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Last Week's Sequencing-Related Papers of Note: Jan 28, 2014


Spatial blockage of ionic current for electrophoretic translocation of DNA through a graphene nanopore.
Lv W, Liu S, Li X, Wu R.
Electrophoresis. 2014 Jan 23. [Epub ahead of print]

ngsTools: methods for population genetics analyses from next-generation sequencing data.
Fumagalli M, Vieira FG, Linderoth T, Nielsen R.
Bioinformatics. 2014 Jan 23. [Epub ahead of print]

Transmissable dog cancer genome reveals the origin and history of an ancient cell lineage.
Murchison EP, Wedge DC, Alexandrov LB, Fu B, et al.
Science. 2014 Jan 24;343(6169):437-40.

Feasibility of whole RNA sequencing from single-cell mRNA amplification.
Xu Y, Hu H, Zheng J, Li B.
Genet Res Int. 2013;2013:724124.

STORMSeq: An open-source, user-friendly pipeline for processing personal genomics data in the cloud.
Karczewski KJ, Fernald GH, Martin AR1, Snyder M, et al.
PLoS One. 2014 Jan 15;9(1):e84860.

Comparison of RNA-seq and microarray in transcriptome profiling of activated T cells.
Zhao S, Fung-Leung WP, Bittner A, Ngo K, Liu X.
PLoS One. 2014 Jan 16;9(1):e78644.

Genome sequencing highlights the dynamic early history of dogs.
Freedman AH, Gronau I, Schweizer RM, Ortega-Del Vecchyo D, et al.
PLoS Genet. 2014 Jan;10(1):e1004016.

Which specimens from a museum collection will yield DNA barcodes? A time series study of spiders in alcohol.
Miller JA, Beentjes KK, van Helsdingen P, Ijland S.
Zookeys. 2013 Dec 30;(365):245-61.

Super-resolution optical DNA mapping via DNA methyltransferase-directed click chemistry.
Vranken C, Deen J, Dirix L, Stakenborg T, et al.
Nucleic Acids Res. 2014 Jan 21. [Epub ahead of print]

BLESS: Bloom-filter-based error correction solution for high-throughput sequencing reads.
Heo Y, Wu XL, Chen D, Ma J, Hwu WM.
Bioinformatics. 2014 Jan 21. [Epub ahead of print]

Microbial phylogenetic profiling with the Pacific Biosciences sequencing platform.
Fichot EB, Norman RS.
Microbiome. 2013 Mar 4;1(1):10.

Molecular indexing enables quantitative targeted RNA sequencing and reveals poor efficiencies in standard library preparations.
Fu GK, Xu W, Wilhelmy J, Mindrinos MN, et al.
Proc Natl Acad Sci U S A. 2014 Jan 21. [Epub ahead of print]

AG-NGS: A powerful and user-friendly computing application for the semi-automated preparation of next-generation sequencing libraries using open liquid handling platforms.
Callejas S, Alvarez R, Benguria A, Dopazo A.
Biotechniques. 2014 Jan;56(1):28-35.

High precision fabrication and positioning of nanoelectrodes in a nanopore.
Ivanov AP, Freedman KJ, Kim M, Albrecht T, Edel JB.
ACS Nano. 2014 Jan 21. [Epub ahead of print]

SeqBench: Integrated solution for the management and analysis of exome sequencing data.
Dander A, Pabinger S, Sperk M, Fischer M, et al.
BMC Res Notes. 2014 Jan 20;7(1):43.

Exploring genome characteristics and sequence quality without a reference.
Simpson JT.
Bioinformatics. 2014 Jan 17. [Epub ahead of print]

The Scan

Lung Cancer Response to Checkpoint Inhibitors Reflected in Circulating Tumor DNA

In non-small cell lung cancer patients, researchers find in JCO Precision Oncology that survival benefits after immune checkpoint blockade coincide with a dip in ctDNA levels.

Study Reviews Family, Provider Responses to Rapid Whole-Genome Sequencing Follow-up

Investigators identified in the European Journal of Human Genetics variable follow-up practices after rapid whole-genome sequencing.

BMI-Related Variants Show Age-Related Stability in UK Biobank Participants

Researchers followed body mass index variant stability with genomic structural equation modeling and genome-wide association studies of 40- to 72-year olds in PLOS Genetics.

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.