Table of Contents

Commentary

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Darwinian alchemy: Human genes from noncoding DNA
- Adam Siepel
Genome Res. October 2009 19: 1693-1695; doi:10.1101/gr.098376.109

Article

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Comparative genomics of protoploid Saccharomycetaceae
- The Génolevures Consortium,
- Jean-Luc Souciet,
- Bernard Dujon,
- Claude Gaillardin,
- Mark Johnston,
- Philippe V. Baret,
- Paul Cliften,
- David J. Sherman,
- Jean Weissenbach,
- Eric Westhof,
- Patrick Wincker,
- Claire Jubin,
- Julie Poulain,
- Valérie Barbe,
- Béatrice Ségurens,
- François Artiguenave,
- Véronique Anthouard,
- Benoit Vacherie,
- Marie-Eve Val,
- Robert S. Fulton,
- Patrick Minx,
- Richard Wilson,
- Pascal Durrens,
- Géraldine Jean,
- Christian Marck,
- Tiphaine Martin,
- Macha Nikolski,
- Thomas Rolland,
- Marie-Line Seret,
- Serge Casarégola,
- Laurence Despons,
- Cécile Fairhead,
- Gilles Fischer,
- Ingrid Lafontaine,
- Véronique Leh,
- Marc Lemaire,
- Jacky de Montigny,
- Cécile Neuvéglise,
- Agnès Thierry,
- Isabelle Blanc-Lenfle,
- Claudine Bleykasten,
- Julie Diffels,
- Emilie Fritsch,
- Lionel Frangeul,
- Adrien Goëffon,
- Nicolas Jauniaux,
- Rym Kachouri-Lafond,
- Célia Payen,
- Serge Potier,
- Lenka Pribylova,
- Christophe Ozanne,
- Guy-Franck Richard,
- Christine Sacerdot,
- Marie-Laure Straub,
- and Emmanuel Talla
Genome Res. October 2009 19: 1696-1709; Published in Advance June 12, 2009, doi:10.1101/gr.091546.109
OPEN ACCESS ARTICLE

Methods

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Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing
- J. Douglas Freeman,
- René L. Warren,
- John R. Webb,
- Brad H. Nelson,
- and Robert A. Holt
Genome Res. October 2009 19: 1817-1824; Published in Advance June 18, 2009, doi:10.1101/gr.092924.109
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Next-generation tag sequencing for cancer gene expression profiling
- A. Sorana Morrissy,
- Ryan D. Morin,
- Allen Delaney,
- Thomas Zeng,
- Helen McDonald,
- Steven Jones,
- Yongjun Zhao,
- Martin Hirst,
- and Marco A. Marra
Genome Res. October 2009 19: 1825-1835; Published in Advance June 18, 2009, doi:10.1101/gr.094482.109
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Quantitative phenotyping via deep barcode sequencing
- Andrew M. Smith,
- Lawrence E. Heisler,
- Joseph Mellor,
- Fiona Kaper,
- Michael J. Thompson,
- Mark Chee,
- Frederick P. Roth,
- Guri Giaever,
- and Corey Nislow
Genome Res. October 2009 19: 1836-1842; Published in Advance July 21, 2009, doi:10.1101/gr.093955.109
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Direct multiplex sequencing (DMPS)—a novel method for targeted high-throughput sequencing of ancient and highly degraded DNA
- Mathias Stiller,
- Michael Knapp,
- Udo Stenzel,
- Michael Hofreiter,
- and Matthias Meyer
Genome Res. October 2009 19: 1843-1848; Published in Advance July 27, 2009, doi:10.1101/gr.095760.109
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Genome-wide comparisons of variation in linkage disequilibrium
- Yik Y. Teo,
- Andrew E. Fry,
- Kanishka Bhattacharya,
- Kerrin S. Small,
- Dominic P. Kwiatkowski,
- and Taane G. Clark
Genome Res. October 2009 19: 1849-1860; Published in Advance June 18, 2009, doi:10.1101/gr.092189.109
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The human protein coevolution network
- Elisabeth R.M. Tillier and
- Robert L. Charlebois
Genome Res. October 2009 19: 1861-1871; Published in Advance August 20, 2009, doi:10.1101/gr.092452.109
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Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns
- Christoph Kaleta,
- Luís Filipe de Figueiredo,
- and Stefan Schuster
Genome Res. October 2009 19: 1872-1883; Published in Advance June 18, 2009, doi:10.1101/gr.090639.108

