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Last Week's Sequencing-Related Papers of Note: May 6, 2014


Resequencing studies of nonmodel organisms using closely related reference genomes: optimal experimental designs and bioinformatics approaches for population genomics.
Nevado B, Ramos-Onsins SE, Perez-Enciso M.
Mol Ecol. 2014 Apr;23(7):1764-79.

Quantifying alternative splicing from paired-end RNA-sequencing data.
Rossell D, Stephan-Otto Attolini C, Kroiss M, Stöcker A.
Ann Appl Stat. 2014 Mar;8(1):309-330.

Towards error-free profiling of immune repertoires.
Shugay M, Britanova OV, Merzlyak EM, Turchaninova MA, et al.
Nat Methods. 2014 May 4. [Epub ahead of print]

Expanded genetic codes in next generation sequencing enable decontamination and mitochondrial enrichment.
McKernan KJ, Spangler J, Zhang L, Tadigotla V, et al.
PLoS One. 2014 May 2;9(5):e96492.

Reconstructing the DNA methylation maps of the Neandertal and the Denisovan.
Gokhman D, Lavi E, Prüfer K, Fraga MF, et al.
Science. 2014 May 2;344(6183):523-527.

ReadXplorer - visualization and analysis of mapped sequences.
Hilker R, Stadermann KB, Doppmeier D, Kalinowski J, et al.
Bioinformatics. 2014 Apr 30. [Epub ahead of print]

Impact of artifact removal on ChIP quality metrics in ChIP-seq and ChIP-exo data.
Carroll TS, Liang Z, Salama R, Stark R, de Santiago I.
Front Genet. 2014 Apr 10;5:75.

Microfluidic single-cell whole-transcriptome sequencing.
Streets AM, Zhang X, Cao C, Pang Y, et al.
Proc Natl Acad Sci U S A. 2014 Apr 29. [Epub ahead of print]

A programmable method for massively parallel targeted sequencing.
Hopmans ES, Natsoulis G, Bell JM, Grimes SM, et al.
Nucleic Acids Res. 2014 Apr 29. [Epub ahead of print]

Transcript mapping based on dRNA-seq data.
Bischler T, Kopf M, Voß B.
BMC Bioinformatics. 2014 Apr 29;15(1):122.

RECLU: a pipeline to discover reproducible transcriptional start sites and their alternative regulation using capped analysis of gene expression (CAGE).
Ohmiya H, Vitezic M, Frith MC, Itoh M, et al.
BMC Genomics. 2014 Apr 25;15(1):269.

The Scan

Purnell Choppin Dies

Purnell Choppin, a virologist who led the Howard Hughes Medical Institute, has died at 91, according to the Washington Post.

Effectiveness May Decline, Data From Israel Suggests

The New York Times reports that new Israeli data suggests a decline in Pfizer-BioNTech SARS-CoV-2 vaccine effectiveness against Delta variant infection, though protection against severe disease remains high.

To See Future Risk

Slate looks into the use of polygenic risk scores in embryo screening.

PLOS Papers on Methicillin-Resistant Staphylococcus, Bone Marrow Smear Sequencing, More

In PLOS this week: genomic analysis of methicillin-resistant Staphylococcus pseudintermedius, archived bone marrow sequencing, and more.