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


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

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.