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Last Week's Sequencing-Related Papers of Note: Feb 25, 2014

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Assessing single nucleotide variant detection and genotype calling on whole-genome sequenced individuals.
Cheng AY, Teo YY, Ong RT.
Bioinformatics. 2014 Feb 19. [Epub ahead of print]


Detecting authorized and unauthorized genetically modified organisms containing vip3A by real-time PCR and next-generation sequencing.
Liang C1, van Dijk JP, Scholtens IM, Staats M, et al.
Anal Bioanal Chem. 2014 Feb 20. [Epub ahead of print]


Synthesis of nucleoside 5'-tetraphosphates containing terminal fluorescent labels via activated cyclic trimetaphosphate.
Mohamady S, Taylor SD.
J Org Chem. 2014 Feb 19. [Epub ahead of print]


Detection of structural variants involving repetitive regions in the reference genome.
Lee H, Popodi E, Foster PL, Tang H.
J Comput Biol. 2014 Feb 19. [Epub ahead of print]


Integrated genomic characterization reveals novel, therapeutically relevant drug targets in FGFR and EGFR pathways in sporadic intrahepatic cholangiocarcinoma.
Borad MJ, Champion MD, Egan JB, Liang WS, et al.
PLOS Genet. 2014 Feb 13;10(2):e1004135.


The Spirodela polyrhiza genome reveals insights into its neotenous reduction fast growth and aquatic lifestyle.
Wang W, Haberer G, Gundlach H, Gläßer C, et al.
Nat Commun. 2014 Feb 19;5:3311.


Atomically thin molybdenum disulfide nanopores with high sensitivity for DNA translocation.
Liu K, Feng J, Kis A, Radenovic A.
ACS Nano. 2014 Feb 18. [Epub ahead of print]


SeqGSEA: a Bioconductor package for gene set enrichment analysis of RNA-seq data integrating differential expression and splicing.
Wang X, Cairns MJ.
Bioinformatics. 2014 Feb 17. [Epub ahead of print]


Fifty thousand years of Arctic vegetation and megafaunal diet.
Willerslev E, Davison J, Moora M, Zobel M, et al.
Nature. 2014 Feb 6;506(7486):47-51.


SOAPdenovo-Trans: De novo transcriptome assembly with short RNA-seq reads.
Xie Y, Wu G, Tang J, Luo R, et al.
Bioinformatics. 2014 Feb 13. [Epub ahead of print]


Massively parallel single-cell RNA-seq for marker-free decomposition of tissues into cell types.
Jaitin DA, Kenigsberg E, Keren-Shaul H, Elefant N, et al.
Science. 2014 Feb 14;343(6172):776-9.


Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls.
Zook JM, Chapman B, Wang J, Mittelman D, et al.
Nat Biotechnol. 2014 Feb 16. [Epub ahead of print]


Sequencing, assembling, and correcting draft genomes using recombinant populations.
Hahn MW, Zhang SV, Moyle LC.
G3 (Bethesda). 2014 Feb 13. [Epub ahead of print]


Ancient whole genome enrichment using baits built from modern DNA.
Enk J, Devault A, Kuch M, Murgha Y, et al.
Mol Biol Evol. 2014 Feb 13. [Epub ahead of print]


Finding the needle in the haystack: Differentiating "identical" twins in paternity testing and forensics by ultra-deep next generation sequencing.
Weber-Lehmann J, Schilling E, Gradl G, Richter DC, et al.
Forensic Sci Int Genet. 2014 Mar;9C:42-46.
(See our coverage of this paper here.)


My-Forensic-Loci-queries (MyFLq) framework for analysis of forensic STR data generated by massive parallel sequencing.
Van Neste C, Vandewoestyne M, Van Criekinge W, Deforce D, Van Nieuwerburgh F.
Forensic Sci Int Genet. 2014 Mar;9C:1-8.

The Scan

And For Adolescents

The US Food and Drug Administration has authorized the Pfizer-BioNTech SARS-CoV-2 vaccine for children between the ages of 12 and 15 years old.

Also of Concern to WHO

The Wall Street Journal reports that the World Health Organization has classified the SARS-CoV-2 variant B.1.617 as a "variant of concern."

Test for Them All

The New York Times reports on the development of combined tests for SARS-CoV-2 and other viruses like influenza.

PNAS Papers on Oral Microbiome Evolution, Snake Toxins, Transcription Factor Binding

In PNAS this week: evolution of oral microbiomes among hominids, comparative genomic analysis of snake toxins, and more.