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In Print: Last Week's Sequencing-Related Papers of Note: Feb 5, 2013


Comparative study of RNA-seq- and microarray-derived coexpression networks in Arabidopsis thaliana.
Giorgi FM, Fabbro CD, Licausi F.
Bioinformatics. 2013 Feb 1. [Epub ahead of print]

Filtering duplicate reads from 454 pyrosequencing data.
Balzer S, Malde K, Grohme MA, Jonassen I.
Bioinformatics. 2013 Feb 1. [Epub ahead of print]

RepeatExplorer: a Galaxy-based web server for genome-wide characterization of eukaryotic repetitive elements from next generation sequence reads.
Novák P, Neumann P, Pech J, Steinhaisl J, Macas J.
Bioinformatics. 2013 Feb 1. [Epub ahead of print]

Using GBrowse 2.0 to visualize and share next-generation sequence data.
Stein LD.
Brief Bioinform. 2013 Feb 1. [Epub ahead of print]

An improved Genotyping By Sequencing (GBS) approach offering increased versatility and efficiency of SNP discovery and genotyping.
Sonah H, Bastien M, Iquira E, Tardivel A, et al.
PLoS One. 2013;8(1):e54603.

A single cell level based method for copy number variation analysis by low coverage massively parallel sequencing.
Zhang C, Zhang C, Chen S, Yin X, et al.
PLoS One. 2013;8(1):e54236.

Low frequency clonal mutations recoverable by deep sequencing in patients with aplastic anemia.
Lane AA, Odejide O, Kopp N, Kim S, et al.
Leukemia. 2013 Feb 1. [Epub ahead of print]

Metagenomic profile of gut microbiota in children during cholera and recovery.
Monira S, Nakamura S, Gotoh K, Izutsu K, et al.
Gut Pathog. 2013 Feb 1;5(1):1.

DNA translocation through a nanopore in a single-layered doped semiconductor membrane.
Jou IA, Melnikov DV, McKinney CR, Gracheva ME.
Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Dec;86(6-1):061906.

Detection of common copy number variation with application to population clustering from next generation sequencing data.
Duan J, Zhang JG, Deng HW, Wang YP.
Conf Proc IEEE Eng Med Biol Soc. 2012 Aug;2012:1246-9.

MosaicFinder: Identification of fused gene families in sequence similarity networks.
Jachiet PA, Pogorelcnik R, Berry A, Lopez P, Bapteste E.
Bioinformatics. 2013 Jan 30. [Epub ahead of print]

Gene capture coupled to high-throughput sequencing as a strategy for targeted metagenome exploration.
Denonfoux J, Parisot N, Dugat-Bony E, Biderre-Petit C, et al.
DNA Res. 2013 Jan 30. [Epub ahead of print]

Maximum likelihood estimation of frequencies of known haplotypes from pooled sequence data.
Kessner D, Turner T, Novembre J.
Mol Biol Evol. 2013 Jan 30. [Epub ahead of print]

Comparative analysis of tandem repeats from hundreds of species reveals unique insights into centromere evolution.
Melters DP, Bradnam KR, Young HA, Telis N, et al.
Genome Biol. 2013 Jan 30;14(1):R10.

High-throughput sequencing reveals extraordinary fluidity of miRNA, piRNA, and siRNA pathways in nematodes.
Shi Z, Montgomery TA, Qi Y, Ruvkun G.
Genome Res. 2013 Jan 30. [Epub ahead of print]

HTQC: a fast quality control toolkit for Illumina sequencing data.
Yang X, Liu D, Liu F, Wu J, et al.
BMC Bioinformatics. 2013 Jan 31;14(1):33.

BioGranat-IG: A network analysis tool to suggest mechanisms of genetic heterogeneity from exome sequencing data.
Dand N, Sprengel F, Ahlers V, Schlitt T.
Bioinformatics. 2013 Jan 29. [Epub ahead of print]

Inferring the kinetics of stochastic gene expression from single-cell RNA-sequencing data.
Kim JK, Marioni JC.
Genome Biol. 2013 Jan 28;14(1):R7.

Gene copy-number polymorphism caused by retrotransposition in humans.
Schrider DR, Navarro FC, Galante PA, Parmigiani RB, et al.
PLoS Genet. 2013 Jan;9(1):e1003242.

Fast and accurate read mapping with approximate seeds and multiple backtracking.
Siragusa E, Weese D, Reinert K.
Nucleic Acids Res. 2013 Jan 28. [Epub ahead of print]

Genome-wide localization of exosome components to active promoters and chromatin insulators in Drosophila.
Lim SJ, Boyle PJ, Chinen M, Dale RK, Lei EP.
Nucleic Acids Res. 2013 Jan 28. [Epub ahead of print]

Sequencing and de novo assembly of the Western tarnished plant bug (Lygus Hesperus) transcriptome.
Hull JJ, Geib SM, Fabrick JA, Brent CS.
PLoS One. 2013;8(1):e55105.

AbCD: Arbitrary coverage design for sequencing-based genetic studies.
Kang J, Huang KC, Xu Z, Wang Y, et al.
Bioinformatics. 2013 Jan 28. [Epub ahead of print]