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In Print: Last Week's Sequencing-Related Papers of Note: Jun 11, 2013

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Error analysis of idealized nanopore sequencing.
O'Donnell CR, Wang H, Dunbar WB.
Electrophoresis. 2013 Jun 7. [Epub ahead of print]


Identification of household bacterial community and analysis of species shared with human microbiome.
Jeon YS, Chun J, Kim BS.
Curr Microbiol. 2013 Jun 7. [Epub ahead of print]


Whole exome sequencing reveals minimal differences between cell line and whole blood derived DNA.
Schafer CM, Campbell NG, Cai G, Yu F, et al.
Genomics. 2013 Jun 3. [Epub ahead of print]


REDItools: high-throughput RNA editing detection made easy.
Picardi E, Pesole G.
Bioinformatics. 2013 Jun 5. [Epub ahead of print]


Sequencing viral genomes from a single isolated plaque.
Depew J, Zhou B, McCorrison JM, Wentworth DE, et al.
Virol J. 2013 Jun 6;10(1):181.


SOAP3-dp: fast, accurate and sensitive GPU-based short read aligner.
Luo R, Wong T, Zhu J, Liu CM, et al.
PLoS One. 2013 May 31;8(5):e65632.


Complete genome phasing of family quartet by combination of genetic, physical and population-based phasing analysis.
Lajugie J, Mukhopadhyay R, Schizas M, Lailler N, et al.
PLoS One. 2013 May 31;8(5):e64571.


Encore: genetic association interaction network centrality pipeline and application to SLE exome data.
Davis NA, Lareau CA, White BC, Pandey A, et al.
Genet Epidemiol. 2013 Jun 5. [Epub ahead of print]


Clustering Acinetobacter strains by optical mapping.
Hall BG, Kirkup BC, Riley MC, Barlow M.
Genome Biol Evol. 2013 Jun 5. [Epub ahead of print]


Characterization of the fungal microbiome (mycobiome) in fecal samples from dogs.
Foster ML, Dowd SE, Stephenson C, Steiner JM, Suchodolski JS.
Vet Med Int. 2013;2013:658373. Epub 2013 Apr 23.


A hierarchical Bayesian model for estimating and inferring differential isoform expression for multi-sample RNA-seq data.
Vardhanabhuti S, Li M, Li H.
Stat Biosci. 2013 May 1;5(1):119-137.


Single nucleotide polymorphism typing with massively parallel sequencing for human identification.
Seo SB, King JL, Warshauer DH, Davis CP, et al.
Int J Legal Med. 2013 Jun 5. [Epub ahead of print]


NGS++: a library for rapid prototyping of epigenomics software tools.
Nordell Markovits A, Joly Beauparlant C, Toupin D, Wang S, et al.
Bioinformatics. 2013 Jun 4. [Epub ahead of print]


Isaac: Ultra-fast whole genome secondary analysis on Illumina sequencing platforms.
Raczy C, Petrovski R, Saunders CT, Chorny I, et al.
Bioinformatics. 2013 Jun 4. [Epub ahead of print]


Modeling the DNA copy number aberration patterns in observational high-throughput cancer data.
van Wieringen WN, Roś BP, Wilting SM.
Stat Appl Genet Mol Biol. 2013 Apr 19;12(2):143-74.


DNA origami nanopores for controlling DNA translocation.
Hernández-Ainsa S, Bell NA, Thacker VV, Göpfrich K, et al.
ACS Nano. 2013 Jun 4. [Epub ahead of print]


Radiation resistance of sequencing chips for in situ life detection.
Carr CE, Rowedder H, Lui CS, Zlatkovsky I, et al.
Astrobiology. 2013 Jun 4. [Epub ahead of print]


Draft genome sequence, and a sequence-defined genetic linkage map of the legume crop species Lupinus angustifolius L.
Yang H, Tao Y, Zheng Z, Zhang Q, et al.
PLoS One. 2013 May 29;8(5):e64799.


Comparative transcriptome profiling reveals different expression patterns in Xanthomonas oryzae pv. oryzae strains with putative virulence-relevant genes.
Zhang F, Du Z, Huang L, Cruz CV, et al.
PLoS One. 2013 May 29;8(5):e64267.


Informed and automated k-mer size selection for genome assembly.
Chikhi R, Medvedev P.
Bioinformatics. 2013 Jun 3. [Epub ahead of print]


Relating genes to function: identifying enriched transcription factors using the ENCODE ChIP-seq significance tool.
Auerbach RK, Chen B, Butte AJ.
Bioinformatics. 2013 Jun 3. [Epub ahead of print]


A quantitative reference transcriptome for Nematostella vectensis early embryonic development: a pipeline for de novo assembly in emerging model systems.
Tulin S, Aguiar D, Istrail S, Smith J.
Evodevo. 2013 Jun 3;4(1):16.


The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color.
Motamayor JC, Mockaitis K, Schmutz J, Haiminen N, et al.
Genome Biol. 2013 Jun 3;14(6):R53.


Estimation of population allele frequencies from next-generation sequencing data: pool-versus individual-based genotyping.
Gautier M, Foucaud J, Gharbi K, Cézard T, et al.
Mol Ecol. 2013 Jun 4. [Epub ahead of print]


On estimation of allele frequencies via next-generation DNA resequencing with barcoding.
Lee JS, Zhao H.
Stat Biosci. 2013 May 1;5(1):26-53.


The non-obese diabetic mouse sequence, annotation and variation resource: an aid for investigating type 1 diabetes.
Steward CA, Gonzalez JM, Trevanion S, Sheppard D, et al.
Database (Oxford). 2013 May 31;2013(0):bat032.

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.