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In Print: Last Week's Sequencing-Related Papers of Note: Sep 17, 2013


Twin mitochondrial sequence analysis.
Bouhlal Y, Martinez S, Gong H, Dumas K, Shieh JT.
Mol Genet Genomic Med. 2013 Sep 1;1(3):174-186.

Effect of DNA extraction methods and sampling techniques on the apparent structure of cow and sheep rumen microbial communities.
Henderson G, Cox F, Kittelmann S, Miri VH, et al.
PLOS One. 2013 Sep 11;8(9):e74787.

A comparison of digital gene expression profiling and methyl DNA immunoprecipitation as methods for gene discovery in honeybee (Apis mellifera) behavioural genomic analyses.
Guan C, Barron AB, He XJ, Wang ZL, et al.
PLOS One. 2013 Sep 9;8(9):e73628.

Quality score based identification and correction of pyrosequencing errors.
Iyer S, Bouzek H, Deng W, Larsen B, et al.
PLOS One. 2013 Sep 5;8(9):e73015.

Distinct mechanisms of DNA sensing based on N-doped carbon nanotubes with enhanced conductance and chemical selectivity.
Kim HS, Lee SJ, Kim YH.
Small. 2013 Sep 4. [Epub ahead of print]

A quality control system for profiles obtained by ChIP sequencing.
Mendoza-Parra MA, Van Gool W, Mohamed Saleem MA, Ceschin DG, Gronemeyer H.
Nucleic Acids Res. 2013 Sep 14. [Epub ahead of print]

Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories.
't Hoen PA, Friedländer MR, Almlöf J, Sammeth M, et al.
Nat Biotechnol. 2013 Sep 15. [Epub ahead of print]

Transcriptome and genome sequencing uncovers functional variation in humans.
Lappalainen T, Sammeth M, Friedländer MR, 't Hoen PA, et al.
Nature. 2013 Sep 15. [Epub ahead of print]

Human gut microbiota community structures in urban and rural populations in Russia.
Tyakht AV, Kostryukova ES, Popenko AS, Belenikin MS, et al.
Nat Commun. 2013 Sep 16;4:2469.

Genome signature-based dissection of human gut metagenomes to extract subliminal viral sequences.
Ogilvie LA, Bowler LD, Caplin J, Dedi C, et al.
Nat Commun. 2013 Sep 16;4:2420.

Reducing assembly complexity of microbial genomes with single-molecule sequencing.
Koren S, Harhay GP, Smith TP, Bono JL, et al.
Genome Biol. 2013 Sep 13;14(9):R101.

BAIT: Organizing genomes and mapping rearrangements in single cells.
Hills M, Neill K, Falconer E, Brinkman R, Lansdorp PM.
Genome Med. 2013 Sep 13;5(9):82.

Modular tagging of amplicons using a single PCR for high-throughput sequencing.
Clarke LJ, Czechowski P, Soubrier J, Stevens MI, Cooper A.
Mol Ecol Resour. 2013 Aug 20. [Epub ahead of print]

Genotyping of human neutrophil antigens (HNA) from whole genome sequencing data.
Chu HT, Lin H, Tsao TT, Chang CF, et al.
BMC Med Genomics. 2013 Sep 12;6(1):31.

Analysis of allele specific expression in mouse liver by RNA-seq: a comparison with "cis"-eQTL identified using genetic linkage.
Lagarrigue S, Martin LJ, Hormozdiari F, Roux PF, et al.
Genetics. 2013 Sep 11. [Epub ahead of print]

Estimating individual admixture proportions from next generation sequencing data.
Skotte L, Korneliussen TS, Albrechtsen A.
Genetics. 2013 Sep 11. [Epub ahead of print]

Distinct polyadenylation landscapes of diverse human tissues revealed by a modified PA-seq strategy.
Ni T, Yang Y, Hafez D, Yang W, et al.
BMC Genomics. 2013 Sep 11;14(1):615.

Evaluating detection limits of next-generation sequencing for the surveillance and monitoring of international marine pests.
Pochon X, Bott NJ, Smith KF, Wood SA.
PLOS One. 2013 Sep 4;8(9):e73935.

