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

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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

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.