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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

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.