007 17: 1614-1625; Published in Advance October 5, 2007, doi:10.1101/gr.6911207
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Systematic condition-dependent annotation of metabolic genes
- Tomer Shlomi,
- Markus Herrgard,
- Vasiliy Portnoy,
- Efrat Naim,
- Bernhard Ø. Palsson,
- Roded Sharan,
- and Eytan Ruppin
Genome Res. November 2007 17: 1626-1633; Published in Advance September 25, 2007, doi:10.1101/gr.6678707
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Functional and evolutionary implications of enhanced genomic analysis of rhomboid intramembrane proteases
- Marius K. Lemberg and
- Matthew Freeman
Genome Res. November 2007 17: 1634-1646; Published in Advance October 15, 2007, doi:10.1101/gr.6425307
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The rise and spread of a new pathogen: Seroresistant Moraxella catarrhalis
- Thierry Wirth,
- Giovanna Morelli,
- Barica Kusecek,
- Alex van Belkum,
- Cindy van der Schee,
- Axel Meyer,
- and Mark Achtman
Genome Res. November 2007 17: 1647-1656; Published in Advance September 25, 2007, doi:10.1101/gr.6122607
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Lateral gene transfer between obligate intracellular bacteria: Evidence from the Rickettsia massiliae genome
- Guillaume Blanc,
- Hiroyuki Ogata,
- Catherine Robert,
- Stéphane Audic,
- Jean-Michel Claverie,
- and Didier Raoult
Genome Res. November 2007 17: 1657-1664; Published in Advance October 4, 2007, doi:10.1101/gr.6742107

Methods

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PennCNV: An integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data
- Kai Wang,
- Mingyao Li,
- Dexter Hadley,
- Rui Liu,
- Joseph Glessner,
- Struan F.A. Grant,
- Hakon Hakonarson,
- and Maja Bucan
Genome Res. November 2007 17: 1665-1674; Published in Advance October 5, 2007, doi:10.1101/gr.6861907

RESOURCES

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Initial sequence and comparative analysis of the cat genome
- Joan U. Pontius,
- James C. Mullikin,
- Douglas R. Smith,
- Agencourt Sequencing Team,
- Kerstin Lindblad-Toh,
- Sante Gnerre,
- Michele Clamp,
- Jean Chang,
- Robert Stephens,
- Beena Neelam,
- Natalia Volfovsky,
- Alejandro A. Schäffer,
- Richa Agarwala,
- Kristina Narfström,
- William J. Murphy,
- Urs Giger,
- Alfred L. Roca,
- Agostinho Antunes,
- Marilyn Menotti-Raymond,
- Naoya Yuhki,
- Jill Pecon-Slattery,
- Warren E. Johnson,
- Guillaume Bourque,
- Glenn Tesler,
- NISC Comparative Sequencing Program,
- and Stephen J. O’Brien
Genome Res. November 2007 17: 1675-1689; doi:10.1101/gr.6380007
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Islands of euchromatin-like sequence and expressed polymorphic sequences within the short arm of human chromosome 21
- Robert Lyle,
- Paola Prandini,
- Kazutoyo Osoegawa,
- Boudewijn ten Hallers,
- Sean Humphray,
- Baoli Zhu,
- Eduardo Eyras,
- Robert Castelo,
- Christine P. Bird,
- Sarantos Gagos,
- Carol Scott,
- Antony Cox,
- Samuel Deutsch,
- Catherine Ucla,
- Marc Cruts,
- Sophie Dahoun,
- Xinwei She,
- Frederique Bena,
- Sheng-Yue Wang,
- Christine Van Broeckhoven,
- Evan E. Eichler,
- Roderic Guigo,
- Jane Rogers,
- Pieter J. de Jong,
- Alexandre Reymond,
- and Stylianos E. Antonarakis
Genome Res. November 2007 17: 1690-1696; Published in Advance September 25, 2007, doi:10.1101/gr.6675307
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SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing
- Juliane C. Dohm,
- Claudio Lottaz,
- Tatiana Borodina,
- and Heinz Himmelbauer
Genome Res. November 2007 17: 1697-1706; Published in Advance October 1, 2007, doi:10.1101/gr.6435207

COMMENTARY

2× genomes—Does depth matter?

ARTICLES

A comprehensive ChIP–chip analysis of E2F1, E2F4, and E2F6 in normal and tumor cells reveals interchangeable roles of E2F family members

Breed relationships facilitate fine-mapping studies: A 7.8-kb deletion cosegregates with Collie eye anomaly across multiple dog breeds

Reductive evolution of architectural repertoires in proteomes and the birth of the tripartite world

LETTERS

Altered adenosine-to-inosine RNA editing in human cancer

Information capture using SNPs from HapMap and whole-genome chips differs in a sample of inflammatory and cardiovascular gene-centric regions from genome-wide estimates

Comparative analysis of chicken chromosome 28 provides new clues to the evolutionary fragility of gene-rich vertebrate regions

An Arabidopsis gene network based on the graphical Gaussian model

Systematic condition-dependent annotation of metabolic genes

Functional and evolutionary implications of enhanced genomic analysis of rhomboid intramembrane proteases

The rise and spread of a new pathogen: Seroresistant Moraxella catarrhalis

Lateral gene transfer between obligate intracellular bacteria: Evidence from the Rickettsia massiliae genome

Methods

PennCNV: An integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data

RESOURCES

Initial sequence and comparative analysis of the cat genome

Islands of euchromatin-like sequence and expressed polymorphic sequences within the short arm of human chromosome 21

SHARCGS, a fast and highly accurate short-read assembly algorithm for de novo genomic sequencing

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