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

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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

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.