Table of Contents

Methods

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Discriminative prediction of mammalian enhancers from DNA sequence
- Dongwon Lee,
- Rachel Karchin,
- and Michael A. Beer
Genome Res. December 2011 21: 2167-2180; Published in Advance August 29, 2011, doi:10.1101/gr.121905.111
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High-throughput semiquantitative analysis of insertional mutations in heterogeneous tumors
- Marco J. Koudijs,
- Christiaan Klijn,
- Louise van der Weyden,
- Jaap Kool,
- Jelle ten Hoeve,
- Daoud Sie,
- Pramudita R. Prasetyanti,
- Eva Schut,
- Sjors Kas,
- Theodore Whipp,
- Edwin Cuppen,
- Lodewyk Wessels,
- David J. Adams,
- and Jos Jonkers
Genome Res. December 2011 21: 2181-2189; Published in Advance August 18, 2011, doi:10.1101/gr.112763.110
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A metabolomic and systems biology perspective on the brain of the Fragile X syndrome mouse model
- Laetitia Davidovic,
- Vincent Navratil,
- Carmela M. Bonaccorso,
- Maria Vincenza Catania,
- Barbara Bardoni,
- and Marc-Emmanuel Dumas
Genome Res. December 2011 21: 2190-2202; Published in Advance September 7, 2011, doi:10.1101/gr.116764.110

Resources

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Simultaneous structural variation discovery among multiple paired-end sequenced genomes
- Fereydoun Hormozdiari,
- Iman Hajirasouliha,
- Andrew McPherson,
- Evan E. Eichler,
- and S. Cenk Sahinalp
Genome Res. December 2011 21: 2203-2212; Published in Advance November 2, 2011, doi:10.1101/gr.120501.111
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Differential expression in RNA-seq: A matter of depth
- Sonia Tarazona,
- Fernando García-Alcalde,
- Joaquín Dopazo,
- Alberto Ferrer,
- and Ana Conesa
Genome Res. December 2011 21: 2213-2223; Published in Advance September 8, 2011, doi:10.1101/gr.124321.111
OPEN ACCESS ARTICLE
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Assemblathon 1: A competitive assessment of de novo short read assembly methods
- Dent Earl,
- Keith Bradnam,
- John St. John,
- Aaron Darling,
- Dawei Lin,
- Joseph Fass,
- Hung On Ken Yu,
- Vince Buffalo,
- Daniel R. Zerbino,
- Mark Diekhans,
- Ngan Nguyen,
- Pramila Nuwantha Ariyaratne,
- Wing-Kin Sung,
- Zemin Ning,
- Matthias Haimel,
- Jared T. Simpson,
- Nuno A. Fonseca,
- İnanç Birol,
- T. Roderick Docking,
- Isaac Y. Ho,
- Daniel S. Rokhsar,
- Rayan Chikhi,
- Dominique Lavenier,
- Guillaume Chapuis,
- Delphine Naquin,
- Nicolas Maillet,
- Michael C. Schatz,
- David R. Kelley,
- Adam M. Phillippy,
- Sergey Koren,
- Shiaw-Pyng Yang,
- Wei Wu,
- Wen-Chi Chou,
- Anuj Srivastava,
- Timothy I. Shaw,
- J. Graham Ruby,
- Peter Skewes-Cox,
- Miguel Betegon,
- Michelle T. Dimon,
- Victor Solovyev,
- Igor Seledtsov,
- Petr Kosarev,
- Denis Vorobyev,
- Ricardo Ramirez-Gonzalez,
- Richard Leggett,
- Dan MacLean,
- Fangfang Xia,
- Ruibang Luo,
- Zhenyu Li,
- Yinlong Xie,
- Binghang Liu,
- Sante Gnerre,
- Iain MacCallum,
- Dariusz Przybylski,
- Filipe J. Ribeiro,
- Shuangye Yin,
- Ted Sharpe,
- Giles Hall,
- Paul J. Kersey,
- Richard Durbin,
- Shaun D. Jackman,
- Jarrod A. Chapman,
- Xiaoqiu Huang,
- Joseph L. DeRisi,
- Mario Caccamo,
- Yingrui Li,
- David B. Jaffe,
- Richard E. Green,
- David Haussler,
- Ian Korf,
- and Benedict Paten
Genome Res. December 2011 21: 2224-2241; Published in Advance September 16, 2011, doi:10.1101/gr.126599.111
OPEN ACCESS ARTICLE

Author Index

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Author Index, Volume 21, 2011
Genome Res. December 2011 21: 2242-2248

Reviewer Index

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Reviewer Index, Volume 21, 2011
Genome Res. December 2011 21: 2249-2253

Research

Homozygosity mapping and targeted genomic sequencing reveal the gene responsible for cerebellar hypoplasia and quadrupedal locomotion in a consanguineous kindred

Relating CNVs to transcriptome data at fine resolution: Assessment of the effect of variant size, type, and overlap with functional regions

Deep-transcriptome and ribonome sequencing redefines the molecular networks of pluripotency and the extracellular space in human embryonic stem cells

Epigenetic regulation of normal human mammary cell type–specific miRNAs

A matter of life or death: How microsatellites emerge in and vanish from the human genome

Phyloepigenomic comparison of great apes reveals a correlation between somatic and germline methylation states

Locus- and domain-dependent control of DNA methylation at mouse B1 retrotransposons during male germ cell development

Delineation of key regulatory elements identifies points of vulnerability in the mitogen-activated signaling network

Emergence of male-biased genes on the chicken Z-chromosome: Sex-chromosome contrasts between male and female heterogametic systems

Genome-wide analysis of retrogene polymorphisms in Drosophila melanogaster

Evidence of abundant stop codon readthrough in Drosophila and other metazoa

Compensation for differences in gene copy number among yeast ribosomal proteins is encoded within their promoters

Chromosome and gene copy number variation allow major structural change between species and strains of Leishmania

Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance

The making of a new pathogen: Insights from comparative population genomics of the domesticated wheat pathogen Mycosphaerella graminicola and its wild sister species

Methods

Discriminative prediction of mammalian enhancers from DNA sequence

High-throughput semiquantitative analysis of insertional mutations in heterogeneous tumors

A metabolomic and systems biology perspective on the brain of the Fragile X syndrome mouse model

Resources

Simultaneous structural variation discovery among multiple paired-end sequenced genomes

Differential expression in RNA-seq: A matter of depth

Assemblathon 1: A competitive assessment of de novo short read assembly methods

Author Index

Author Index, Volume 21, 2011

Reviewer Index

Reviewer Index, Volume 21, 2011

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