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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

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.