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In Print: Last Week's Sequencing-Related Papers of Note: May 22, 2012


Predicting the DNA sequence dependence of nanopore ion current using atomic-resolution Brownian dynamics.
Comer J, Aksimentiev A.
J Phys Chem C Nanomater Interfaces. 2012 Feb 9;116(5):3376-3393. Epub 2012 Jan 9.

Selective enrichment and sequencing of whole mitochondrial genomes in the presence of nuclear encoded mitochondrial pseudogenes (Numts) .
Wolff JN, Shearman DC, Brooks RC, Ballard JW.
PLoS One. 2012;7(5):e37142. Epub 2012 May 14.

Characterization of squamate olfactory receptor genes and their transcripts by the high-throughput sequencing approach.
Dehara Y, Hashiguchi Y, Matsubara K, Yanai T, et al.
Genome Biol Evol. 2012 Jan;4(4):602-16.

Subgenomic analysis of microRNAs in polyploid wheat.
Kantar M, Akpınar BA, Valárik M, Lucas SJ, et al.
Funct Integr Genomics. 2012 May 17. [Epub ahead of print]

OSA: A fast and accurate alignment tool for RNA-seq.
Hu J, Ge H, Newman M, Liu K.
Bioinformatics. 2012 May 15. [Epub ahead of print]

Handling the data management needs of high-throughput sequencing data: SpeedGene, a compression algorithm for the efficient storage of genetic data.
Qiao D, Yip WK, Lange C.
BMC Bioinformatics. 2012 May 16;13(1):100. [Epub ahead of print]

Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next-generation DNA sequencing.
Baird DJ, Hajibabaei M.
Mol Ecol. 2012 Apr;21(8):2039-44.

Identification of microRNAs and natural antisense transcript-originated endogenous siRNAs from small-RNA deep sequencing data.
Zhang W, Zhou X, Xia J, Zhou X.
Methods Mol Biol. 2012;883:221-7.

Computational analysis of RNA-seq.
Givan SA, Bottoms CA, Spollen WG.
Methods Mol Biol. 2012;883:201-19.

Global assembly of expressed sequence tags.
Cheung F.
Methods Mol Biol. 2012;883:193-9.

New virus discovery by deep sequencing of small RNAs.
Singh K, Kaur R, Qiu W.
Methods Mol Biol. 2012;883:177-91.

Isolation and profiling of protein-associated small RNAs.
Zhao H, Lii Y, Zhu P, Jin H.
Methods Mol Biol. 2012;883:165-76.

Detection and quantification of alternative splicing variants using RNA-seq.
Bryant DW Jr, Priest HD, Mockler TC.
Methods Mol Biol. 2012;883:97-110.

Construction of RNA-seq libraries from large and microscopic tissues for the Illumina sequencing platform.
Atamian HS, Kaloshian I.
Methods Mol Biol. 2012;883:47-57.

SuperSAGE: Powerful serial analysis of gene expression.
Matsumura H, Urasaki N, Yoshida K, Krüger DH, et al.
Methods Mol Biol. 2012;883:1-17.

Gene mapping via bulked segregant RNA-seq (BSR-seq) .
Liu S, Yeh CT, Tang HM, Nettleton D, Schnable PS.
PLoS One. 2012;7(5):e36406. Epub 2012 May 7.

Comparative genomics of rhizobia nodulating soybean suggests extensive recruitment of lineage-specific genes in adaptations.
Tian CF, Zhou YJ, Zhang YM, Li QQ, et al.
Proc Natl Acad Sci U S A. 2012 May 14. [Epub ahead of print]

Real-time analysis and selection of methylated DNA by fluorescence-activated single molecule sorting in a nanofluidic channel.
Cipriany BR, Murphy PJ, Hagarman JA, Cerf A, et al.
Proc Natl Acad Sci U S A. 2012 May 14. [Epub ahead of print]

Copy number variation detection and genotyping from exome sequence data.
Krumm N, Sudmant PH, Ko A, O'Roak BJ, et al.
Genome Res. 2012 May 14. [Epub ahead of print]

A new strategy to reduce allelic bias in RNA-seq readmapping.
Vijaya Satya R, Zavaljevski N, Reifman J.
Nucleic Acids Res. 2012 May 14. [Epub ahead of print]

Identification of avian W-linked contigs by short-read sequencing.
Chen N, Bellott DW, Page DC, Clark AG.
BMC Genomics. 2012 May 14;13(1):183. [Epub ahead of print]

SIS: a program to generate draft genome sequence scaffolds for prokaryotes.
Dias Z, Dias U, Setubal JC.
BMC Bioinformatics. 2012 May 14;13(1):96. [Epub ahead of print]

Quantity and quality assessment of DNA extracted from saliva and blood.
Looi ML, Zakaria H, Osman J, Jamal R.
Clin Lab. 2012;58(3-4):307-12.

The Scan

Study Finds Sorghum Genetic Loci Influencing Composition, Function of Human Gut Microbes

Focusing on microbes found in the human gut microbiome, researchers in Nature Communications identified 10 sorghum loci that appear to influence the microbial taxa or microbial metabolite features.

Treatment Costs May Not Coincide With R&D Investment, Study Suggests

Researchers in JAMA Network Open did not find an association between ultimate treatment costs and investments in a drug when they analyzed available data on 60 approved drugs.

Sleep-Related Variants Show Low Penetrance in Large Population Analysis

A limited number of variants had documented sleep effects in an investigation in PLOS Genetics of 10 genes with reported sleep ties in nearly 192,000 participants in four population studies.

Researchers Develop Polygenic Risk Scores for Dozens of Disease-Related Exposures

With genetic data from two large population cohorts and summary statistics from prior genome-wide association studies, researchers came up with 27 exposure polygenic risk scores in the American Journal of Human Genetics.