Resource

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BayesCall: A model-based base-calling algorithm for high-throughput short-read sequencing
- Wei-Chun Kao,
- Kristian Stevens,
- and Yun S. Song
Genome Res. October 2009 19: 1884-1895; Published in Advance August 6, 2009, doi:10.1101/gr.095299.109
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GenGIS: A geospatial information system for genomic data
- Donovan H. Parks,
- Michael Porter,
- Sylvia Churcher,
- Suwen Wang,
- Christian Blouin,
- Jacqueline Whalley,
- Stephen Brooks,
- and Robert G. Beiko
Genome Res. October 2009 19: 1896-1904; Published in Advance July 27, 2009, doi:10.1101/gr.095612.109
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Analysis of the human E2 ubiquitin conjugating enzyme protein interaction network
- Gabriel Markson,
- Christina Kiel,
- Russell Hyde,
- Stephanie Brown,
- Panagoula Charalabous,
- Anja Bremm,
- Jennifer Semple,
- Jonathan Woodsmith,
- Simon Duley,
- Kourosh Salehi-Ashtiani,
- Marc Vidal,
- David Komander,
- Luis Serrano,
- Paul Lehner,
- and Christopher M. Sanderson
Genome Res. October 2009 19: 1905-1911; Published in Advance June 23, 2009, doi:10.1101/gr.093963.109
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Evidence-based gene predictions in plant genomes
- Chengzhi Liang,
- Long Mao,
- Doreen Ware,
- and Lincoln Stein
Genome Res. October 2009 19: 1912-1923; Published in Advance June 18, 2009, doi:10.1101/gr.088997.108

Commentary

Darwinian alchemy: Human genes from noncoding DNA

Article

Comparative genomics of protoploid Saccharomycetaceae

Letter

Unusual composition of a yeast chromosome arm is associated with its delayed replication

Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives

Nucleosomes are well positioned in exons and carry characteristic histone modifications

Chromatin poises miRNA- and protein-coding genes for expression

Recent de novo origin of human protein-coding genes

Relaxation of selective constraints on avian mitochondrial DNA following the degeneration of flight ability

Abundant and dynamically expressed miRNAs, piRNAs, and other small RNAs in the vertebrate Xenopus tropicalis

Abundant primary piRNAs, endo-siRNAs, and microRNAs in a Drosophila ovary cell line

Deterministic protein inference for shotgun proteomics data provides new insights into Arabidopsis pollen development and function

Whole genome sequence of Desulfovibrio magneticus strain RS-1 revealed common gene clusters in magnetotactic bacteria

Inference of the impact of insertion sequence (IS) elements on bacterial genome diversification through analysis of small-size structural polymorphisms in Escherichia coli O157 genomes

Methods

Profiling the T-cell receptor beta-chain repertoire by massively parallel sequencing

Next-generation tag sequencing for cancer gene expression profiling

Quantitative phenotyping via deep barcode sequencing

Direct multiplex sequencing (DMPS)—a novel method for targeted high-throughput sequencing of ancient and highly degraded DNA

Genome-wide comparisons of variation in linkage disequilibrium

The human protein coevolution network

Can the whole be less than the sum of its parts? Pathway analysis in genome-scale metabolic networks using elementary flux patterns

Resource

BayesCall: A model-based base-calling algorithm for high-throughput short-read sequencing

GenGIS: A geospatial information system for genomic data

Analysis of the human E2 ubiquitin conjugating enzyme protein interaction network

Evidence-based gene predictions in plant genomes

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