Table of Contents

Perspective

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Human genomic disease variants: A neutral evolutionary explanation
- Joel T. Dudley,
- Yuseob Kim,
- Li Liu,
- Glenn J. Markov,
- Kristyn Gerold,
- Rong Chen,
- Atul J. Butte,
- and Sudhir Kumar
Genome Res. August 2012 22: 1383-1394; Published in Advance June 4, 2012, doi:10.1101/gr.133702.111

Methods

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Copy number variation detection and genotyping from exome sequence data
- Niklas Krumm,
- Peter H. Sudmant,
- Arthur Ko,
- Brian J. O'Roak,
- Maika Malig,
- Bradley P. Coe,
- NHLBI Exome Sequencing Project,
- Aaron R. Quinlan,
- Deborah A. Nickerson,
- and Evan E. Eichler
Genome Res. August 2012 22: 1525-1532; Published in Advance May 14, 2012, doi:10.1101/gr.138115.112
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Systematic identification of edited microRNAs in the human brain
- Shahar Alon,
- Eyal Mor,
- Francois Vigneault,
- George M. Church,
- Franco Locatelli,
- Federica Galeano,
- Angela Gallo,
- Noam Shomron,
- and Eli Eisenberg
Genome Res. August 2012 22: 1533-1540; Published in Advance April 12, 2012, doi:10.1101/gr.131573.111
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Mutation mapping and identification by whole-genome sequencing
- Ignaty Leshchiner,
- Kristen Alexa,
- Peter Kelsey,
- Ivan Adzhubei,
- Christina A. Austin-Tse,
- Jeffrey D. Cooney,
- Heidi Anderson,
- Matthew J. King,
- Rolf W. Stottmann,
- Maija K. Garnaas,
- Seungshin Ha,
- Iain A. Drummond,
- Barry H. Paw,
- Trista E. North,
- David R. Beier,
- Wolfram Goessling,
- and Shamil R. Sunyaev
Genome Res. August 2012 22: 1541-1548; Published in Advance May 3, 2012, doi:10.1101/gr.135541.111
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Dissection of complex adult traits in a mouse synthetic population
- David T. Burke,
- Kenneth M. Kozloff,
- Shu Chen,
- Joshua L. West,
- Jodi M. Wilkowski,
- Steven A. Goldstein,
- Richard A. Miller,
- and Andrzej T. Galecki
Genome Res. August 2012 22: 1549-1557; Published in Advance May 15, 2012, doi:10.1101/gr.135582.111

Resources

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Genetic dissection of a model complex trait using the Drosophila Synthetic Population Resource
- Elizabeth G. King,
- Chris M. Merkes,
- Casey L. McNeil,
- Steven R. Hoofer,
- Saunak Sen,
- Karl W. Broman,
- Anthony D. Long,
- and Stuart J. Macdonald
Genome Res. August 2012 22: 1558-1566; Published in Advance April 10, 2012, doi:10.1101/gr.134031.111
OPEN ACCESS ARTICLE
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RNA-seq analysis of the C. briggsae transcriptome
- Bora Uyar,
- Jeffrey S.C. Chu,
- Ismael A. Vergara,
- Shu Yi Chua,
- Martin R. Jones,
- Tammy Wong,
- David L. Baillie,
- and Nansheng Chen
Genome Res. August 2012 22: 1567-1580; Published in Advance July 6, 2012, doi:10.1101/gr.134601.111
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HaploMerger: Reconstructing allelic relationships for polymorphic diploid genome assemblies
- Shengfeng Huang,
- Zelin Chen,
- Guangrui Huang,
- Ting Yu,
- Ping Yang,
- Jie Li,
- Yonggui Fu,
- Shaochun Yuan,
- Shangwu Chen,
- and Anlong Xu
Genome Res. August 2012 22: 1581-1588; Published in Advance May 3, 2012, doi:10.1101/gr.133652.111
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MuSiC: Identifying mutational significance in cancer genomes
- Nathan D. Dees,
- Qunyuan Zhang,
- Cyriac Kandoth,
- Michael C. Wendl,
- William Schierding,
- Daniel C. Koboldt,
- Thomas B. Mooney,
- Matthew B. Callaway,
- David Dooling,
- Elaine R. Mardis,
- Richard K. Wilson,
- and Li Ding
Genome Res. August 2012 22: 1589-1598; Published in Advance July 3, 2012, doi:10.1101/gr.134635.111

Perspective

Human genomic disease variants: A neutral evolutionary explanation

Research

Neonatal DNA methylation profile in human twins is specified by a complex interplay between intrauterine environmental and genetic factors, subject to tissue-specific influence

Genome-wide DNA methylation profiles in hematopoietic stem and progenitor cells reveal overrepresentation of ETS transcription factor binding sites

Genome-wide genetic variations are highly correlated with proximal DNA methylation patterns

CBX3 regulates efficient RNA processing genome-wide

Integrative functional genomics identifies an enhancer looping to the SOX9 gene disrupted by the 17q24.3 prostate cancer risk locus

Dynamic transitions in RNA polymerase II density profiles during transcription termination

Global analysis reveals multiple pathways for unique regulation of mRNA decay in induced pluripotent stem cells

Adenosine deaminases that act on RNA induce reproducible changes in abundance and sequence of embryonic miRNAs

A-to-I editing of microRNAs in the mammalian brain increases during development

Effects of ADARs on small RNA processing pathways in C. elegans

Genome sequencing reveals complex speciation in the Drosophila simulans clade

Genomic characterization of the Bacillus cereus sensu lato species: Backdrop to the evolution of Bacillus anthracis

Methods

Copy number variation detection and genotyping from exome sequence data

Systematic identification of edited microRNAs in the human brain

Mutation mapping and identification by whole-genome sequencing

Dissection of complex adult traits in a mouse synthetic population

Resources

Genetic dissection of a model complex trait using the Drosophila Synthetic Population Resource

RNA-seq analysis of the C. briggsae transcriptome

HaploMerger: Reconstructing allelic relationships for polymorphic diploid genome assemblies

MuSiC: Identifying mutational significance in cancer genomes

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