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In Print: Last Week's Sequencing-Related Papers of Note: Apr 30, 2013


miRAuto: An automated user-friendly microRNA prediction tool utilizing plant small RNA sequencing data.
Lee J, Kim DI, Park JH, Choi IY, Shin C.
Mol Cells. 2013 Apr;35(4):342-7.

Quantitative transcriptomics using designed primer-based amplification.
Bhargava V, Ko P, Willems E, Mercola M, Subramaniam S.
Sci Rep. 2013 Apr 29;3:1740.

Differentiation of short single-stranded DNA homopolymers in solid-state nanopores.
Venta K, Shemer G, Puster M, Rodriguez-Manzo JA, et al.
ACS Nano. 2013 Apr 26. [Epub ahead of print]

A strategy for sequencing based on rolling-circle amplification on a microarray.
Gao L, Cui J, Zhou Y, Chen L, et al.
J Biomed Nanotechnol. 2013 Apr;9(4):615-20.

Shimmer: Detection of genetic alterations in tumors using next generation sequence data.
Hansen NF, Gartner JJ, Mei L, Samuels Y, Mullikin JC.
Bioinformatics. 2013 Apr 24. [Epub ahead of print]

A support vector machine for identification of single-nucleotide polymorphisms from next-generation sequencing data.
O'Fallon BD, Wooderchak-Donahue W, Crockett DK.
Bioinformatics. 2013 Apr 24. [Epub ahead of print]

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions.
Kim D, Pertea G, Trapnell C, Pimentel H, et al.
Genome Biol. 2013 Apr 25;14(4):R36.

Systematic biases in DNA copy number originate from isolation procedures.
van Heesch S, Mokry M, Boskova V, Junker W, et al.
Genome Biol. 2013 Apr 24;14(4):R33.

Empirical Bayesian analysis of paired high-throughput sequencing data with a beta-binomial distribution.
Hardcastle TJ, Kelly KA.
BMC Bioinformatics. 2013 Apr 23;14(1):135.

A model based criterion for gene expression calls using RNA-seq data.
Wagner GP, Kin K, Lynch VJ.
Theory Biosci. 2013 Apr 25. [Epub ahead of print]

Allelic imbalance metre (Allim), a new tool for measuring allele-specific gene expression with RNA-seq data.
Pandey RV, Franssen SU, Futschik A, Schlötterer C.
Mol Ecol Resour. 2013 Apr 25. [Epub ahead of print]

BRAT-BW: efficient and accurate mapping of bisulfite-treated reads.
Harris EY, Ponts N, Le Roch KG, Lonardi S.
Bioinformatics. 2012 Jul 1;28(13):1795-6.

Enhanced de novo assembly of high throughput pyrosequencing data using whole genome mapping.
Onmus-Leone F, Hang J, Clifford RJ, Yang Y, Riley et al.
PLoS One. 2013 Apr 17;8(4):e61762.

Bats are a major natural reservoir for hepaciviruses and pegiviruses.
Quan PL, Firth C, Conte JM, Williams SH, et al.
Proc Natl Acad Sci U S A. 2013 Apr 22. [Epub ahead of print]

mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters.
Jónsson H, Ginolhac A, Schubert M, Johnson P, Orlando L.
Bioinformatics. 2013 Apr 23. [Epub ahead of print]

A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor.
Luo MC, Gu YQ, You FM, Deal KR, et al.
Proc Natl Acad Sci U S A. 2013 Apr 22. [Epub ahead of print]

ShortStack: Comprehensive annotation and quantification of small RNA genes.
Axtell MJ.
RNA. 2013 Apr 22. [Epub ahead of print]

Massive functional mapping of a 5'-UTR by saturation mutagenesis, phenotypic sorting and deep sequencing.
Holmqvist E, Reimegård J, Wagner EG.
Nucleic Acids Res. 2013 Apr 22. [Epub ahead of print]

Direct visualization of single molecule translocations through a synthetic nanopores comparable in size to a molecule.
Kurz V, Nelson EM, Shim J, Timp G.
ACS Nano. 2013 Apr 22. [Epub ahead of print]

Meander: visually exploring the structural variome using space-filling curves.
Pavlopoulos GA, Kumar P, Sifrim A, Sakai R, et al.
Nucleic Acids Res. 2013 Apr 19. [Epub ahead of print]

Massively parallel characterization of restriction endonucleases.
Kamps-Hughes N, Quimby A, Zhu Z, Johnson EA.
Nucleic Acids Res. 2013 Apr 19. [Epub ahead of print]

Identification of direct targets and modified bases of RNA cytosine methyltransferases.
Khoddami V, Cairns BR.
Nat Biotechnol. 2013 Apr 21. [Epub ahead of print]

RNA-seq identified a super-long intergenic transcript functioning in adipogenesis.
Yi F, Yang F, Liu X, Chen H, et al.
RNA Biol. 2013 Apr 11;10(6).

De novo semi-alignment of 16S rRNA gene sequences for deep phylogenetic characterization of next generation sequencing data.
Avershina E, Frisli T, Rudi K.
Microbes Environ. 2013 Apr 20. [Epub ahead of print]

ELOPER: Elongation of paired-end reads as a pre-processing tool for improved de novo genome assembly.
Silver DH, Ben-Elazar S, Bogoslavsky A, Yanai I.
Bioinformatics. 2013 Apr 19. [Epub ahead of print]

Transcriptome analysis based on next-generation sequencing of non-model plants producing specialized metabolites of biotechnological interest.
Xiao M, Zhang Y, Chen X, Lee EJ, et al.
J Biotechnol. 2013 Apr 16. [Epub ahead of print]

COHCAP: an integrative genomic pipeline for single-nucleotide resolution DNA methylation analysis.
Warden CD, Lee H, Tompkins JD, Li X, et al.
Nucleic Acids Res. 2013 Apr 17. [Epub ahead of print]

Diagnosis of copy number variation by Illumina next generation sequencing is comparable in performance to oligonucleotide array comparative genomic hybridization.
Hayes JL, Tzika A, Thygesen H, Berri S, et al.
Genomics. 2013 Apr 15. [Epub ahead of print]

Sequencing, de novo assembly, annotation and SSR and SNP detection of sabaigrass (Eulaliopsis binata) transcriptome.
Zou D, Chen X, Zou D.
Genomics. 2013 Apr 15. [Epub ahead of print]