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Papers of Note: Apr 12, 2011


Small RNA library preparation for next-generation sequencing by single ligation, extension and circularization technology.
Kwon YS.
Biotechnol Lett. 2011 Apr 9. [Epub ahead of print]

Efficient and cost effective population resequencing by pooling and in-solution hybridization.
Bansal V, Tewhey R, Leproust EM, Schork NJ.
PLoS One. 2011 Mar 30;6(3):e18353.

A framework for variation discovery and genotyping using next-generation DNA sequencing data.
Depristo MA, Banks E, Poplin R, et al.
Nat Genet. 2011 Apr 10. [Epub ahead of print]

Comrad: a novel algorithmic framework for the integrated analysis of RNA-seq and WGSS data.
McPherson A, Wu C, Hajirasouliha I, et al.
Bioinformatics. 2011 Apr 9. [Epub ahead of print]

Complete characterization of the edited transcriptome of the mitochondrion of Physarum polycephalum using deep sequencing of RNA.
Bundschuh R, Altmüller J, Becker C, Nürnberg P, Gott JM.
Nucleic Acids Res. 2011 Apr 8. [Epub ahead of print]

Amplification of viral RNA from drinking water using TransPlex whole transcriptome amplification.
Parker JK, Chang TY, Meschke JS.
J Appl Microbiol. 2011 Apr 7. Epub ahead of print]

Genomic signatures of strain selection and enhancement in Bacillus atrophaeus var. globigii, a historical biowarfare simulant.
Gibbons HS, Broomall SM, McNew LA, et al.
PLoS One. 2011 Mar 25;6(3):e17836.

Experimental illumination of a fitness landscape.
Hietpas RT, Jensen JD, Bolon DN.
Proc Natl Acad Sci U S A. 2011 Apr 4. [Epub ahead of print]

Thermoelectric method for sequencing DNA.
Nestorova GG, Guilbeau EJ.
Lab Chip. 2011 Apr 5. [Epub ahead of print]

Unlocking the barley genome by chromosomal and comparative genomics.
Mayer KF, Martis M, Hedley PE, et al.
Plant Cell. 2011 Apr 5. [Epub ahead of print]

High-quality DNA sequence capture of 524 disease candidate genes.
Shen P, Wang W, Krishnakumar S, et al.
Proc Natl Acad Sci U S A. 2011 Apr 5. [Epub ahead of print]

Deep sequencing analysis of the developing mouse brain reveals a novel microRNA.
Ling KH, Brautigan PJ, Hahn CN, et al.
BMC Genomics. 2011 Apr 5;12(1):176.

Construction of normalized RNA-seq libraries for next-generation sequencing using the crab duplex-specific nuclease.
Christodoulou DC, Gorham JM, Herman DS, Seidman JG.
Curr Protoc Mol Biol. 2011 Apr;Chapter 4:Unit4.12.

Transitions in bacterial communities along the 2000 km salinity gradient of the Baltic Sea.
Herlemann DP, Labrenz M, Jürgens K, Bertilsson S, Waniek JJ, Andersson AF.
ISME J. 2011 Apr 7. [Epub ahead of print]

DIME: R-package for identifying differential ChIP-seq based on an ensemble of mixture models.
Taslim C, Huang T, Lin S.
Bioinformatics. 2011 Apr 5. [Epub ahead of print]

Correcting errors in short reads by multiple alignments.
Salmela L, Schröder J.
Bioinformatics. 2011 Apr 5. [Epub ahead of print]

High-throughput analysis of the mutagenic and cytotoxic properties of DNA lesions by next-generation sequencing.
Yuan B, Wang J, Cao H, Sun R, Wang Y.
Nucleic Acids Res. 2011 Apr 5. [Epub ahead of print]

Global analysis of gene-level microRNA expression in Arabidopsis using deep sequencing data.
Yang X, Zhang H, Li L.
Genomics. 2011 Apr 4. [Epub ahead of print]

De novo transcriptome sequencing in Salvia miltiorrhiza to identify genes involved in the biosynthesis of active ingredients.
Wenping H, Yuan Z, Jie S, Lijun Z, Zhezhi W
Genomics. 2011 Apr 4. [Epub ahead of print]

Detection and mapping of mtDNA SNPs in Atlantic salmon using high throughput DNA sequencing.
Fridjonsson O, Olafsson K, Tompsett S, et al.
BMC Genomics. 2011 Apr 7;12(1):179.

The Scan

Transcriptomic, Epigenetic Study Appears to Explain Anti-Viral Effects of TB Vaccine

Researchers report in Science Advances on an interferon signature and long-term shifts in monocyte cell DNA methylation in Bacille Calmette-Guérin-vaccinated infant samples.

DNA Storage Method Taps Into Gene Editing Technology

With a dual-plasmid system informed by gene editing, researchers re-wrote DNA sequences in E. coli to store Charles Dickens prose over hundreds of generations, as they recount in Science Advances.

Researchers Model Microbiome Dynamics in Effort to Understand Chronic Human Conditions

Investigators demonstrate in PLOS Computational Biology a computational method for following microbiome dynamics in the absence of longitudinally collected samples.

New Study Highlights Role of Genetics in ADHD

Researchers report in Nature Genetics on differences in genetic architecture between ADHD affecting children versus ADHD that persists into adulthood or is diagnosed in adults.