Table of Contents

Commentary

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Every genome sequence needs a good map
- Harris A. Lewin,
- Denis M. Larkin,
- Joan Pontius,
- and Stephen J. O'Brien
Genome Res. November 2009 19: 1925-1928; Published in Advance July 13, 2009, doi:10.1101/gr.094557.109

Perspective

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Phylogenomics of primates and their ancestral populations
- Adam Siepel
Genome Res. November 2009 19: 1929-1941; Published in Advance October 3, 2009, doi:10.1101/gr.084228.108

Methods

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Rapid inexpensive genome-wide association using pooled whole blood
- Jamie E. Craig,
- Alex W. Hewitt,
- Amy E. McMellon,
- Anjali K. Henders,
- Lingjun Ma,
- Leanne Wallace,
- Shiwani Sharma,
- Kathryn P. Burdon,
- Peter M. Visscher,
- Grant W. Montgomery,
- and Stuart MacGregor
Genome Res. November 2009 19: 2075-2080; Published in Advance October 3, 2009, doi:10.1101/gr.094680.109
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Rapid identification of homologous recombinants and determination of gene copy number with reference/query pyrosequencing (RQPS)
- Zhenyi Liu,
- Anna C. Obenauf,
- Michael R. Speicher,
- and Raphael Kopan
Genome Res. November 2009 19: 2081-2089; Published in Advance October 1, 2009, doi:10.1101/gr.093856.109
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Distinguishing direct versus indirect transcription factor–DNA interactions
- Raluca Gordân,
- Alexander J. Hartemink,
- and Martha L. Bulyk
Genome Res. November 2009 19: 2090-2100; Published in Advance August 3, 2009, doi:10.1101/gr.094144.109
OPEN ACCESS ARTICLE
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An ensemble model of competitive multi-factor binding of the genome
- Todd Wasson and
- Alexander J. Hartemink
Genome Res. November 2009 19: 2101-2112; Published in Advance August 31, 2009, doi:10.1101/gr.093450.109
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Automatic analysis of dividing cells in live cell movies to detect mitotic delays and correlate phenotypes in time
- Nathalie Harder,
- Felipe Mora-Bermúdez,
- William J. Godinez,
- Annelie Wünsche,
- Roland Eils,
- Jan Ellenberg,
- and Karl Rohr
Genome Res. November 2009 19: 2113-2124; Published in Advance October 1, 2009, doi:10.1101/gr.092494.109

Resource

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LookSeq: A browser-based viewer for deep sequencing data
- Heinrich Magnus Manske and
- Dominic P. Kwiatkowski
Genome Res. November 2009 19: 2125-2132; Published in Advance August 13, 2009, doi:10.1101/gr.093443.109
OPEN ACCESS ARTICLE
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mGene: Accurate SVM-based gene finding with an application to nematode genomes
- Gabriele Schweikert,
- Alexander Zien,
- Georg Zeller,
- Jonas Behr,
- Christoph Dieterich,
- Cheng Soon Ong,
- Petra Philips,
- Fabio De Bona,
- Lisa Hartmann,
- Anja Bohlen,
- Nina Krüger,
- Sören Sonnenburg,
- and Gunnar Rätsch
Genome Res. November 2009 19: 2133-2143; Published in Advance June 29, 2009, doi:10.1101/gr.090597.108
OPEN ACCESS ARTICLE
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Windshield splatter analysis with the Galaxy metagenomic pipeline
- Sergei Kosakovsky Pond,
- Samir Wadhawan,
- Francesca Chiaromonte,
- Guruprasad Ananda,
- Wen-Yu Chung,
- James Taylor,
- Anton Nekrutenko,
- and The Galaxy Team
Genome Res. November 2009 19: 2144-2153; Published in Advance October 9, 2009, doi:10.1101/gr.094508.109
OPEN ACCESS ARTICLE
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Singapore Genome Variation Project: A haplotype map of three Southeast Asian populations
- Yik-Ying Teo,
- Xueling Sim,
- Rick T.H. Ong,
- Adrian K.S. Tan,
- Jieming Chen,
- Erwin Tantoso,
- Kerrin S. Small,
- Chee-Seng Ku,
- Edmund J.D. Lee,
- Mark Seielstad,
- and Kee-Seng Chia
Genome Res. November 2009 19: 2154-2162; Published in Advance August 21, 2009, doi:10.1101/gr.095000.109
OPEN ACCESS ARTICLE

Commentary

Every genome sequence needs a good map

Perspective

Phylogenomics of primates and their ancestral populations

Letter

Population genomics in a disease targeted primary cell model

Coexpression network based on natural variation in human gene expression reveals gene interactions and functions

Elucidation of the ELK1 target gene network reveals a role in the coordinate regulation of core components of the gene regulation machinery

The presence of RNA polymerase II, active or stalled, predicts epigenetic fate of promoter CpG islands

Exon-trapping mediated by the human retrotransposon SVA

5′-Transducing SVA retrotransposon groups spread efficiently throughout the human genome

Relative contribution of sequence and structure features to the mRNA binding of Argonaute/EIF2C–miRNA complexes and the degradation of miRNA targets

Complex selection on 5′ splice sites in intron-rich organisms

Allele-specific DNA methylation in mouse strains is mainly determined by cis-acting sequences

Deeply conserved chordate noncoding sequences preserve genome synteny but do not drive gene duplicate retention

Profiling the repertoire of phenotypes influenced by environmental cues that occur during asexual reproduction

Repertoire and evolution of miRNA genes in four divergent nematode species

Methods

Rapid inexpensive genome-wide association using pooled whole blood

Rapid identification of homologous recombinants and determination of gene copy number with reference/query pyrosequencing (RQPS)

Distinguishing direct versus indirect transcription factor–DNA interactions

An ensemble model of competitive multi-factor binding of the genome

Automatic analysis of dividing cells in live cell movies to detect mitotic delays and correlate phenotypes in time

Resource

LookSeq: A browser-based viewer for deep sequencing data

mGene: Accurate SVM-based gene finding with an application to nematode genomes

Windshield splatter analysis with the Galaxy metagenomic pipeline

Singapore Genome Variation Project: A haplotype map of three Southeast Asian populations

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