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In Print: Last Week's Sequencing-Related Papers of Note: Oct 29, 2013


Next-generation sequencing reveals how RNA catalysts evolve from random space.
Ameta S, Winz ML, Previti C, Jäschke A.
Nucleic Acids Res. 2013 Oct 23. [Epub ahead of print]

Semiconductor-based DNA sequencing of histone modification states.
Cheng CS, Rai K, Garber M, Hollinger A, et al.
Nat Commun. 2013 Oct 25;4:2672.

Single-cell genome and metatranscriptome sequencing reveal metabolic interactions of an alkane-degrading methanogenic community.
Embree M, Nagarajan H, Movahedi N, Chitsaz H, Zengler K.
ISME J. 2013 Oct 24. [Epub ahead of print]

Compact representation of k-mer de Bruijn graphs for genome read assembly.
Rødland EA.
BMC Bioinformatics. 2013 Oct 23;14(1):313.

SeqPig: simple and scalable scripting for large sequencing data sets in Hadoop.
Schumacher A, Pireddu L, Niemenmaa M, Kallio A, et al.
Bioinformatics. 2013 Oct 22. [Epub ahead of print]

A hierarchical Poisson log-normal model for network inference from RNA sequencing data.
Gallopin M, Rau A, Jaffrézic F.
PLoS One. 2013 Oct 17;8(10):e77503.

dPeak: High resolution identification of transcription factor binding sites from PET and SET ChIP-seq data.
Chung D, Park D, Myers K, Grass J, et al.
PLoS Comput Biol. 2013 Oct;9(10):e1003246.

PacBio sequencing of gene families − a case study with wheat gluten genes.
Zhang W, Ciclitira P, Messing J.
Gene. 2013 Oct 18. [Epub ahead of print]

eALPS: Estimating abundance levels in pooled sequencing using available genotyping data.
Eskin I, Hormozdiari F, Conde L, Riby J, et al.
J Comput Biol. 2013 Oct 21. [Epub ahead of print]

A nanopore-nanofiber mesh biosensor to control DNA translocation.
Squires AH, Hersey JS, Grinstaff MW, Meller A.
J Am Chem Soc. 2013 Oct 21. [Epub ahead of print]

Combining different mRNA capture methods to analyze the transcriptome: analysis of the Xenopus laevis transcriptome.
Blower MD, Jambhekar A, Schwarz DS, Toombs JA.
PLoS One. 2013 Oct 15;8(10):e77700.

AutoAssemblyD: a graphical user interface system for several genome assemblers.
Veras AA, de Sá PH, Azevedo V, Silva A, Ramos RT.
Bioinformation. 2013 Sep 23;9(16):840-1.

PEAR: A fast and accurate Illumina Paired-End reAd mergeR.
Zhang J, Kobert K, Flouri T, Stamatakis A.
Bioinformatics. 2013 Oct 18. [Epub ahead of print]

Metagenomic species profiling using universal phylogenetic marker genes.
Sunagawa S, Mende DR, Zeller G, Izquierdo-Carrasco F, et al.
Nat Methods. 2013 Oct 20. [Epub ahead of print]

Quantitative assessment of single-cell RNA-sequencing methods.
Wu AR, Neff NF, Kalisky T, Dalerba P, et al.
Nat Methods. 2013 Oct 20. [Epub ahead of print]