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In Print: Last Week's Sequencing-Related Papers of Note: Aug 6, 2013


RNA-DNA differences in human mitochondria restore ancestral form of 16S ribosomal RNA.
Bar-Yaacov D, Avital G, Levin L, Richards A, et al.
Genome Res. 2013 Aug 2. [Epub ahead of print]

Massively parallel sequencing of Chikso (Korean brindle cattle) to discover genome-wide SNPs and InDels.
Choi JW, Liao X, Park S, Jeon HJ, et al.
Mol Cells. 2013 Aug 1. [Epub ahead of print]

AlienTrimmer: A tool to quickly and accurately trim off multiple short contaminant sequences from high-throughput sequencing reads.
Criscuolo A, Brisse S.
Genomics. 2013 Aug 1. [Epub ahead of print]

Improving transcriptome assembly through error correction of high-throughput sequence reads.
Macmanes MD, Eisen MB.
PeerJ. 2013 Jul 23;1:e113. Print 2013.

Genome-wide association studies using single nucleotide polymorphism markers developed by re-sequencing of the genomes of cultivated tomato.
Shirasawa K, Fukuoka H, Matsunaga H, Kobayashi Y, et al.
DNA Res. 2013 Jul 31. [Epub ahead of print]

Estimating exome genotyping accuracy by comparing to data from large scale sequencing projects.
Heinrich V, Kamphans T, Stange J, Parkhomchuk D, et al.
Genome Med. 2013 Jul 31;5(7):69.

De novo assembly of the Streptomyces sp. strain Mg1 genome using PacBio single-molecule sequencing.
Hoefler BC, Konganti K, Straight PD.
Genome Announc. 2013 Aug 1;1(4).

Low-pass DNA sequencing of 1200 Sardinians reconstructs European Y-chromosome phylogeny.
Francalacci P, Morelli L, Angius A, Berutti R, et al.
Science. 2013 Aug 2;341(6145):565-9.

Sequencing Y chromosomes resolves discrepancy in time to common ancestor of males versus females.
Poznik GD, Henn BM, Yee MC, Sliwerska E, et al.
Science. 2013 Aug 2;341(6145):562-5.

Global gene expression response of a population exposed to benzene: A pilot study exploring the use of RNA-sequencing technology.
Thomas R, McHale CM, Lan Q, Hubbard AE, et al.
Environ Mol Mutagen. 2013 Aug 1. [Epub ahead of print]

Emulsion PCR-coupled target enrichment: An effective fishing method for high-throughput sequencing of poorly preserved ancient DNA.
Kihana M, Mizuno F, Sawafuji R, Wang L, Ueda S.
Gene. 2013 Jul 27. [Epub ahead of print]

Indel and Carryforward Correction (ICC): A new analysis approach for processing 454 pyrosequencing data.
Deng W, Maust BS, Westfall DH, Chen L, et al.
Bioinformatics. 2013 Jul 29. [Epub ahead of print]

Comparison of direct boiling method with commercial kits for extracting fecal microbiome DNA by Illumina sequencing of 16S rRNA tags.
Peng X, Yu KQ, Deng GH, Jiang YX, et al.
J Microbiol Methods. 2013 Jul 27. [Epub ahead of print]

Whole-genome resequencing of Hanwoo (Korean cattle) and insight into regions of homozygosity.
Lee KT, Chung WH, Lee SY, Choi JW, et al.
BMC Genomics. 2013 Jul 30;14(1):519.

Genetic measurement of memory B-cell recall using antibody repertoire sequencing.
Vollmers C, Sit RV, Weinstein JA, Dekker CL, Quake SR.
Proc Natl Acad Sci U S A. 2013 Jul 29. [Epub ahead of print]

PCR-induced transitions are the major source of error in cleaned ultra-deep pyrosequencing data.
Brodin J, Mild M, Hedskog C, Sherwood E, et al.
PLoS One. 2013 Jul 23;8(7):e70388.

A microfluidic DNA library preparation platform for next-generation sequencing.
Kim H, Jebrail MJ, Sinha A, Bent ZW, et al.
PLoS One. 2013 Jul 22;8(7):e68988.

Advantages of single-molecule real-time sequencing in high-GC content genomes.
Shin SC, Ahn do H, Kim SJ, Lee H, et al.
PLoS One. 2013 Jul 23;8(7):e68824.

A microfluidic device for preparing next generation DNA sequencing libraries and for automating other laboratory protocols that require one or more column chromatography steps.
Tan SJ, Phan H, Gerry BM, Kuhn A, et al.
PLoS One. 2013 Jul 24;8(7):e64084.

Sequencing and annotated analysis of the Holstein cow genome.
Kõks S, Lilleoja R, Reimann E, Salumets A, et al.
Mamm Genome. 2013 Jul 27. [Epub ahead of print]

MiTCR: software for T-cell receptor sequencing data analysis.
Bolotin DA, Shugay M, Mamedov IZ, Putintseva EV, et al.
Nat Methods. 2013 Jul 28. [Epub ahead of print]

Rapid and accurate large-scale genotyping of duplicated genes and discovery of interlocus gene conversions.
Nuttle X, Huddleston J, O'Roak BJ, Antonacci F, et al.
Nat Methods. 2013 Jul 28. [Epub ahead of print]

Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing.
Xue Z, Huang K, Cai C, Cai L, et al.
Nature. 2013 Jul 28. [Epub ahead of print]

An optimal test with maximum average power while controlling FDR with application to RNA-seq data.
Si Y, Liu P.
Biometrics. 2013 Jul 26:1-12. [Epub ahead of print]