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Recent Sequencing-Related Papers of Note: Aug 26, 2014


Probing molecular pathways for DNA orientational trapping, unzipping and translocation in nanopores by using a tunable overhang sensor.
Wang Y, Tian K, Hunter LL, Ritzo B, Gu LQ.
Nanoscale. 2014 Aug 21. [Epub ahead of print]

Choice of reference sequence and assembler for alignment of Listeria monocytogenes short-read sequence data greatly influences rates of error in SNP analyses.
Pightling AW, Petronella N, Pagotto F.
PLOS One. 2014 Aug 21;9(8):e104579.

Development of a prokaryotic universal primer for simultaneous analysis of bacteria and archaea using next-generation sequencing.
Takahashi S, Tomita J, Nishioka K, Hisada T, Nishijima M.
PLOS One. 2014 Aug 21;9(8):e105592.

FACTERA: a practical method for the discovery of genomic rearrangements at breakpoint resolution.
Newman AM, Bratman SV, Stehr H, Lee LJ, et al.
Bioinformatics. 2014 Aug 20. [Epub ahead of print]

Poretools: a toolkit for analyzing nanopore sequence data.
Loman NJ, Quinlan AR.
Bioinformatics. 2014 Aug 20. [Epub ahead of print]

Acceleration of short and long DNA read mapping without loss of accuracy using suffix array.
Tárraga J, Arnau V, Martínez H, Moreno R, et al.
Bioinformatics. 2014 Aug 20. [Epub ahead of print]

OptiType: precision HLA typing from next-generation sequencing data.
Szolek A, Schubert B, Mohr C, Sturm M, et al.
Bioinformatics. 2014 Aug 20. [Epub ahead of print]

Performance comparison of second- and third-generation sequencers using a bacterial genome with two chromosomes.
Miyamoto M, Motooka D, Gotoh K, Imai T, et al.
BMC Genomics. 2014 Aug 21;15(1):699.

Profile hidden Markov models for the detection of viruses within metagenomic sequence data.
Skewes-Cox P, Sharpton TJ, Pollard KS, DeRisi JL.
PLOS One. 2014 Aug 20;9(8):e105067.

A quantitative comparison of single-cell whole genome amplification methods.
de Bourcy CF, De Vlaminck I, Kanbar JN, Wang J, et al.
PLOS One. 2014 Aug 19;9(8):e105585.

MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm.
Wu YW, Tang YH, Tringe SG, Simmons BA, Singer SW.
Microbiome. 2014 Aug 1;2:26.

The CNVrd2 package: measurement of copy number at complex loci using high-throughput sequencing data.
Nguyen HT, Merriman TR, Black MA.
Front Genet. 2014 Aug 1;5:248.

ExaBayes: massively parallel Bayesian tree inference for the whole-genome era.
Aberer AJ, Kobert K, Stamatakis A.
Mol Biol Evol. 2014 Aug 18. [Epub ahead of print]

A high-throughput sequencing ecotoxicology study of freshwater bacterial communities and their responses to tebuconazole.
Noémie P, Simon R, Joan A, Stéphane P, et al.
FEMS Microbiol Ecol. 2014 Aug 18. [Epub ahead of print]

Evaluation of exome sequencing to estimate tumor burden in plasma.
Klevebring D, Neiman M, Sundling S, Eriksson L, et al.
PLOS One. 2014 Aug 18;9(8):e104417.

A method to evaluate genome-wide methylation in archival formalin-fixed, paraffin-embedded ovarian epithelial cells.
Li Q, Li M, Ma L, Li W, et al.
PLOS One. 2014 Aug 18;9(8):e104481.

A rank-based sequence aligner with applications in phylogenetic analysis.
Dinu LP, Ionescu RT, Tomescu AI.
PLOS One. 2014 Aug 18;9(8):e104006.

Degenerate adaptor sequences for detecting PCR duplicates in reduced representation sequencing data improve genotype-calling accuracy.
Tin MM, Rheindt FE, Cros E, Mikheyev AS.
Mol Ecol Resour. 2014 Aug 11. [Epub ahead of print]

Haplotype counting by next-generation sequencing for ultrasensitive human DNA detection.
Debeljak M, Freed DN, Welch JA, Haley L, et al.
J Mol Diagn. 2014 Sep;16(5):495-503.

Sequencing of captive target transcripts identifies the network of regulated genes and functions of primate-specific miR-522.
Tan SM, Kirchner R, Jin J, Hofmann O, et al.
Cell Rep. 2014 Aug 12. [Epub ahead of print]

Targeted sequencing by proximity ligation for comprehensive variant detection and local haplotyping.
de Vree PJ, de Wit E, Yilmaz M, van de Heijning M, et al.
Nat Biotechnol. 2014 Aug 17. [Epub ahead of print]
(See our coverage of this paper here.)

A comprehensive insight into bacterial virulence in drinking water using 454 pyrosequencing and Illumina high-throughput sequencing.
Huang K, Zhang XX, Shi P, Wu B, Ren H.
Ecotoxicol Environ Saf. 2014 Aug 14;109C:15-21.

Discovery of common sequences absent in the human reference genome using pooled samples from next generation sequencing.
Liu Y, Koyutürk M, Maxwell S, Xiang M, et al.
BMC Genomics. 2014 Aug 16;15(1):685.

Using familial information for variant filtering in high-throughput sequencing studies.
Bahlo M, Tankard R, Lukic V, Oliver KL, Smith KR.
Hum Genet. 2014 Aug 17. [Epub ahead of print]