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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

Purnell Choppin Dies

Purnell Choppin, a virologist who led the Howard Hughes Medical Institute, has died at 91, according to the Washington Post.

Effectiveness May Decline, Data From Israel Suggests

The New York Times reports that new Israeli data suggests a decline in Pfizer-BioNTech SARS-CoV-2 vaccine effectiveness against Delta variant infection, though protection against severe disease remains high.

To See Future Risk

Slate looks into the use of polygenic risk scores in embryo screening.

PLOS Papers on Methicillin-Resistant Staphylococcus, Bone Marrow Smear Sequencing, More

In PLOS this week: genomic analysis of methicillin-resistant Staphylococcus pseudintermedius, archived bone marrow sequencing, and more.