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In Print: Last Week's Sequencing-Related Papers of Note: Jul 3, 2012


The PhyloPythiaS web server for taxonomic assignment of metagenome sequences.
Patil KR, Roune L, McHardy AC.
PLoS One. 2012;7(6):e38581.

RSeQC: Quality control of RNA-seq experiments.
Wang L, Wang S, Li W.
Bioinformatics. 2012 Jun 27. [Epub ahead of print]

Efficient recovery of whole blood RNA — a comparison of commercial RNA extraction protocols for high-throughput applications in wildlife species.
Schwochow D, Serieys LE, Wayne RK, Thalmann O.
BMC Biotechnol. 2012 Jun 27;12(1):33.

SVM2: an improved paired-end-based tool for the detection of small genomic structural variations using high-throughput single-genome resequencing data.
Chiara M, Pesole G, Horner DS.
Nucleic Acids Res. 2012 Jun 25. [Epub ahead of print]

Genome sequence of the model medicinal mushroom Ganoderma lucidum.
Chen S, Xu J, Liu C, Zhu Y, et al.
Nat Commun. 2012 Jun 26;3:913.

Rapid genome-scale mapping of chromatin accessibility in tissue.
Grøntved L, Bandle R, John S, Baek S, et al.
Epigenetics Chromatin. 2012 Jun 26;5(1):10.

Genomic sequencing of Plasmodium falciparum malaria parasites from Senegal reveals the demographic history of the population.
Chang HH, Park DJ, Galinsky KJ, Schaffner SF, et al.
Mol Biol Evol. 2012 Jun 24. [Epub ahead of print]

Toward almost closed genomes with GapFiller.
Boetzer M, Pirovano W.
Genome Biol. 2012 Jun 25;13(6):R56.

Changes in genome content generated via segregation of non-allelic homologs.
Liu S, Ying K, Yeh CT, Yang J, et al.
Plant J. 2012 Jun 25. [Epub ahead of print]

The Scan

Study Finds Sorghum Genetic Loci Influencing Composition, Function of Human Gut Microbes

Focusing on microbes found in the human gut microbiome, researchers in Nature Communications identified 10 sorghum loci that appear to influence the microbial taxa or microbial metabolite features.

Treatment Costs May Not Coincide With R&D Investment, Study Suggests

Researchers in JAMA Network Open did not find an association between ultimate treatment costs and investments in a drug when they analyzed available data on 60 approved drugs.

Sleep-Related Variants Show Low Penetrance in Large Population Analysis

A limited number of variants had documented sleep effects in an investigation in PLOS Genetics of 10 genes with reported sleep ties in nearly 192,000 participants in four population studies.

Researchers Develop Polygenic Risk Scores for Dozens of Disease-Related Exposures

With genetic data from two large population cohorts and summary statistics from prior genome-wide association studies, researchers came up with 27 exposure polygenic risk scores in the American Journal of Human Genetics.