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Last Week's Sequencing-Related Papers of Note: Feb 4, 2014


Yersinia pestis and the Plague of Justinian 541-543 AD: a genomic analysis.
Wagner DM, Klunk J, Harbeck M, Devault A, et al.
Lancet Infect Dis. 2014 Jan 27. [Epub ahead of print]

Finding the missing honey bee genes: lessons learned from a genome upgrade.
Elsik CG, Worley KC, Bennett AK, Beye M, et al.
BMC Genomics. 2014 Jan 30;15(1):86.

Variant calling in low-coverage whole genome sequencing of a Native American population sample.
Bizon C, Spiegel M, Chasse SA, Gizer IR, et al.
BMC Genomics. 2014 Jan 30;15(1):85.

QTrim: a novel tool for the quality trimming of sequence reads generated using the Roche/454 sequencing platform.
Shrestha RK, Lubinsky B, Bansode VB, Moinz MB, et al.
BMC Bioinformatics. 2014 Jan 30;15(1):33.

Poly(A)-tail profiling reveals an embryonic switch in translational control.
Subtelny AO, Eichhorn SW, Chen GR, Sive H, Bartel DP.
Nature. 2014 Jan 29. [Epub ahead of print]

SHEAR: sample heterogeneity estimation and assembly by reference.
Landman SR, Hwang TH, Silverstein KA, Li Y, et al.
BMC Genomics. 2014 Jan 29;15(1):84.

Launching genomics into the cloud: deployment of Mercury, a next generation sequence analysis pipeline.
Reid JG, Carroll A, Veeraraghavan N, Dahdouli M, et al.
BMC Bioinformatics. 2014 Jan 29;15(1):30.

Caught in the middle with multiple displacement amplification: the myth of pooling for avoiding multiple displacement amplification bias in a metagenome.
Marine R, McCarren C, Vorrasane V, Nasko D, et al.
Microbiome. 2014 Jan 30;2(1):3.

HTSstation: a web application and open-access libraries for high-throughput sequencing data analysis.
David FP, Delafontaine J, Carat S, Ross FJ, et al.
PLOS One. 2014 Jan 27;9(1):e85879.

NGSANE: a lightweight production informatics framework for high throughput data analysis.
Buske FA, French HJ, Smith MA, Clark SJ, Bauer DC.
Bioinformatics. 2014 Jan 26. [Epub ahead of print]

Parseq: reconstruction of microbial transcription landscape from RNA-seq read counts using state-space models.
Mirauta B, Nicolas P, Richard H.
Bioinformatics. 2014 Jan 27. [Epub ahead of print]

CUSHAW3: sensitive and accurate base-space and color-space short-read alignment with hybrid seeding.
Liu Y, Popp B, Schmidt B.
PLOS One. 2014 Jan 22;9(1):e86869.

PSCC: sensitive and reliable population-scale copy number variation detection method based on low coverage sequencing.
Li X, Chen S, Xie W, Vogel I, et al.
PLOS One. 2014 Jan 21;9(1):e85096.

Correction of sequence-dependent ambiguous bases (Ns) from the 454 pyrosequencing system.
Shin S, Park J.
Nucleic Acids Res. 2014 Jan 23. [Epub ahead of print]

Cloud-based bioinformatics workflow platform for large-scale next-generation sequencing analyses.
Liu B, Li J, Liu C.
J Biomed Inform. 2014 Jan 22. [Epub ahead of print]

ROVER variant caller: read-pair overlap considerate variant-calling software applied to PCR-based massively parallel sequencing datasets.
Pope BJ, Nguyen-Dumont T, Hammet F, Park DJ.
Source Code Biol Med. 2014 Jan 24;9(1):3.

From cheek swabs to consensus sequences: an A to Z protocol for high-throughput DNA sequencing of complete human mitochondrial genomes.
Clarke AC, Prost S, Stanton JA, White WT, et al.
BMC Genomics. 2014 Jan 25;15(1):68.

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.