Table of Contents

Methods

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A comprehensively molecular haplotype-resolved genome of a European individual
- Eun-Kyung Suk,
- Gayle K. McEwen,
- Jorge Duitama,
- Katja Nowick,
- Sabrina Schulz,
- Stefanie Palczewski,
- Stefan Schreiber,
- Dustin T. Holloway,
- Stephen McLaughlin,
- Heather Peckham,
- Clarence Lee,
- Thomas Huebsch,
- and Margret R. Hoehe
Genome Res. October 2011 21: 1672-1685; Published in Advance August 3, 2011, doi:10.1101/gr.125047.111
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Trans genomic capture and sequencing of primate exomes reveals new targets of positive selection
- Renee D. George,
- Graham McVicker,
- Rachel Diederich,
- Sarah B. Ng,
- Alexandra P. MacKenzie,
- Willie J. Swanson,
- Jay Shendure,
- and James H. Thomas
Genome Res. October 2011 21: 1686-1694; Published in Advance July 27, 2011, doi:10.1101/gr.121327.111
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Efficient cross-species capture hybridization and next-generation sequencing of mitochondrial genomes from noninvasively sampled museum specimens
- Victor C. Mason,
- Gang Li,
- Kristofer M. Helgen,
- and William J. Murphy
Genome Res. October 2011 21: 1695-1704; Published in Advance August 31, 2011, doi:10.1101/gr.120196.111
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True single-molecule DNA sequencing of a pleistocene horse bone
- Ludovic Orlando,
- Aurelien Ginolhac,
- Maanasa Raghavan,
- Julia Vilstrup,
- Morten Rasmussen,
- Kim Magnussen,
- Kathleen E. Steinmann,
- Philipp Kapranov,
- John F. Thompson,
- Grant Zazula,
- Duane Froese,
- Ida Moltke,
- Beth Shapiro,
- Michael Hofreiter,
- Khaled A.S. Al-Rasheid,
- M. Thomas P. Gilbert,
- and Eske Willerslev
Genome Res. October 2011 21: 1705-1719; Published in Advance July 29, 2011, doi:10.1101/gr.122747.111
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Characterization of complex chromosomal rearrangements by targeted capture and next-generation sequencing
- Nara L.M. Sobreira,
- Veena Gnanakkan,
- Michael Walsh,
- Beth Marosy,
- Elizabeth Wohler,
- George Thomas,
- Julie E. Hoover-Fong,
- Ada Hamosh,
- Sarah J. Wheelan,
- and David Valle
Genome Res. October 2011 21: 1720-1727; Published in Advance September 2, 2011, doi:10.1101/gr.122986.111
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A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data
- Daniel A. Skelly,
- Marnie Johansson,
- Jennifer Madeoy,
- Jon Wakefield,
- and Joshua M. Akey
Genome Res. October 2011 21: 1728-1737; Published in Advance August 26, 2011, doi:10.1101/gr.119784.110
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Application of microdroplet PCR for large-scale targeted bisulfite sequencing
- H. Kiyomi Komori,
- Sarah A. LaMere,
- Ali Torkamani,
- G. Traver Hart,
- Steve Kotsopoulos,
- Jason Warner,
- Michael L. Samuels,
- Jeff Olson,
- Steven R. Head,
- Phillip Ordoukhanian,
- Pauline L. Lee,
- Darren R. Link,
- and Daniel R. Salomon
Genome Res. October 2011 21: 1738-1745; Published in Advance July 14, 2011, doi:10.1101/gr.116863.110

Resources

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Genome-based analysis of the nonhuman primate Macaca fascicularis as a model for drug safety assessment
- Martin Ebeling,
- Erich Küng,
- Angela See,
- Clemens Broger,
- Guido Steiner,
- Marco Berrera,
- Tobias Heckel,
- Leonardo Iniguez,
- Thomas Albert,
- Roland Schmucki,
- Hermann Biller,
- Thomas Singer,
- and Ulrich Certa
Genome Res. October 2011 21: 1746-1756; Published in Advance August 23, 2011, doi:10.1101/gr.123117.111
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Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity
- Lingyun Song,
- Zhancheng Zhang,
- Linda L. Grasfeder,
- Alan P. Boyle,
- Paul G. Giresi,
- Bum-Kyu Lee,
- Nathan C. Sheffield,
- Stefan Gräf,
- Mikael Huss,
- Damian Keefe,
- Zheng Liu,
- Darin London,
- Ryan M. McDaniell,
- Yoichiro Shibata,
- Kimberly A. Showers,
- Jeremy M. Simon,
- Teresa Vales,
- Tianyuan Wang,
- Deborah Winter,
- Zhuzhu Zhang,
- Neil D. Clarke,
- Ewan Birney,
- Vishwanath R. Iyer,
- Gregory E. Crawford,
- Jason D. Lieb,
- and Terrence S. Furey
Genome Res. October 2011 21: 1757-1767; Published in Advance July 12, 2011, doi:10.1101/gr.121541.111
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Research

Loss of exon identity is a common mechanism of human inherited disease

Analysis of alternative splicing associated with aging and neurodegeneration in the human brain

Large-scale methylation domains mark a functional subset of neuronally expressed genes

DNA methylation profiles of human active and inactive X chromosomes

Genome-wide analysis distinguishes hyperglycemia regulated epigenetic signatures of primary vascular cells

The human gut virome: Inter-individual variation and dynamic response to diet

Copy number variation analysis in the great apes reveals species-specific patterns of structural variation

Gorilla genome structural variation reveals evolutionary parallelisms with chimpanzee

Regulation of nucleosome landscape and transcription factor targeting at tissue-specific enhancers by BRG1

Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration

Methods

A comprehensively molecular haplotype-resolved genome of a European individual

Trans genomic capture and sequencing of primate exomes reveals new targets of positive selection

Efficient cross-species capture hybridization and next-generation sequencing of mitochondrial genomes from noninvasively sampled museum specimens

True single-molecule DNA sequencing of a pleistocene horse bone

Characterization of complex chromosomal rearrangements by targeted capture and next-generation sequencing

A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data

Application of microdroplet PCR for large-scale targeted bisulfite sequencing

Resources

Genome-based analysis of the nonhuman primate Macaca fascicularis as a model for drug safety assessment

Open chromatin defined by DNaseI and FAIRE identifies regulatory elements that shape cell-type identity

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