Table of Contents

Perspective

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Assembly of large genomes using second-generation sequencing
- Michael C. Schatz,
- Arthur L. Delcher,
- and Steven L. Salzberg
Genome Res. September 2010 20: 1165-1173; Published in Advance May 27, 2010, doi:10.1101/gr.101360.109

Research

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The initial peopling of the Americas: A growing number of founding mitochondrial genomes from Beringia
- Ugo A. Perego,
- Norman Angerhofer,
- Maria Pala,
- Anna Olivieri,
- Hovirag Lancioni,
- Baharak Hooshiar Kashani,
- Valeria Carossa,
- Jayne E. Ekins,
- Alberto Gómez-Carballa,
- Gabriela Huber,
- Bettina Zimmermann,
- Daniel Corach,
- Nora Babudri,
- Fausto Panara,
- Natalie M. Myres,
- Walther Parson,
- Ornella Semino,
- Antonio Salas,
- Scott R. Woodward,
- Alessandro Achilli,
- and Antonio Torroni
Genome Res. September 2010 20: 1174-1179; Published in Advance June 29, 2010, doi:10.1101/gr.109231.110
OPEN ACCESS ARTICLE
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Susceptibility to chronic pain following nerve injury is genetically affected by CACNG2
- Jonathan Nissenbaum,
- Marshall Devor,
- Ze'ev Seltzer,
- Mathias Gebauer,
- Martin Michaelis,
- Michael Tal,
- Ruslan Dorfman,
- Merav Abitbul-Yarkoni,
- Yan Lu,
- Tina Elahipanah,
- Sonia delCanho,
- Anne Minert,
- Kaj Fried,
- Anna-Karin Persson,
- Hagai Shpigler,
- Erez Shabo,
- Benjamin Yakir,
- Anne Pisanté,
- and Ariel Darvasi
Genome Res. September 2010 20: 1180-1190; Published in Advance August 5, 2010, doi:10.1101/gr.104976.110
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An 8q24 gene desert variant associated with prostate cancer risk confers differential in vivo activity to a MYC enhancer
- Nora F. Wasserman,
- Ivy Aneas,
- and Marcelo A. Nobrega
Genome Res. September 2010 20: 1191-1197; Published in Advance July 13, 2010, doi:10.1101/gr.105361.110
OPEN ACCESS ARTICLE
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Gene amplification as double minutes or homogeneously staining regions in solid tumors: Origin and structure
- Clelia Tiziana Storlazzi,
- Angelo Lonoce,
- Maria C. Guastadisegni,
- Domenico Trombetta,
- Pietro D'Addabbo,
- Giulia Daniele,
- Alberto L'Abbate,
- Gemma Macchia,
- Cecilia Surace,
- Klaas Kok,
- Reinhard Ullmann,
- Stefania Purgato,
- Orazio Palumbo,
- Massimo Carella,
- Peter F. Ambros,
- and Mariano Rocchi
Genome Res. September 2010 20: 1198-1206; Published in Advance July 14, 2010, doi:10.1101/gr.106252.110
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MicroRNA, mRNA, and protein expression link development and aging in human and macaque brain
- Mehmet Somel,
- Song Guo,
- Ning Fu,
- Zheng Yan,
- Hai Yang Hu,
- Ying Xu,
- Yuan Yuan,
- Zhibin Ning,
- Yuhui Hu,
- Corinna Menzel,
- Hao Hu,
- Michael Lachmann,
- Rong Zeng,
- Wei Chen,
- and Philipp Khaitovich
Genome Res. September 2010 20: 1207-1218; Published in Advance July 20, 2010, doi:10.1101/gr.106849.110
OPEN ACCESS ARTICLE
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Chickens possess centromeres with both extended tandem repeats and short non-tandem-repetitive sequences
- Wei-Hao Shang,
- Tetsuya Hori,
- Atsushi Toyoda,
- Jun Kato,
- Kris Popendorf,
- Yasubumi Sakakibara,
- Asao Fujiyama,
- and Tatsuo Fukagawa
Genome Res. September 2010 20: 1219-1228; Published in Advance June 9, 2010, doi:10.1101/gr.106245.110
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Patching gaps in plant genomes results in gene movement and erosion of colinearity
- Thomas Wicker,
- Jan P. Buchmann,
- and Beat Keller
Genome Res. September 2010 20: 1229-1237; Published in Advance June 7, 2010, doi:10.1101/gr.107284.110
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Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq
- Tingting Lu,
- Guojun Lu,
- Danlin Fan,
- Chuanrang Zhu,
- Wei Li,
- Qiang Zhao,
- Qi Feng,
- Yan Zhao,
- Yunli Guo,
- Wenjun Li,
- Xuehui Huang,
- and Bin Han
Genome Res. September 2010 20: 1238-1249; Published in Advance July 13, 2010, doi:10.1101/gr.106120.110
OPEN ACCESS ARTICLE
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Genome-wide mapping of nuclear mitochondrial DNA sequences links DNA replication origins to chromosomal double-strand break formation in Schizosaccharomyces pombe
- Sandrine Lenglez,
- Damien Hermand,
- and Anabelle Decottignies
Genome Res. September 2010 20: 1250-1261; Published in Advance August 5, 2010, doi:10.1101/gr.104513.109

