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In Print: Last Week's Sequencing-Related Papers of Note: Jan 22, 2013


NSeq: a multithreaded Java application for finding positioned nucleosomes from sequencing data.
Nellore A, Bobkov K, Howe E, Pankov A, et al.
Front Genet. 2012;3:320.

Co-phylog: an assembly-free phylogenomic approach for closely related organisms.
Yi H, Jin L.
Nucleic Acids Res. 2013 Jan 18. [Epub ahead of print]

CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model.
Wang L, Park HJ, Dasari S, Wang S, et al.
Nucleic Acids Res. 2013 Jan 17. [Epub ahead of print]

Detecting miRNAs in deep-sequencing data: a software performance comparison and evaluation.
Williamson V, Kim A, Xie B, McMichael GO, et al.
Brief Bioinform. 2013 Jan;14(1):36-45.

DNA-binding specificities of human transcription factors.
Jolma A, Yan J, Whitington T, Toivonen J, et al.
Cell. 2013 Jan 17;152(1-2):327-339.

Xenobiotics shape the physiology and gene expression of the active human gut microbiome.
Maurice CF, Haiser HJ, Turnbaugh PJ.
Cell. 2013 Jan 17;152(1-2):39-50.

Lessons learned from microsatellite development for nonmodel organisms using 454 pyrosequencing.
Schoebel CN, Brodbeck S, Buehler D, Cornejo C, et al.
J Evol Biol. 2013 Jan 17. doi: 10.1111/jeb.12077. [Epub ahead of print]

Grape RNA-seq analysis pipeline environment.
Knowles D, Röder M, Merkel A, Guigó R.
Bioinformatics. 2013 Jan 17. [Epub ahead of print]

Optimizing nucleic acid extraction from thyroid fine-needle aspiration cells in stained slides, formalin-fixed/paraffin-embedded tissues, and long-term stored blood samples.
Kizys MM, Cardoso MG, Lindsey SC, Harada MY, et al.
Arq Bras Endocrinol Metabol. 2012 Dec;56(9):618-26.

Identifying personal genomes by surname inference.
Gymrek M, McGuire AL, Golan D, Halperin E, Erlich Y.
Science. 2013 Jan 18;339(6117):321-4.

Deep sequencing of RNA from ancient maize kernels.
Fordyce SL, Avila-Arcos MC, Rasmussen M, Cappellini E, et al.
PLoS One. 2013;8(1):e50961.

Deep sequencing of small RNAs identifies canonical and non-canonical miRNA and endogenous siRNAs in mammalian somatic tissues.
Castellano L, Stebbing J.
Nucleic Acids Res. 2013 Jan 15. [Epub ahead of print]

In-solution hybrid capture of bisulfite-converted DNA for targeted bisulfite sequencing of 174 ADME genes.
Ivanov M, Kals M, Kacevska M, Metspalu A, et al.
Nucleic Acids Res. 2013 Jan 15. [Epub ahead of print]

DSK: k-mer counting with very low memory usage.
Rizk G, Lavenier D, Chikhi R.
Bioinformatics. 2013 Jan 16. [Epub ahead of print]

Dynamic DNA methylation across diverse human cell lines and tissues.
Varley KE, Gertz J, Bowling KM, Parker SL, et al.
Genome Res. 2013 Jan 16. [Epub ahead of print]

Differences in sequencing technologies improve the retrieval of anammox bacterial genome from metagenomes.
Gori F, Green Tringe S, Folino G, van Hijum SA, et al.
BMC Genomics. 2013 Jan 16;14(1):7.

Development and validation of microsatellite markers for Brachiaria ruziziensis obtained by partial genome assembly of Illumina single-end reads.
Silva PI, Martins AM, Gouvea EG, Pessoa-Filho M, Ferreira ME.
BMC Genomics. 2013 Jan 16;14(1):17.

Double restriction-enzyme digestion improves the coverage and accuracy of genome-wide CpG methylation profiling by reduced representation bisulfite sequencing.
Wang J, Xia Y, Li L, Gong D, et al.
BMC Genomics. 2013 Jan 16;14(1):11.

FUSIM: a software tool for simulating fusion transcripts.
Bruno AE, Miecznikowski JC, Qin M, Wang J, Liu S.
BMC Bioinformatics. 2013 Jan 16;14(1):13.

SRAdb: query and use public next-generation sequencing data from within R.
Zhu Y, Stephens RM, Meltzer PS, Davis SR.
BMC Bioinformatics. 2013 Jan 17;14(1):19.

BM-BC: a Bayesian method of base calling for Solexa sequence data.
Ji Y, Mitra R, Quintana F, Jara A, et al.
BMC Bioinformatics. 2012;13 Suppl 13:S6.

Accuracy of RNA-seq and its dependence on sequencing depth.
Cai G, Li H, Lu Y, Huang X, et al.
BMC Bioinformatics. 2012;13 Suppl 13:S5.

MetAMOS: a modular and open source metagenomic assembly and analysis pipeline.
Treangen TJ, Koren S, Sommer DD, Liu B, et al.
Genome Biol. 2013 Jan 15;14(1):R2.

A physical, genetic and functional sequence assembly of the barley genome.
International Barley Genome Sequencing Consortium, Mayer KF, Waugh R, Brown JW, et al.
Nature. 2012 Nov 29;491(7426):711-6.

A novel Bayesian network inference algorithm for integrative analysis of heterogeneous deep sequencing data.
Liu Y, Qiao N, Zhu S, Su M, et al.
Cell Res. 2013 Jan 15. [Epub ahead of print]

Ion Torrent-based transcriptional assessment of a Corynebacterium pseudotuberculosis equi strain reveals denaturing high-performance liquid chromatography a promising rRNA depletion method.
Castro TL, Seyffert N, Ramos RT, Barbosa S, et al.
Microb Biotechnol. 2013 Jan 15. [Epub ahead of print]