Table of Contents

Editorial

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Scope note
Genome Res. May 2011 21: xi

Insight/Outlook

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Genomic contributions to Mendelian disease
- Aravinda Chakravarti
Genome Res. May 2011 21: 643-644; doi:10.1101/gr.123554.111

Perspective

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Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression
- Lesley T. MacNeil and
- Albertha J.M. Walhout
Genome Res. May 2011 21: 645-657; Published in Advance February 4, 2011, doi:10.1101/gr.097378.109

Research

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Exome sequencing and disease-network analysis of a single family implicate a mutation in KIF1A in hereditary spastic paraparesis
- Yaniv Erlich,
- Simon Edvardson,
- Emily Hodges,
- Shamir Zenvirt,
- Pramod Thekkat,
- Avraham Shaag,
- Talya Dor,
- Gregory J. Hannon,
- and Orly Elpeleg
Genome Res. May 2011 21: 658-664; Published in Advance April 12, 2011, doi:10.1101/gr.117143.110
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Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes
- Axel M. Hillmer,
- Fei Yao,
- Koichiro Inaki,
- Wah Heng Lee,
- Pramila N. Ariyaratne,
- Audrey S.M. Teo,
- Xing Yi Woo,
- Zhenshui Zhang,
- Hao Zhao,
- Leena Ukil,
- Jieqi P. Chen,
- Feng Zhu,
- Jimmy B.Y. So,
- Manuel Salto-Tellez,
- Wan Ting Poh,
- Kelson F.B. Zawack,
- Niranjan Nagarajan,
- Song Gao,
- Guoliang Li,
- Vikrant Kumar,
- Hui Ping J. Lim,
- Yee Yen Sia,
- Chee Seng Chan,
- See Ting Leong,
- Say Chuan Neo,
- Poh Sum D. Choi,
- Hervé Thoreau,
- Patrick B.O. Tan,
- Atif Shahab,
- Xiaoan Ruan,
- Jonas Bergh,
- Per Hall,
- Valère Cacheux-Rataboul,
- Chia-Lin Wei,
- Khay Guan Yeoh,
- Wing-Kin Sung,
- Guillaume Bourque,
- Edison T. Liu,
- and Yijun Ruan
Genome Res. May 2011 21: 665-675; Published in Advance April 5, 2011, doi:10.1101/gr.113555.110
OPEN ACCESS ARTICLE
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Transcriptional consequences of genomic structural aberrations in breast cancer
- Koichiro Inaki,
- Axel M. Hillmer,
- Leena Ukil,
- Fei Yao,
- Xing Yi Woo,
- Leah A. Vardy,
- Kelson Folkvard Braaten Zawack,
- Charlie Wah Heng Lee,
- Pramila Nuwantha Ariyaratne,
- Yang Sun Chan,
- Kartiki Vasant Desai,
- Jonas Bergh,
- Per Hall,
- Thomas Choudary Putti,
- Wai Loon Ong,
- Atif Shahab,
- Valere Cacheux-Rataboul,
- Radha Krishna Murthy Karuturi,
- Wing-Kin Sung,
- Xiaoan Ruan,
- Guillaume Bourque,
- Yijun Ruan,
- and Edison T. Liu
Genome Res. May 2011 21: 676-687; Published in Advance April 5, 2011, doi:10.1101/gr.113225.110
OPEN ACCESS ARTICLE
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Neurons show distinctive DNA methylation profile and higher interindividual variations compared with non-neurons
- Kazuya Iwamoto,
- Miki Bundo,
- Junko Ueda,
- Michael C. Oldham,
- Wataru Ukai,
- Eri Hashimoto,
- Toshikazu Saito,
- Daniel H. Geschwind,
- and Tadafumi Kato
Genome Res. May 2011 21: 688-696; Published in Advance April 5, 2011, doi:10.1101/gr.112755.110
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Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements
- Ofir Hakim,
- Myong-Hee Sung,
- Ty C. Voss,
- Erik Splinter,
- Sam John,
- Peter J. Sabo,
- Robert E. Thurman,
- John A. Stamatoyannopoulos,
- Wouter de Laat,
- and Gordon L. Hager
Genome Res. May 2011 21: 697-706; Published in Advance April 6, 2011, doi:10.1101/gr.111153.110
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Core promoter T-blocks correlate with gene expression levels in C. elegans
- Vladislav Grishkevich,
- Tamar Hashimshony,
- and Itai Yanai
Genome Res. May 2011 21: 707-717; Published in Advance March 2, 2011, doi:10.1101/gr.113381.110
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Nucleosome fragility reveals novel functional states of chromatin and poises genes for activation
- Yuanxin Xi,
- Jianhui Yao,
- Rui Chen,
- Wei Li,
- and Xiangwei He
Genome Res. May 2011 21: 718-724; Published in Advance March 1, 2011, doi:10.1101/gr.117101.110
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Genetic architecture of regulatory variation in Arabidopsis thaliana
- Xu Zhang,
- Andrew J. Cal,
- and Justin O. Borevitz
Genome Res. May 2011 21: 725-733; Published in Advance April 5, 2011, doi:10.1101/gr.115337.110
OPEN ACCESS ARTICLE

