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In Print: Last Week's Sequencing-Related Papers of Note: Jul 2, 2013


The Million Mutation Project: A new approach to genetics in Caenorhabditis elegans.
Thompson O, Edgley M, Strasbourger P, Flibotte S, et al.
Genome Res. 2013 Jun 25. [Epub ahead of print]

Laser microdissection coupled with RNA-seq analysis of porcine enterocytes infected with an obligate intracellular pathogen (Lawsonia intracellularis) .
Vannucci FA, Foster DN, Gebhart CJ.
BMC Genomics. 2013 Jun 24;14(1):421.

Lessons learned from implementing a national infrastructure in Sweden for storage and analysis of next-generation sequencing data.
Lampa S, Dahlö M, Olason PI, Hagberg J, Spjuth O.
Gigascience. 2013 Jun 25;2(1):9.

Beyond classification: gene-family phylogenies from shotgun metagenomic reads enable accurate community analysis.
Riesenfeld SJ, Pollard KS.
BMC Genomics. 2013 Jun 22;14(1):419.

A filtering method to generate high quality short reads using Illumina paired-end technology.
Eren AM, Vineis JH, Morrison HG, Sogin ML.
PLoS One. 2013 Jun 17;8(6):e66643.

A strategy to capture and characterize the synaptic transcriptome.
Puthanveettil SV, Antonov I, Kalachikov S, Rajasethupathy P, et al.
Proc Natl Acad Sci U S A. 2013 Apr 30;110(18):7464-9.

miReader: discovering novel miRNAs in species without sequenced genome.
Jha A, Shankar R.
PLoS One. 2013 Jun 21;8(6):e66857.

A re-sequencing based assessment of genomic heterogeneity and fast neutron-induced deletions in a common bean cultivar.
O'Rourke JA, Iniguez LP, Bucciarelli B, Roessler J, et al.
Front Plant Sci. 2013 Jun 25;4:210.

Estimating absolute methylation levels at single CpG resolution from methylation enrichment and restriction enzyme sequencing methods.
Stevens M, Cheng JB, Li D, Xie M, et al.
Genome Res. 2013 Jun 26. [Epub ahead of print]

Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm.
Zhang B, Zhou Y, Lin N, Lowdon RF, et al.
Genome Res. 2013 Jun 26. [Epub ahead of print]

Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse.
Orlando L, Ginolhac A, Zhang G, Froese D, et al.
Nature. 2013 Jun 26. [Epub ahead of print]

Bi-PROF: Bisulfite profiling of target regions using 454 GS FLX Titanium technology.
Gries J, Schumacher D, Arand J, Lutsik P, et al.
Epigenetics. 2013 Jun 10;8(7).

Pressure-controlled motion of single polymers through solid-state nanopores.
Lu B, Hoogerheide D, Zhao Q, Zhang H, et al.
Nano Lett. 2013 Jun 26. [Epub ahead of print]

Rainbow: a tool for large-scale whole-genome sequencing data analysis using cloud computing.
Zhao S, Prenger K, Smith L, Messina T, et al.
BMC Genomics. 2013 Jun 27;14(1):425.

Taxonomic profiling and metagenome analysis of a microbial community from a habitat contaminated with industrial discharges.
Shah V, Zakrzewski M, Wibberg D, Eikmeyer F, et al.
Microb Ecol. 2013 Jun 25. [Epub ahead of print]

Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden.
Long Q, Rabanal FA, Meng D, Huber CD, et al.
Nat Genet. 2013 Jun 23. [Epub ahead of print]

DNase I-hypersensitive exons colocalize with promoters and distal regulatory elements.
Mercer TR, Edwards SL, Clark MB, Neph SJ, et al.
Nat Genet. 2013 Jun 23. [Epub ahead of print]

A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italic) .
Jia G, Huang X, Zhi H, Zhao Y, et al.
Nat Genet. 2013 Jun 23. [Epub ahead of print]

Comparison of the distal gut microbiota from people and animals in Africa.
Ellis RJ, Bruce KD, Jenkins C, Stothard JR, et al.
PLoS One. 2013;8(1):e54783.

The Scan

Not Yet a Permanent One

NPR says the lack of a permanent Food and Drug Administration commissioner has "flummoxed" public health officials.

Unfair Targeting

Technology Review writes that a new report says the US has been unfairly targeting Chinese and Chinese-American individuals in economic espionage cases.

Limited Rapid Testing

The New York Times wonders why rapid tests for COVID-19 are not widely available in the US.

Genome Research Papers on IPAFinder, Structural Variant Expression Effects, Single-Cell RNA-Seq Markers

In Genome Research this week: IPAFinder method to detect intronic polyadenylation, influence of structural variants on gene expression, and more.