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Recent Sequencing-Related Papers of Note: Aug 12, 2014

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SciClone: inferring clonal architecture and tracking the spatial and temporal patterns of tumor evolution.
Miller CA, White BS, Dees ND, Griffith M, et al.
PLOS Comput Biol. 2014 Aug 7;10(8):e1003665.


Validation of high throughput sequencing and microbial forensics applications.
Budowle B, Connell ND, Bielecka-Oder A, Colwell RR, et al.
Investig Genet. 2014 Jul 30;5:9.


leeHom: adaptor trimming and merging for Illumina sequencing reads.
Renaud G, Stenzel U, Kelso J.
Nucleic Acids Res. 2014 Aug 6. [Epub ahead of print]


Enhancing the detection of barcoded reads in high throughput DNA sequencing data by controlling the false discovery rate.
Buschmann T, Zhang R, Brash DE, Bystrykh LV.
BMC Bioinformatics. 2014 Aug 7;15(1):264.


Comparative genomics of 274 Vibrio cholerae genomes reveals mobile functions structuring three niche dimensions.
Dutilh BE, Thompson CC, Vicente AC, Marin MA, et al.
BMC Genomics. 2014 Aug 5;15(1):654.


Cell fate inclination within 2-cell and 4-cell mouse embryos revealed by single-cell RNA sequencing.
Biase F, Cao X, Zhong S.
Genome Res. 2014 Aug 5. [Epub ahead of print]


Selective whole genome amplification for re-sequencing target microbial species from complex natural samples.
Leichty AR, Brisson D.
Genetics. 2014 Aug 5. [Epub ahead of print]


A new system identification approach to identify genetic variants in sequencing studies for a binary phenotype.
Kang G, Bi W, Zhao Y, Zhang JF, et al.
Hum Hered. 2014 Jul 30;78(2):104-116.


DNAApp: a mobile application for sequencing data analysis.
Nguyen PV, Verma CS, Gan SK.
Bioinformatics. 2014 Aug 5. [Epub ahead of print]


Cytosine deamination is a major cause of baseline noise in next-generation sequencing.
Chen G, Mosier S, Gocke CD, Lin MT, Eshleman JR.
Mol Diagn Ther. 2014 Aug 5. [Epub ahead of print]


Distinctive thanatomicrobiome signatures found in the blood and internal organs of humans.
Can I, Javan GT, Pozhitkov AE, Noble PA.
J Microbiol Methods. 2014 Aug 1. [Epub ahead of print]


The complete mitochondrial genome of Leizhou goat Capra hircus (Bovidae; Caprinae).
Sun LQ, Guo GL, Wu JY, Zhang L.
Mitochondrial DNA. 2014 Jul 31:1-2.


Tn5 transposase and tagmentation procedures for massively-scaled sequencing projects.
Picelli S, Björklund AK, Reinius B, Sagasser S, et al.
Genome Res. 2014 Jul 30. [Epub ahead of print]


The DNA methylation landscape of human early embryos.
Guo H, Zhu P, Yan L, Li R, et al.
Nature. 2014 Jul 31;511(7511):606-610.


Whole genome sequencing of the Mycobacterium tuberculosis Manila sub-lineage results in better resolution than MIRU-VNTR and spoligotype.
Jamieson FB, Teatero S, Guthrie JL, Neemuchwala A, et al.
J Clin Microbiol. 2014 Jul 30. [Epub ahead of print]


Validation and assessment of variant calling pipelines for next-generation sequencing.
Pirooznia M, Kramer M, Parla J, Goes F, et al.
Hum Genomics. 2014 Jul 30;8(1):14.


Employing whole genome mapping for optimal de novo assembly of bacterial genomes.
Xavier BB, Sabirova J, Pieter M, Hernalsteens JP, et al.
BMC Res Notes. 2014 Jul 30;7(1):484.


Fast and sensitive alignment of microbial whole genome sequencing reads to large sequence datasets on a desktop PC: application to metagenomic datasets and pathogen identification.
Pongor LS, Vera R, Ligeti B.
PLOS One. 2014 Jul 31;9(7):e103441.


Transcriptome of the female synganglion of the black-legged tick Ixodes scapularis (acari: Ixodidae) with comparison between Illumina and 454 systems.
Egekwu N, Sonenshine DE, Bissinger BW, Roe RM.
PLOS One. 2014 Jul 30;9(7):e102667.


Rapid detection, complete genome sequencing, and phylogenetic analysis of porcine deltacoronavirus.
Marthaler D, Raymond L, Jiang Y, Collins J, et al.
Emerg Infect Dis. 2014 Aug;20(8).


Whole-genome bisulfite sequencing of multiple individuals reveals complementary roles of promoter and gene body methylation in transcriptional regulation.
Lou S, Lee HM, Qin H, Li JW, et al.
Genome Biol. 2014 Jul 30;15(7):408.


Single-cell genome-wide bisulfite sequencing for assessing epigenetic heterogeneity.
Smallwood SA, Lee HJ, Angermueller C, Krueger F, et al.
Nat Methods. 2014 Aug;11(8):817-20.


Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle.
Daetwyler HD, Capitan A, Pausch H, Stothard P, et al.
Nat Genet. 2014 Aug;46(8):858-65.


Mutational signatures in Helicobacter pylori-induced gastric cancer: lessons from new sequencing technologies.
Derks S, Bass AJ.
Gastroenterology. 2014 Aug;147(2):267-9.


Using next-generation RNA sequencing to identify imprinted genes.
Wang X, Clark AG.
Heredity (Edinb). 2014 Aug;113(2):156-66.


A bead-based normalization for uniform sequencing depth (BeNUS) protocol for multi-samples sequencing exemplified by HLA-B.
Hosomichi K, Mitsunaga S, Nagasaki H, Inoue I.
BMC Genomics. 2014 Aug 4;15(1):645.


Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex.
Pollen AA, Nowakowski TJ, Shuga J, Wang X, et al.
Nat Biotechnol. 2014 Aug 3. [Epub ahead of print]

The Scan

Another Resignation

According to the Wall Street Journal, a third advisory panel member has resigned following the US Food and Drug Administration's approval of an Alzheimer's disease drug.

Novavax Finds Its Vaccine Effective

Reuters reports Novavax's SARS-CoV-2 vaccine is more than 90 percent effective in preventing COVID-19.

Can't Be Used

The US Food and Drug Administration says millions of vaccine doses made at an embattled manufacturing facility cannot be used, the New York Times reports.

PLOS Papers on Frozen Shoulder GWAS, Epstein-Barr Effects on Immune Cell Epigenetics, More

In PLOS this week: genome-wide association study of frozen shoulder, epigenetic patterns of Epstein-Barr-infected B lymphocyte cells, and more.