Genomic prediction in maize breeding populations with genotyping-by-sequencing.
Crossa J, Beyene Y, Kassa S, Pérez P, et al.
G3 (Bethesda). 2013 Sep 10. [Epub ahead of print]

Next-generation anchor based phylogeny (NexABP): constructing phylogeny from next-generation sequencing data.
Roychowdhury T, Vishnoi A, Bhattacharya A.
Sci Rep. 2013 Sep 11;3:2634.

Target capture and massively parallel sequencing of ultraconserved elements (UCEs) for comparative studies at shallow evolutionary time scales.
Smith BT, Harvey MG, Faircloth BC, Glenn TC, Brumfield RT.
Syst Biol. 2013 Sep 10. [Epub ahead of print]

Toward a statistically explicit understanding of de novo sequence assembly.
Howison M, Dunn CW, Zapata F.
Bioinformatics. 2013 Sep 10. [Epub ahead of print]

BioPig: a Hadoop-based analytic toolkit for large-scale sequence data.
Nordberg H, Bhatia K, Wang K, Wang Z.
Bioinformatics. 2013 Sep 10. [Epub ahead of print]

HMCan: a method for detecting chromatin modifications in cancer samples using ChIP-seq data.
Ashoor H, Hérault A, Kamoun A, Radvanyi F, et al.
Bioinformatics. 2013 Sep 9. [Epub ahead of print]

Levenshtein error-correcting barcodes for multiplexed DNA sequencing.
Buschmann T, Bystrykh LV.
BMC Bioinformatics. 2013 Sep 11;14(1):272.

Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data.
Rapaport F, Khanin R, Liang Y, Pirun M, et al.
Genome Biol. 2013 Sep 10;14(9):R95.

Mining RNA-seq data for infections and contaminations.
Bonfert T, Csaba G, Zimmer R, Friedel CC.
PLOS One. 2013 Sep 3;8(9):e73071.

Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments.
Dabney J, Knapp M, Glocke I, Gansauge MT, et al.
Proc Natl Acad Sci U S A. 2013 Sep 9. [Epub ahead of print]

De novo sequencing of short interfering ribonucleic acids facilitated by use of tandem mass spectrometry with ion mobility spectrometry.
Fisher HC, Smith M, Ashcroft AE.
Rapid Commun Mass Spectrom. 2013 Oct 30;27(20):2247-54.

Signatures of rapid evolution in urban and rural transcriptomes of white-footed mice (Peromyscus leucopus) in the New York metropolitan area.
Harris SE, Munshi-South J, Obergfell C, O'Neill R.
PLOS One. 2013 Aug 28;8(8):e74938.

Primate genome architecture influences structural variation mechanisms and functional consequences.
Gokcumen O, Tischler V, Tica J, Zhu Q, et al.
Proc Natl Acad Sci U S A. 2013 Sep 6. [Epub ahead of print]

A short-read multiplex sequencing method for reliable, cost-effective and high-throughput genotyping in large-scale studies.
Cao H, Wang Y, Zhang W, Chai X, et al.
Hum Mutat. 2013 Sep 6. [Epub ahead of print]

A microbial profiling method for the human microbiota using high-throughput sequencing.
Tseng HH, Hullar MA, Li F, Lampe JW, et al.
Metagenomics (Cairo). 2013;2:235646.

Accelerating the design of biomimetic materials by integrating RNA-seq with proteomics and materials science.
Guerette PA, Hoon S, Seow Y, Raida M, et al.
Nat Biotechnol. 2013 Sep 8. [Epub ahead of print]

Centroid based clustering of high throughput sequencing reads based on n-mer counts.
Solovyov A, Lipkin WI.
BMC Bioinformatics. 2013 Sep 8;14(1):268.

L_RNA_scaffolder: scaffolding genomes with transcripts.
Xue W, Li JT, Zhu YP, Hou GY, et al.
BMC Genomics. 2013 Sep 8;14(1):604.