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Recent Sequencing-Related Papers of Note: May 27, 2014


Graphene sculpturene nanopores for DNA nucleobase sensing.
Sadeghi H, Algharagholy LA, Pope T, Bailey SW, et al.
J Phys Chem B. 2014 May 21. [Epub ahead of print]

Draft sequences of the radish (Raphanus sativus L.) genome.
Kitashiba H, Li F, Hirakawa H, Kawanabe T, et al.
DNA Res. 2014 May 16. [Epub ahead of print]

Precise estimates of mutation rate and spectrum in yeast.
Zhu YO, Siegal ML, Hall DW, Petrov DA.
Proc Natl Acad Sci U S A. 2014 May 20. [Epub ahead of print]

Microbial community profiling of human saliva using shotgun metagenomic sequencing.
Hasan NA, Young BA, Minard-Smith AT, Saeed K, et al.
PLOS One. 2014 May 20;9(5):e97699.

Exploration and retrieval of whole-metagenome sequencing samples.
Seth S, Välimäki N, Kaski S, Honkela A.
Bioinformatics. 2014 May 19. [Epub ahead of print]

CLImAT: accurate detection of copy number alteration and loss of heterozygosity in impure and aneuploid tumor samples using whole-genome sequencing data.
Yu Z, Liu Y, Shen Y, Wang M, Li A.
Bioinformatics. 2014 May 19. [Epub ahead of print]

SparkSeq: fast, scalable, cloud-ready tool for the interactive genomic data analysis with nucleotide precision.
Wiewiórka MS, Messina A, Pacholewska A, Maffioletti S, et al.
Bioinformatics. 2014 May 19. [Epub ahead of print]

Molecular traces of alternative social organization in a termite genome.
Terrapon N, Li C, Robertson HM, Ji L4, Meng X, et al.
Nat Commun. 2014 May 20;5:3636.

GPU-BSM: A GPU-based tool to map bisulfite-treated reads.
Manconi A, Orro A, Manca E, Armano G, Milanesi L.
PLOS One. 2014 May 19;9(5):e97277.

HIV-1 Quasispecies delineation by tag linkage deep sequencing.
Wu NC, De La Cruz J, Al-Mawsawi LQ, Olson CA, et al.
PLOS One. 2014 May 19;9(5):e97505.

Fast assembly of the mitochondrial genome of a plant parasitic nematode (Meloidogyne graminicola) using next generation sequencing.
Besnard G, Jühling F, Chapuis E, Zedane L, et al.
C R Biol. 2014 May;337(5):295-301.

Direct, concurrent measurements of the forces and currents affecting DNA in a nanopore with comparable topography.
Nelson EM, Li H, Timp G.
ACS Nano. 2014 May 19. [Epub ahead of print]

The Scan

Purnell Choppin Dies

Purnell Choppin, a virologist who led the Howard Hughes Medical Institute, has died at 91, according to the Washington Post.

Effectiveness May Decline, Data From Israel Suggests

The New York Times reports that new Israeli data suggests a decline in Pfizer-BioNTech SARS-CoV-2 vaccine effectiveness against Delta variant infection, though protection against severe disease remains high.

To See Future Risk

Slate looks into the use of polygenic risk scores in embryo screening.

PLOS Papers on Methicillin-Resistant Staphylococcus, Bone Marrow Smear Sequencing, More

In PLOS this week: genomic analysis of methicillin-resistant Staphylococcus pseudintermedius, archived bone marrow sequencing, and more.