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Volume 12 Issue 7
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Comment |
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Food of the dogs
Gregory A Petsko Genome Biology 2011, 12:122 (25 July 2011)
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Editor’s summary
Human evolution and the Paleofood movement
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An integrated strategy for identification of both sharp and broad peaks from next-generation sequencing data
Weiqun Peng, Keji Zhao Genome Biology 2011, 12:120 (25 July 2011)
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Editor’s summary
Keji Zhao discusses Genome Biology's method article on ZINBA, a novel peak-finding tool developed by Jason Lieb and colleagues
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Sex lethal and upstream ORFs: a bait-and-trap system for ribosomes
Peng Yao, Paul L Fox Genome Biology 2011, 12:121 (25 July 2011)
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Editor’s summary
Research highlight on a novel mechanism of eukaryotic gene regulation
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Review |
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Atg8: an autophagy-related ubiquitin-like protein family
Tomer Shpilka, Hilla Weidberg, Shmuel Pietrokovski, Zvulun Elazar Genome Biology 2011, 12:226 (27 July 2011)
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Editor’s summary
The Atg8 family of autophagy-related ubiquitin-like proteins mediate remodeling of intracellular membranes and interact with many proteins to regulate trafficking and autophagy
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Research |
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A comparative analysis of DNA methylation across human embryonic stem cell lines
Pao-Yang Chen, Suhua Feng, Jong Joo, Steve E Jacobsen, Matteo Pellegrini Genome Biology 2011, 12:R62 (6 July 2011)
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Editor’s summary
A comparison of DNA methylation in three human embryonic stem cell lines
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Genome sequence and global sequence variation map with 5.5 million SNPs in Chinese rhesus macaque
Xiaodong Fang, Yanfeng Zhang, Rui Zhang, Lixin Yang, Ming Li, Kaixiong Ye, Xiaosen Guo, Jun Wang, Bing Su Genome Biology 2011, 12:R63 (6 July 2011)
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Editor’s summary
The first genome of a Chinese rhesus macaque includes millions of SNPs relative to the (Indian) reference genome
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Small RNA sequencing reveals miR-642a-3p as a novel adipocyte-specific microRNA and miR-30 as a key regulator of human adipogenesis
Laure-Emmanuelle Zaragosi, Brigitte Wdziekonski, Kevin Brigand, Phi Villageois, Bernard Mari, Rainer Waldmann, Christian Dani, Pascal Barbry Genome Biology 2011, 12:R64 (18 July 2011)
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Editor’s summary
The miR-30 family of miRNAs is found to regulate adipogenesis by targeting RUNX2 mRNA
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Proteome-wide evidence for enhanced positive Darwinian selection within intrinsically disordered regions in proteins
Johan Nilsson, Mats Grahn, Anthony PH Wright Genome Biology 2011, 12:R65 (19 July 2011)
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Editor’s summary
Enhanced positive codon selection in the intrinsically disordered regions of yeast proteins
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The minimal kinome of Giardia lamblia illuminates early kinase evolution and unique parasite biology
Gerard Manning, David S Reiner, Tineke Lauwaet, Michael Dacre, Alias Smith, Yufeng Zhai, Staffan Svard, Frances D Gillin Genome Biology 2011, 12:R66 (25 July 2011)
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Editor’s summary
Comparison of sequenced genomes of Giardia lamblia reveals that it has the fewest number of kinases of any known eukaryote
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Targeted enrichment beyond the consensus coding DNA sequence exome reveals exons with higher variant densities
Matthew N Bainbridge, Min Wang, Yuanqing Wu, Irene Newsham, Donna M Muzny, John L Jefferies, Thomas J Albert, Daniel L Burgess, Richard A Gibbs Genome Biology 2011, 12:R68 (25 July 2011)
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Editor’s summary
Extension of exome capture beyond the commonly targeted regions reveals much higher variant densities in predicted exons
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Extensive characterization of NF-κB binding uncovers non-canonical motifs and advances the interpretation of genetic functional traits
Daniel Wong, Ana Teixeira, Spyros Oikonomopoulos, Peter Humburg, Imtiaz Lone, David Saliba, Trevor Siggers, Martha Bulyk, Dimitar Angelov, Stefan Dimitrov, Irina A Udalova, Jiannis Ragoussis Genome Biology 2011, 12:R70 (29 July 2011)
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Editor’s summary
Protein binding microarrays and Electrophoretic Mobility Shift Assay-Sequencing reveal non-canonical NFkappaB binding sites associated with polymorphisms
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ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions
Naim U Rashid, Paul G Giresi, Joseph G Ibrahim, Wei Sun, Jason D Lieb Genome Biology 2011, 12:R67 (25 July 2011)
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Editor’s summary
ZINBA is a method for analyzing peaks in next generation sequencing datasets such as ChIP-seq or DNase-seq
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ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data
Brad A Friedman, Tom Maniatis Genome Biology 2011, 12:R69 (28 July 2011)
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Editor’s summary
A web-based RNA-seq and microarray analysis tool
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Correspondence |
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Sequencing the genome of the Burmese python (Python molurus bivittatus) as a model for studying extreme adaptations in snakes
Todd A Castoe, AP Jason de Koning, Kathryn T Hall, Ken D Yokoyama, Wanjun Gu, Eric N Smith, Cédric Feschotte, Peter Uetz, David A Ray, Jason Dobry, Robert Bogden, Stephen P Mackessy, Anne M Bronikowski, Wesley C Warren, Stephen M Secor, David D Pollock Genome Biology 2011, 12:406 (28 July 2011)
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Editor’s summary
The genome of the Burmese python is being sequenced, providing insights into the unique anatomy, physiology, and evolution of snakes
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