Table of Contents

Perspectives

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Genetic basis of kidney cancer: Role of genomics for the development of disease-based therapeutics
- W. Marston Linehan
Genome Res. November 2012 22: 2089-2100; Published in Advance October 4, 2012, doi:10.1101/gr.131110.111
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Translating genomic information into clinical medicine: Lung cancer as a paradigm
- Mia A. Levy,
- Christine M. Lovly,
- and William Pao
Genome Res. November 2012 22: 2101-2108; Published in Advance September 27, 2012, doi:10.1101/gr.131128.111
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Methods

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Observation of dually decoded regions of the human genome using ribosome profiling data
- Audrey M. Michel,
- Kingshuk Roy Choudhury,
- Andrew E. Firth,
- Nicholas T. Ingolia,
- John F. Atkins,
- and Pavel V. Baranov
Genome Res. November 2012 22: 2219-2229; Published in Advance May 16, 2012, doi:10.1101/gr.133249.111
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Ultrafast genome-wide scan for SNP–SNP interactions in common complex disease
- Snehit Prabhu and
- Itsik Pe'er
Genome Res. November 2012 22: 2230-2240; Published in Advance July 5, 2012, doi:10.1101/gr.137885.112
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Paired-end sequencing of Fosmid libraries by Illumina
- Louise J.S. Williams,
- Diana G. Tabbaa,
- Na Li,
- Aaron M. Berlin,
- Terrance P. Shea,
- Iain MacCallum,
- Michael S. Lawrence,
- Yotam Drier,
- Gad Getz,
- Sarah K. Young,
- David B. Jaffe,
- Chad Nusbaum,
- and Andreas Gnirke
Genome Res. November 2012 22: 2241-2249; Published in Advance July 16, 2012, doi:10.1101/gr.138925.112
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nFuse: Discovery of complex genomic rearrangements in cancer using high-throughput sequencing
- Andrew McPherson,
- Chunxiao Wu,
- Alexander W. Wyatt,
- Sohrab Shah,
- Colin Collins,
- and S. Cenk Sahinalp
Genome Res. November 2012 22: 2250-2261; Published in Advance June 28, 2012, doi:10.1101/gr.136572.111
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Spark: A navigational paradigm for genomic data exploration
- Cydney B. Nielsen,
- Hamid Younesy,
- Henriette O'Geen,
- Xiaoqin Xu,
- Andrew R. Jackson,
- Aleksandar Milosavljevic,
- Ting Wang,
- Joseph F. Costello,
- Martin Hirst,
- Peggy J. Farnham,
- and Steven J.M. Jones
Genome Res. November 2012 22: 2262-2269; Published in Advance September 7, 2012, doi:10.1101/gr.140665.112
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Finished bacterial genomes from shotgun sequence data
- Filipe J. Ribeiro,
- Dariusz Przybylski,
- Shuangye Yin,
- Ted Sharpe,
- Sante Gnerre,
- Amr Abouelleil,
- Aaron M. Berlin,
- Anna Montmayeur,
- Terrance P. Shea,
- Bruce J. Walker,
- Sarah K. Young,
- Carsten Russ,
- Chad Nusbaum,
- Iain MacCallum,
- and David B. Jaffe
Genome Res. November 2012 22: 2270-2277; Published in Advance July 24, 2012, doi:10.1101/gr.141515.112
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Systematic elucidation and in vivo validation of sequences enriched in hindbrain transcriptional control
- Grzegorz M. Burzynski,
- Xylena Reed,
- Leila Taher,
- Zachary E. Stine,
- Takeshi Matsui,
- Ivan Ovcharenko,
- and Andrew S. McCallion
Genome Res. November 2012 22: 2278-2289; Published in Advance July 3, 2012, doi:10.1101/gr.139717.112
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Integration of ChIP-seq and machine learning reveals enhancers and a predictive regulatory sequence vocabulary in melanocytes
- David U. Gorkin,
- Dongwon Lee,
- Xylena Reed,
- Christopher Fletez-Brant,
- Seneca L. Bessling,
- Stacie K. Loftus,
- Michael A. Beer,
- William J. Pavan,
- and Andrew S. McCallion
Genome Res. November 2012 22: 2290-2301; Published in Advance September 27, 2012, doi:10.1101/gr.139360.112

Resource

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A miRNA-regulatory network explains how dysregulated miRNAs perturb oncogenic processes across diverse cancers
- Christopher L. Plaisier,
- Min Pan,
- and Nitin S. Baliga
Genome Res. November 2012 22: 2302-2314; Published in Advance June 28, 2012, doi:10.1101/gr.133991.111
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Perspectives

Genetic basis of kidney cancer: Role of genomics for the development of disease-based therapeutics

Translating genomic information into clinical medicine: Lung cancer as a paradigm

Research

The transcriptional landscape and mutational profile of lung adenocarcinoma

Whole-exome sequencing combined with functional genomics reveals novel candidate driver cancer genes in endometrial cancer

A functional methylome map of ulcerative colitis

Guthrie card methylomics identifies temporally stable epialleles that are present at birth in humans

Nurture trumps nature in a longitudinal survey of salivary bacterial communities in twins from early adolescence to early adulthood

Genistein and bisphenol A exposure cause estrogen receptor 1 to bind thousands of sites in a cell type-specific manner

Cohesin regulates tissue-specific expression by stabilizing highly occupied cis-regulatory modules

Drosophila CTCF tandemly aligns with other insulator proteins at the borders of H3K27me3 domains

Nature and function of insulator protein binding sites in the Drosophila genome

The BEAF-32 insulator coordinates genome organization and function during the evolution of Drosophila species

Genome-wide search for novel human uORFs and N-terminal protein extensions using ribosomal footprinting

Methods

Observation of dually decoded regions of the human genome using ribosome profiling data

Ultrafast genome-wide scan for SNP–SNP interactions in common complex disease

Paired-end sequencing of Fosmid libraries by Illumina

nFuse: Discovery of complex genomic rearrangements in cancer using high-throughput sequencing

Spark: A navigational paradigm for genomic data exploration

Finished bacterial genomes from shotgun sequence data

Systematic elucidation and in vivo validation of sequences enriched in hindbrain transcriptional control

Integration of ChIP-seq and machine learning reveals enhancers and a predictive regulatory sequence vocabulary in melanocytes

Resource

A miRNA-regulatory network explains how dysregulated miRNAs perturb oncogenic processes across diverse cancers

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