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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]

The Scan

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.