Methods

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High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes
- Adam D. Ewing and
- Haig H. Kazazian, Jr
Genome Res. September 2010 20: 1262-1270; Published in Advance May 20, 2010, doi:10.1101/gr.106419.110
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Methylation profiling in individuals with uniparental disomy identifies novel differentially methylated regions on chromosome 15
- Andrew J. Sharp,
- Eugenia Migliavacca,
- Yann Dupre,
- Elisavet Stathaki,
- Mohammad Reza Sailani,
- Alessandra Baumer,
- Albert Schinzel,
- Deborah J. Mackay,
- David O. Robinson,
- Gilda Cobellis,
- Luigi Cobellis,
- Han G. Brunner,
- Bernhard Steiner,
- and Stylianos E. Antonarakis
Genome Res. September 2010 20: 1271-1278; Published in Advance July 14, 2010, doi:10.1101/gr.108597.110
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Bisulfite Patch PCR enables multiplexed sequencing of promoter methylation across cancer samples
- Katherine Elena Varley and
- Robi David Mitra
Genome Res. September 2010 20: 1279-1287; Published in Advance July 13, 2010, doi:10.1101/gr.101212.109
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High-throughput profiling of amino acids in strains of the Saccharomyces cerevisiae deletion collection
- Sara J. Cooper,
- Gregory L. Finney,
- Shauna L. Brown,
- Sven K. Nelson,
- Jay Hesselberth,
- Michael J. MacCoss,
- and Stanley Fields
Genome Res. September 2010 20: 1288-1296; Published in Advance July 7, 2010, doi:10.1101/gr.105825.110

Resources

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The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
- Aaron McKenna,
- Matthew Hanna,
- Eric Banks,
- Andrey Sivachenko,
- Kristian Cibulskis,
- Andrew Kernytsky,
- Kiran Garimella,
- David Altshuler,
- Stacey Gabriel,
- Mark Daly,
- and Mark A. DePristo
Genome Res. September 2010 20: 1297-1303; Published in Advance July 19, 2010, doi:10.1101/gr.107524.110
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Structural and operational complexity of the Geobacter sulfurreducens genome
- Yu Qiu,
- Byung-Kwan Cho,
- Young Seoub Park,
- Derek Lovley,
- Bernhard Ø. Palsson,
- and Karsten Zengler
Genome Res. September 2010 20: 1304-1311; Published in Advance June 30, 2010, doi:10.1101/gr.107540.110

Perspective

Assembly of large genomes using second-generation sequencing

Research

The initial peopling of the Americas: A growing number of founding mitochondrial genomes from Beringia

Susceptibility to chronic pain following nerve injury is genetically affected by CACNG2

An 8q24 gene desert variant associated with prostate cancer risk confers differential in vivo activity to a MYC enhancer

Gene amplification as double minutes or homogeneously staining regions in solid tumors: Origin and structure

MicroRNA, mRNA, and protein expression link development and aging in human and macaque brain

Chickens possess centromeres with both extended tandem repeats and short non-tandem-repetitive sequences

Patching gaps in plant genomes results in gene movement and erosion of colinearity

Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq

Genome-wide mapping of nuclear mitochondrial DNA sequences links DNA replication origins to chromosomal double-strand break formation in Schizosaccharomyces pombe

Methods

High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes

Methylation profiling in individuals with uniparental disomy identifies novel differentially methylated regions on chromosome 15

Bisulfite Patch PCR enables multiplexed sequencing of promoter methylation across cancer samples

High-throughput profiling of amino acids in strains of the Saccharomyces cerevisiae deletion collection

Resources

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

Structural and operational complexity of the Geobacter sulfurreducens genome

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