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Last Week's Sequencing-Related Papers of Note: Feb 11, 2014


SASI-seq: sample assurance spike-ins, and highly differentiating 384 barcoding for Illumina sequencing.
Quail MA, Smith M, Jackson D, Leonard S, et al.
BMC Genomics. 2014 Feb 7;15(1):110.

A rat RNA-seq transcriptomic BodyMap across 11 organs and 4 developmental stages.
Yu Y, Fuscoe JC, Zhao C, Guo C, et al.
Nat Commun. 2014 Feb 10;5:3230.

Pore-size reduction protocol for SiN membrane nanopore using the thermal reflow in nanoimprinting for nanobio-based sensing.
Lee DS, Song HW, Choi CG, Jung MY.
J Biomed Opt. 2014 May 1;19(5):51211.

The HTS barcode checker pipeline, a tool for automated detection of illegally traded species from high-throughput sequencing data.
Lammers Y, Peelen T, Vos RA, Gravendeel B.
BMC Bioinformatics. 2014 Feb 6;15(1):44.

A simple method for gene phasing using mate pair sequencing.
Cradic KW, Murphy SJ, Drucker TM, Sikkink RA, et al.
BMC Med Genet. 2014 Feb 6;15(1):19.

Improving read mapping using additional prefix grams.
Kim J, Li C, Xie X.
BMC Bioinformatics. 2014 Feb 5;15(1):42.

Re-sequencing expands our understanding of the phenotypic impact of variants at GWAS loci.
Service SK, Teslovich TM, Fuchsberger C, Ramensky V, et al.
PLOS Genet. 2014 Jan 30;10(1):e1004147.

Relationship estimation from whole-genome sequence data.
Li H, Glusman G, Hu H, Shankaracharya, et al.
PLOS Genet. 2014 Jan 30;10(1):e1004144.

Empirical assessment of RAD sequencing for interspecific phylogeny.
Cruaud A, Gautier M, Galan M, Foucaud J, et al.
Mol Biol Evol. 2014 Feb 3. [Epub ahead of print]

Regulating the transport of DNA through biofriendly nanochannels in a thin solid membrane.
Wang D, Harrer S, Luan B, Stolovitzky G, et al.
Sci Rep. 2014 Feb 5;4:3985.

Comparison of three next-generation sequencing platforms for metagenomic sequencing and identification of pathogens in blood.
Frey KG, Herrera-Galeano JE, Redden CL, Luu TV, et al.
BMC Genomics. 2014 Feb 4;15(1):96.

Comprehensive analysis to improve the validation rate for single nucleotide variants detected by next-generation sequencing.
Park MH, Rhee H, Park JH, Woo HM, et al.
PLOS One. 2014 Jan 29;9(1):e86664.

Whole-genome sequence of a flatfish provides insights into ZW sex chromosome evolution and adaptation to a benthic lifestyle.
Chen S, Zhang G, Shao C, Huang Q, et al.
Nat Genet. 2014 Feb 2. [Epub ahead of print]

Voom: precision weights unlock linear model analysis tools for RNA-seq read counts.
Law CW, Chen Y, Shi W, Smyth GK.
Genome Biol. 2014 Feb 3;15(2):R29.

Origin of current blockades in nanopore translocation experiments.
Kesselheim S, Müller W, Holm C.
Phys Rev Lett. 2014 Jan 10;112(1):018101.

Escape of DNA from a weakly biased thin nanopore: experimental evidence for a universal diffusive behavior.
Hoogerheide DP, Albertorio F, Golovchenko JA.
Phys Rev Lett. 2013 Dec 13;111(24):248301.

The Scan

Genetic Tests Lead to Potential Prognostic Variants in Dutch Children With Dilated Cardiomyopathy

Researchers in Circulation: Genomic and Precision Medicine found that the presence of pathogenic or likely pathogenic variants was linked to increased risk of death and poorer outcomes in children with pediatric dilated cardiomyopathy.

Fragile X Syndrome Mutations Found With Comprehensive Testing Method

Researchers in Clinical Chemistry found fragile X syndrome expansions and other FMR1 mutations with ties to the intellectual disability condition using a long-range PCR and long-read sequencing approach.

Team Presents Strategy for Speedy Species Detection in Metagenomic Sequence Data

A computational approach presented in PLOS Computational Biology produced fewer false-positive species identifications in simulated and authentic metagenomic sequences.

Genetic Risk Factors for Hypertension Can Help Identify Those at Risk for Cardiovascular Disease

Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.