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

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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.

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