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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

WHO Seeks Booster Pause

According to CNN, the World Health Organization is calling for a moratorium on administering SARS-CoV-2 vaccine boosters until more of the world has received initial doses.

For Those Long Legs

With its genome sequence and subsequent RNAi analyses, researchers have examined the genes that give long legs to daddy longlegs, New Scientist says.

September Plans

The New York Times reports that the US Food and Drug Administration is aiming for early September for full approval of the Pfizer-BioNTech SARS-CoV-2 vaccine.

Nucleic Acids Research Papers on Targeting DNA Damage Response, TSMiner, VarSAn

In Nucleic Acids Research this week: genetic changes affecting DNA damage response inhibitor response, "time-series miner" approach, and more.