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Recent Sequencing-Related Papers of Note: Sep 23, 2014


Parallel single cancer cell whole genome amplification using button-valve assisted mixing in nanoliter chambers.
Yang Y, Swennenhuis JF, Rho HS, Le Gac S, Terstappen LW.
PLOS One. 2014 Sep 18;9(9):e107958.

Improved nucleosome-positioning algorithm iNPS for accurate nucleosome positioning from sequencing data.
Chen W, Liu Y, Zhu S, et al.
Nat Commun. 2014 Sep 18;5:4909.

A microfluidic whole genome amplification device for single cell sequencing.
Yu Z, Lu S, Huang Y.
Anal Chem. 2014 Sep 18. [Epub ahead of print]

Label-free optical detection of biomolecular translocation through nanopore arrays.
Ivankin A, Henley RY, Larkin J, Carson S, et al.
ACS Nano. 2014 Sep 18. [Epub ahead of print]

Ancient human genomes suggest three ancestral populations for present-day Europeans.
Lazaridis I, Patterson N, Mittnik A, Renaud G, et al.
Nature. 2014 Sep 18;513(7518):409-13.

Optimization of extraction of circulating RNAs from plasma - enabling small RNA sequencing.
Spornraft M, Kirchner B, Haase B, Benes V, et al.
PLOS One. 2014 Sep 17;9(9):e107259.

Genome-wide map of regulatory interactions in the human genome.
Heidari N, Phanstiel DH, He C, Grubert F, et al.
Genome Res. 2014 Sep 16. [Epub ahead of print]

cnvCapSeq: detecting copy number variation in long-range targeted resequencing data.
Bellos E, Kumar V, Lin C, Maggi J, et al.
Nucleic Acids Res. 2014 Sep 16. [Epub ahead of print]

Using normalization to resolve RNA-seq biases caused by amplification from minimal input.
Ager-Wick E, Henkel CV, Haug TM, Weltzien FA.
Physiol Genomics. 2014 Sep 16. [Epub ahead of print]

Next-generation sequencing of 16S ribosomal RNA gene amplicons.
Sanschagrin S, Yergeau E.
J Vis Exp. 2014 Aug 29;(90).

Collection and extraction of saliva DNA for next generation sequencing.
Goode MR, Cheong SY, Li N, Ray WC, Bartlett CW.
J Vis Exp. 2014 Aug 27;(90).

Hyb-Seq: Combining target enrichment and genome skimming for plant phylogenomics.
Weitemier K, Straub SC, Cronn RC, Fishbein M, et al.
Appl Plant Sci. 2014 Aug 29;2(9).

SAGE: String-overlap Assembly of GEnomes.
Ilie L, Haider B, Molnar M, Solis-Oba R.
BMC Bioinformatics. 2014 Sep 15;15(1):302.

TELP, a sensitive and versatile library construction method for next-generation sequencing.
Peng X, Wu J, Brunmeir R, Kim SY, et al.
Nucleic Acids Res. 2014 Sep 15. [Epub ahead of print]

SSB binding to single-stranded DNA probed using solid-state nanopore sensors.
Japrung D, Bahrami A, Nadzeyka A, Peto L, et al.
J Phys Chem B. 2014 Sep 15. [Epub ahead of print]

Application of Ion Torrent sequencing to the assessment of the effect of alkali ballast water treatment on microbial community diversity.
Fujimoto M, Moyerbrailean GA, Noman S, Gizicki JP, et al.
PLOS One. 2014 Sep 15;9(9):e107534.

The Scan

Another Resignation

According to the Wall Street Journal, a third advisory panel member has resigned following the US Food and Drug Administration's approval of an Alzheimer's disease drug.

Novavax Finds Its Vaccine Effective

Reuters reports Novavax's SARS-CoV-2 vaccine is more than 90 percent effective in preventing COVID-19.

Can't Be Used

The US Food and Drug Administration says millions of vaccine doses made at an embattled manufacturing facility cannot be used, the New York Times reports.

PLOS Papers on Frozen Shoulder GWAS, Epstein-Barr Effects on Immune Cell Epigenetics, More

In PLOS this week: genome-wide association study of frozen shoulder, epigenetic patterns of Epstein-Barr-infected B lymphocyte cells, and more.