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Last Week's Sequencing-Related Papers of Note: Jan 21, 2014

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XS: a FASTQ read simulator.
Pratas DR, Pinho AJ, Rodrigues JM.
BMC Res Notes. 2014 Jan 16;7(1):40.


Phenotype to genotype using forward-genetic Mu-seq for identification and functional classification of maize mutants.
Hunter CT, Suzuki M, Saunders J, Wu S, et al.
Front Plant Sci. 2014 Jan 7;4:545.


The locust genome provides insight into swarm formation and long-distance flight.
Wang X, Fang X, Yang P, Jiang X, et al.
Nat Commun. 2014 Jan 14;5:2957.


Technical variations in low-input RNA-seq methodologies.
Bhargava V, Head SR, Ordoukhanian P, Mercola M, Subramaniam S.
Sci Rep. 2014 Jan 14;4:3678.


Reconstructing complex regions of genomes using long-read sequencing technology.
Huddleston J, Ranade S, Malig M, Antonacci F, et al.
Genome Res. 2014 Jan 13. [Epub ahead of print]


Whole genome sequence of a Turkish individual.
Dogan H, Can H, Otu HH.
PLoS One. 2014 Jan 9;9(1):e85233.


Transforming RNA-seq data to improve the performance of prognostic gene signatures.
Zwiener I, Frisch B, Binder H.
PLoS One. 2014 Jan 8;9(1):e85150.


An integrated framework for discovery and genotyping of genomic variants from high-throughput sequencing experiments.
Duitama J, Quintero JC, Cruz DF, Quintero C, et al.
Nucleic Acids Res. 2014 Jan 11. [Epub ahead of print]


BlindCall: ultra-fast base-calling of high-throughput sequencing data by blind deconvolution.
Ye C, Hsiao C, Bravo HC.
Bioinformatics. 2014 Jan 9. [Epub ahead of print]


Transcriptome in vivo analysis (TIVA) of spatially defined single cells in live tissue.
Lovatt D, Ruble BK, Lee J, Dueck H, et al.
Nat Methods. 2014 Jan 12. [Epub ahead of print]


Genome sequencing accuracy by RCA-seq versus long PCR template cloning and sequencing in identification of human papillomavirus type 58.
Wang X, Li Y, Ni T, Xie X, et al.
Cell Biosci. 2014 Jan 13;4(1):5.

The Scan

Just Breathing

A new analysis suggests that most Mycobacterium tuberculosis is spread by aerosols from breathing, rather than by coughing, the New York Times reports.

Just Like This One

NPR reports that the World Health Organization has hired a South African biotech company to recreate mRNA vaccine for SARS-CoV-2 that is similar to the one developed by Moderna.

Slow Start

The Wall Street Journal reports that Biogen's Alzheimer's disease treatment had revenues for July through September that totaled $300,000.

Genome Research Papers on Cancer Chromatin, Splicing in the Thymus, Circular RNAs in Cancer

In Genome Research this week: analysis of bivalent chromatin sites, RBFOX splicing factors' role in thymic epithelial cells, and more.