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In Print: Last Week's Sequencing-Related Papers of Note: Apr 16, 2013


Extracellular vesicle-mediated transfer of donor genomic DNA to recipient cells is a novel mechanism for genetic influence between cells.
Cai J, Han Y, Ren H, Chen C, et al.
J Mol Cell Biol. 2013 Apr 11. [Epub ahead of print]

Roles for transcript leaders in translation and mRNA decay revealed by transcript leader sequencing.
Arribere JA, Gilbert WV.
Genome Res. 2013 Apr 11. [Epub ahead of print]

Reflex: intramolecular barcoding of long-range PCR products for sequencing multiple pooled DNAs.
Casbon JA, Slatter AF, Musgrave-Brown E, Osborne RJ, et al.
Nucleic Acids Res. 2013 Apr 10. [Epub ahead of print]

High-resolution mapping of in vivo genomic transcription factor binding sites using in situ DNase I footprinting and ChIP-seq.
Chumsakul O, Nakamura K, Kurata T, Sakamoto T, et al.
DNA Res. 2013 Apr 11. [Epub ahead of print]

Species identification and profiling of complex microbial communities using shotgun Illumina sequencing of 16S rRNA amplicon sequences.
Ong SH, Kukkillaya VU, Wilm A, Lay C, et al.
PLoS One. 2013 Apr 8;8(4)

An electro-hydrodynamics-based model for the ionic conductivity of solid-state nanopores during DNA translocation.
Luan B, Stolovitzky G.
Nanotechnology. 2013 Apr 12;24(19):195702.

CMG-Biotools, a free workbench for basic comparative microbial genomics.
Vesth T, Lagesen K, Acar O, Ussery D.
PLoS One. 2013;8(4):e60120.

Genome-wide quantitative identification of DNA differentially methylated sites in Arabidopsis seedlings growing at different water potential.
Colaneri AC, Jones AM.
PLoS One. 2013;8(4):e59878.

Comprehensive characterization of human genome variation by high coverage whole-genome sequencing of forty four Caucasians.
Shen H, Li J, Zhang J, Xu C, et al.
PLoS One. 2013;8(4):e59494.

Probing DNA shape and methylation state on a genomic scale with DNase I.
Lazarovici A, Zhou T, Shafer A, Dantas Machado AC, et al.
Proc Natl Acad Sci U S A. 2013 Apr 1. [Epub ahead of print]

The use of RelocaTE and unassembled short reads to produce high-resolution snapshots of transposable element generated diversity in rice.
Robb SM, Lu L, Valencia E, Burnette JM 3rd, et al.
G3 (Bethesda). 2013 Apr 5. pii: g3.112.005348v1.

High throughput transcriptome analysis of lipid metabolism in Syrian hamster liver in absence of an annotated genome.
Schmucki R, Berrera M, Küng E, Lee S, et al.
BMC Genomics. 2013 Apr 10;14(1):237.

Generation of mast cells from mouse fetus: analysis of differentiation and functionality, and transcriptome profiling using next generation sequencer.
Fukuishi N, Igawa Y, Kunimi T, Hamano H, et al.
PLoS One. 2013;8(4):e60837.

Transcriptome sequencing and analysis of wild amur ide (Leuciscus waleckii) inhabiting an extreme alkaline-saline lake reveals insights into stress adaptation.
Xu J, Ji P, Wang B, Zhao L, et al.
PLoS One. 2013;8(4):e59703.

Comprehensively identifying and characterizing the missing gene sequences in human reference genome with integrated analytic approaches.
Chen G, Wang C, Shi L, Tong W, et al.
Hum Genet. 2013 Apr 10. [Epub ahead of print]

Robustness of gut microbiota of healthy adults in response to probiotic intervention revealed by high-throughput pyrosequencing.
Kim SW, Suda W, Kim S, Oshima K, et al.
DNA Res. 2013 Apr 9. [Epub ahead of print]

Differential principal component analysis of ChIP-seq.
Ji H, Li X, Wang QF, Ning Y.
Proc Natl Acad Sci U S A. 2013 Apr 8. [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.