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Papers of Note: Jun 21, 2011


Temporal analysis of the honey bee microbiome reveals four novel viruses and seasonal prevalence of known viruses, nosema, and crithidia.
Runckel C, Flenniken ML, Engel JC, et al.
PLoS One. 2011;6(6):e20656.

Genome-wide analysis of the relationships between DNaseI HS, histone modifications and gene expression reveals distinct modes of chromatin domains.
Shu W, Chen H, Bo X, Wang S.
Nucleic Acids Res. 2011 Jun 17. [Epub ahead of print]

Deep small RNA sequencing from the nematode Ascaris reveals conservation, functional diversification, and novel developmental profiles.
Wang J, Czech B, Crunk A, et al.
Genome Res. 2011 Jun 17. [Epub ahead of print]

Meta-IDBA: a de novo assembler for metagenomic data.
Peng Y, Leung HC, Yiu SM, Chin FY.
Bioinformatics. 2011 Jul 1;27(13):i94-i101.

Dynamic profiling of mRNA turnover reveals gene-specific and system-wide regulation of mRNA decay.
Munchel SE, Shultzaberger RK, Takizawa N, Weis K.
Mol Biol Cell. 2011 Jun 16. [Epub ahead of print]

Short read Illumina data for the de novo assembly of a non-model snail species transcriptome (Radix balthica, Basommatophora, Pulmonata), and a comparison of assembler performance.
Feldmeyer B, Wheat CW, Krezdorn N, et al.
BMC Genomics. 2011 Jun 16;12(1):317.

Illumina-based analysis of microbial community diversity.
Degnan PH, Ochman H.
ISME J. 2011 Jun 16. [Epub ahead of print]

Evaluation of next-generation sequencing software in mapping and assembly.
Bao S, Jiang R, Kwan W, et al.
J Hum Genet. 2011 Jun 16. [Epub ahead of print]

Multiplexed microsatellite recovery using massively parallel sequencing.
Jennings TN, Knaus BJ, Mullins TD, et al.
Mol Ecol Resour. 2011 Jun 16. [Epub ahead of print]

PRGmatic: an efficient pipeline for collating genome-enriched second-generation sequencing data using a 'provisional-reference genome'.
Hird SM, Brumfield RT, Carstens BC.
Mol Ecol Resour. 2011 Jul;11(4):743-8.

jMHC: software assistant for multilocus genotyping of gene families using next-generation amplicon sequencing.
Stuglik MT, Radwan J, Babik W.
Mol Ecol Resour. 2011 Jul;11(4):739-42.

High-throughput microsatellite isolation through 454 GS-FLX Titanium pyrosequencing of enriched DNA libraries.
Malausa T, Gilles A, Meglécz E, et al.
Mol Ecol Resour. 2011 Jul;11(4):638-644.

Second generation sequencing allows for mtDNA mixture deconvolution and high resolution detection of heteroplasmy.
Holland MM, McQuillan MR, O'Hanlon KA.
Croat Med J. 2011 Jun 15;52(3):299-313.

Efficient alignment of pyrosequencing reads for re-sequencing applications.
Fernandes F, da Fonseca PG, Russo LM, et al.
BMC Bioinformatics. 2011 May 16;12(1):163.

Characterization of single-nucleotide variation in Indian-origin Rhesus macaques (Macaca mulatta).
Fawcett GL, Raveendran M, Rio Deiros D, et al.
BMC Genomics. 2011 Jun 13;12(1):311.

Nanopore translocation dynamics of a single DNA-bound protein.
Spiering A, Getfert S, Sischka A, et al.
Nano Lett. 2011 Jun 13. [Epub ahead of print]

Fluorogenic DNA sequencing in PDMS microreactors.
Sims PA, Greenleaf WJ, Duan H, Xie XS.
Nat Methods. 2011 Jun 12. [Epub ahead of print]

Saliva is a reliable and practical source of germline DNA for genome-wide studies in chronic lymphocytic leukemia.
Rasi S, Bruscaggin A, Rinaldi A, et al.
Leuk Res. 2011 Jun 8. [Epub ahead of print]

Estimation of allele frequency and association mapping using next-generation sequencing data.
Kim SY, Lohmueller KE, Albrechtsen A, et al.
BMC Bioinformatics. 2011 Jun 11;12(1):231.

Controlling DNA translocation through gate modulation of nanopore wall surface charges.
He Y, Tsutsui M, Fan C, Taniguchi M, Kawai T.
ACS Nano. 2011 Jun 13. [Epub ahead of print]

The Scan

Single-Cell Sequencing Points to Embryo Mosaicism

Mosaicism may affect preimplantation genetic tests for aneuploidy, a single-cell sequencing-based analysis of almost three dozen embryos in PLOS Genetics finds.

Rett Syndrome Mouse Model Study Points to RNA Editing Possibilities

Investigators targeted MECP2 in mutant mouse models of Rett syndrome, showing in PNAS that they could restore its expression and dial down symptoms.

Investigators Find Shared, Distinct Genetic Contributors to Childhood Hodgkin Lymphoma

An association study in JAMA Network Open uncovers risk variants within and beyond the human leukocyte antigen locus.

Transcriptomic, Epigenetic Study Appears to Explain Anti-Viral Effects of TB Vaccine

Researchers report in Science Advances on an interferon signature and long-term shifts in monocyte cell DNA methylation in Bacille Calmette-Guérin-vaccinated infant samples.