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In Print: Sequencing-Related Papers of Note of the Last Two Weeks: Dec 31, 2013


Rapid single-colony whole-genome sequencing of bacterial pathogens.
Köser CU, Fraser LJ, Ioannou A, Becq J, et al.
J Antimicrob Chemother. 2013 Dec 25. [Epub ahead of print]

Efficient selection of biomineralizing DNA aptamers using deep sequencing and population clustering.
Bawazer LA, Newman AM, Gu Q, Ibish A, et al.
ACS Nano. 2013 Dec 23. [Epub ahead of print]

Quantitative single-cell RNA-seq with unique molecular identifiers.
Islam S, Zeisel A, Joost S, La Manno G, et al.
Nat Methods. 2013 Dec 22. [Epub ahead of print]

PennSeq: accurate isoform-specific gene expression quantification in RNA-seq by modeling non-uniform read distribution.
Hu Y, Liu Y, Mao X, Jia C, et al.
Nucleic Acids Res. 2013 Dec 20. [Epub ahead of print]

The utility of shallow RNA-seq for documenting differential gene expression in genes with high and low levels of expression.
Atallah J, Plachetzki DC, Jasper WC, Johnson BR.
PLOS One. 2013 Dec 16;8(12):e84160.

A universal method for species identification of mammals utilizing next generation sequencing for the analysis of DNA mixtures.
Tillmar AO, Dell'amico B, Welander J, Holmlund G.
PLOS One. 2013 Dec 16;8(12):e83761.

Combining DGE and RNA-sequencing data to identify new polyA+ non-coding transcripts in the human genome.
Philippe N, Bou Samra E, Boureux A, Mancheron A, et al.
Nucleic Acids Res. 2013 Dec 18. [Epub ahead of print]

A FIB induced boiling mechanism for rapid nanopore formation.
Das K, Freund JB, Johnson HT.
Nanotechnology. 2013 Dec 20;25(3):035303.

Inferring short tandem repeat variation from paired-end short reads.
Cao MD, Tasker E, Willadsen K, Imelfort M, et al.
Nucleic Acids Res. 2013 Dec 17. [Epub ahead of print]

Summarizing specific profiles in Illumina sequencing from whole-genome amplified DNA.
Tsai IJ, Hunt M, Holroyd N, Huckvale T, et al.
DNA Res. 2013 Dec 18. [Epub ahead of print]

The complete genome sequence of a Neanderthal from the Altai Mountains.
Prüfer K, Racimo F, Patterson N, Jay F, et al.
Nature. 2013 Dec 18. [Epub ahead of print]

Ultrashort single-walled carbon nanotubes in a lipid bilayer as a new nanopore sensor.
Liu L, Yang C, Zhao K, Li J, Wu HC.
Nat Commun. 2013 Dec 19;4:2989.

Sequencing error correction without a reference genome.
Sleep JA, Schreiber AW, Baumann U.
BMC Bioinformatics. 2013 Dec 18;14(1):367.

Evaluation of assembly strategies using RNA-seq data associated with grain development of wheat (Triticum aestivum L.).
Li HZ, Gao X, Li XY, Chen QJ, et al.
PLOS One. 2013 Dec 12;8(12):e83530.

Widespread misinterpretable ChIP-seq bias in yeast.
Park D, Lee Y, Bhupindersingh G, Iyer VR.
PLOS One. 2013 Dec 9;8(12):e83506.

Large-scale quality analysis of published ChIP-seq data.
Marinov GK, Kundaje A, Park PJ, Wold BJ.
G3. 2013 Dec 17. [Epub ahead of print]

Quantitative PCR as a predictor of aligned ancient DNA read counts following targeted enrichment.
Enk J, Rouillard JM, Poinar H.
Biotechniques. 2013 Dec;55(6):300-9.

RNA-seq optimization with eQTL gold standards.
Ellis SE, Gupta S, Ashar FN, Bader JS, et al.
BMC Genomics. 2013 Dec 17;14(1):892.

A high-throughput Sanger strategy for human mitochondrial genome sequencing.
Lyons EA, Scheible MK, Sturk-Andreaggi K, Irwin JA, Just RS.
BMC Genomics. 2013 Dec 16;14(1):881.

Synthesis of 3'-O-fluorescently mono-modified reversible terminators and their uses in sequencing-by-synthesis.
Kim DR, Kim TS, Kim E, Min SJ, et al.
Bioorg Med Chem Lett. 2014 Jan 1;24(1):209-13.