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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

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.