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Papers of Note: Oct 19, 2010


Mutation discovery by targeted genomic enrichment of multiplexed barcoded samples.
Nijman IJ, Mokry M, van Boxtel R, Toonen P, et al.
Nat Methods. 2010 Oct 17. [Epub ahead of print]

Ab initio identification of transcription start sites in the rhesus macaque genome by histone modification and RNA-seq.
Liu Y, Han D, Han Y, Yan Z, et al.
Nucleic Acids Res. 2010 Oct 14. [Epub ahead of print]

COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer.
Forbes SA, Bindal N, Bamford S, Cole C, et al.
Nucleic Acids Res. 2010 Oct 15. [Epub ahead of print]

Comparing de novo assemblers for 454 transcriptome data.
Kumar S, Blaxter ML.
BMC Genomics. 2010 Oct 16;11(1):571.

Data structures and compression algorithms for high-throughput sequencing technologies.
Daily K, Rigor P, Christley S, Xie X, Baldi P.
BMC Bioinformatics. 2010 Oct 14;11(1):514.

Somatic structural rearrangements in genetically engineered mouse mammary tumors.
Varela I, Klijn C, Stephens P, Mudie LJ, et al.
Genome Biol. 2010 Oct 13;11(10):R100.

Exome sequencing, ANGPTL3 mutations, and familial combined hypolipidemia.
Musunuru K, Pirruccello JP, Do R, Peloso GM, et al.
N Engl J Med. 2010 Oct 13. [Epub ahead of print]

Ultra-deep sequencing reveals the microRNA expression pattern of the human stomach.
Ribeiro-Dos-Santos A, Khayat AS, Silva A, Alencar DO, et al.
PLoS One. 2010 Oct 8;5(10). pii: e13205.

Geoseq: a tool for dissecting deep-sequencing datasets.
Gurtowski J, Cancio A, Shah H, George A, et al.
BMC Bioinformatics. 2010 Oct 12;11(1):506. [Epub ahead of print]

Representativeness of microsatellite distributions in genomes, as revealed by 454 GS-FLX Titanium pyrosequencing.
Martin JF, Pech N, Meglecz E, Ferreira S, et al.
BMC Genomics. 2010 Oct 12;11(1):560. [Epub ahead of print]

Genome-wide double-stranded RNA sequencing reveals the functional significance of base-paired RNAs in Arabidopsis.
Zheng Q, Ryvkin P, Li F, Dragomir I, et al.
PLoS Genet. 2010 Sep 30;6(9). pii: e1001141.

Use of robotics in high-throughput DNA sequencing.
Keeney S.
Methods Mol Biol. 2011;688:227-37.

Simulation of ion conduction in α-hemolysin nanopores with covalently attached β-cyclodextrin based on Boltzmann transport Monte Carlo model.
Toghraee R, Lee KI, Papke D, Chiu SW, et al.
J Comput Theor Nanosci. 2010 Dec;7(12):2555-2567.

Individuality in gut microbiota composition is a complex polygenic trait shaped by multiple environmental and host genetic factors.
Benson AK, Kelly SA, Legge R, Ma F, et al.
Proc Natl Acad Sci U S A. 2010 Oct 11. [Epub ahead of print]

Microbes and Health Sackler Colloquium: Human oral, gut, and plaque microbiota in patients with atherosclerosis.
Koren O, Spor A, Felin J, Fåk F, et al.
Proc Natl Acad Sci U S A. 2010 Oct 11. [Epub ahead of print]

A classification model for G-to-A hypermutation in hepatitis B virus ultra-deep pyrosequencing reads.
Reuman EC, Margeridon-Thermet S, Caudill HB, Liu T, et al.
Bioinformatics. 2010 Oct 11. [Epub ahead of print]

A comparison of DNA sequencing and the hydrolysis probe analysis (TaqMan assay) for knockdown resistance (kdr) mutations in Anopheles gambiae from the Republic of the Congo.
Choi KS, Spillings BL, Coetzee M, Hunt RH, Koekemoer LL.
Malar J. 2010 Oct 12;9(1):278.

Error tolerant indexing and alignment of short reads with covering template families.
Giladi E, Healy J, Myers G, Hart C, et al.
J Comput Biol. 2010 Oct;17(10):1279-93.

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.