Methods

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Efficient storage of high throughput DNA sequencing data using reference-based compression
- Markus Hsi-Yang Fritz,
- Rasko Leinonen,
- Guy Cochrane,
- and Ewan Birney
Genome Res. May 2011 21: 734-740; Published in Advance January 18, 2011, doi:10.1101/gr.114819.110
OPEN ACCESS ARTICLE
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Differential genome-wide profiling of tandem 3′ UTRs among human breast cancer and normal cells by high-throughput sequencing
- Yonggui Fu,
- Yu Sun,
- Yuxin Li,
- Jie Li,
- Xingqiang Rao,
- Chong Chen,
- and Anlong Xu
Genome Res. May 2011 21: 741-747; Published in Advance April 7, 2011, doi:10.1101/gr.115295.110
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Calling Cards enable multiplexed identification of the genomic targets of DNA-binding proteins
- Haoyi Wang,
- David Mayhew,
- Xuhua Chen,
- Mark Johnston,
- and Robi David Mitra
Genome Res. May 2011 21: 748-755; Published in Advance April 6, 2011, doi:10.1101/gr.114850.110
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Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and “resurrected” pseudogenes in the mouse genome
- Markus Brosch,
- Gary I. Saunders,
- Adam Frankish,
- Mark O. Collins,
- Lu Yu,
- James Wright,
- Ruth Verstraten,
- David J. Adams,
- Jennifer Harrow,
- Jyoti S. Choudhary,
- and Tim Hubbard
Genome Res. May 2011 21: 756-767; Published in Advance April 1, 2011, doi:10.1101/gr.114272.110
OPEN ACCESS ARTICLE

Resources

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Maximum-likelihood estimation of recent shared ancestry (ERSA)
- Chad D. Huff,
- David J. Witherspoon,
- Tatum S. Simonson,
- Jinchuan Xing,
- W. Scott Watkins,
- Yuhua Zhang,
- Therese M. Tuohy,
- Deborah W. Neklason,
- Randall W. Burt,
- Stephen L. Guthery,
- Scott R. Woodward,
- and Lynn B. Jorde
Genome Res. May 2011 21: 768-774; Published in Advance February 8, 2011, doi:10.1101/gr.115972.110
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Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis
- Riu Yamashita,
- Nuankanya P. Sathira,
- Akinori Kanai,
- Kousuke Tanimoto,
- Takako Arauchi,
- Yoshiaki Tanaka,
- Shin-ichi Hashimoto,
- Sumio Sugano,
- Kenta Nakai,
- and Yutaka Suzuki
Genome Res. May 2011 21: 775-789; Published in Advance March 3, 2011, doi:10.1101/gr.110254.110
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Exhaustive T-cell repertoire sequencing of human peripheral blood samples reveals signatures of antigen selection and a directly measured repertoire size of at least 1 million clonotypes
- René L. Warren,
- J. Douglas Freeman,
- Thomas Zeng,
- Gina Choe,
- Sarah Munro,
- Richard Moore,
- John R. Webb,
- and Robert A. Holt
Genome Res. May 2011 21: 790-797; Published in Advance February 24, 2011, doi:10.1101/gr.115428.110
OPEN ACCESS ARTICLE
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MicroRNA programs in normal and aberrant stem and progenitor cells
- Christopher P. Arnold,
- Ruoying Tan,
- Baiyu Zhou,
- Si-Biao Yue,
- Steven Schaffert,
- Joseph R. Biggs,
- Regis Doyonnas,
- Miao-Chia Lo,
- John M. Perry,
- Valérie M. Renault,
- Alessandra Sacco,
- Tim Somervaille,
- Patrick Viatour,
- Anne Brunet,
- Michael L. Cleary,
- Linheng Li,
- Julien Sage,
- Dong-Er Zhang,
- Helen M. Blau,
- Caifu Chen,
- and Chang-Zheng Chen
Genome Res. May 2011 21: 798-810; Published in Advance March 30, 2011, doi:10.1101/gr.111385.110

Erratum

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Erratum
Genome Res. May 2011 21: 811

Editorial

Scope note

Insight/Outlook

Genomic contributions to Mendelian disease

Perspective

Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression

Research

Exome sequencing and disease-network analysis of a single family implicate a mutation in KIF1A in hereditary spastic paraparesis

Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes

Transcriptional consequences of genomic structural aberrations in breast cancer

Neurons show distinctive DNA methylation profile and higher interindividual variations compared with non-neurons

Diverse gene reprogramming events occur in the same spatial clusters of distal regulatory elements

Core promoter T-blocks correlate with gene expression levels in C. elegans

Nucleosome fragility reveals novel functional states of chromatin and poises genes for activation

Genetic architecture of regulatory variation in Arabidopsis thaliana

Methods

Efficient storage of high throughput DNA sequencing data using reference-based compression

Differential genome-wide profiling of tandem 3′ UTRs among human breast cancer and normal cells by high-throughput sequencing

Calling Cards enable multiplexed identification of the genomic targets of DNA-binding proteins

Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and “resurrected” pseudogenes in the mouse genome

Resources

Maximum-likelihood estimation of recent shared ancestry (ERSA)

Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis

Exhaustive T-cell repertoire sequencing of human peripheral blood samples reveals signatures of antigen selection and a directly measured repertoire size of at least 1 million clonotypes

MicroRNA programs in normal and aberrant stem and progenitor cells

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Erratum

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