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In Print: Last Week's Sequencing-Related Papers of Note: Apr 10, 2012


Improving RNA-seq precision with MapAl.
Labaj PP, Linggi BE, Wiley HS, Kreil DP.
Front Genet. 2012;3:28. Epub 2012 Apr 2.

Digital polymerase chain reaction in an array of femtoliter PDMS microreactors.
Men Y, Fu Y, Chen Z, Sims PA, et al.
Anal Chem. 2012 Apr 7. [Epub ahead of print]

Highly multiplexed and strand-specific single-cell RNA 5' end sequencing.
Islam S, Kjällquist U, Moliner A, Zajac P, et al.
Nat Protoc. 2012 Apr 5;7(5):813-28.

The genomic basis of adaptive evolution in threespine sticklebacks.
Jones FC, Grabherr MG, Chan YF, Russell P, et al.
Nature. 2012 Apr 4;484(7392):55-61.

VESPA: software to facilitate genomic annotation of prokaryotic organisms through integration of proteomic and transcriptomic data.
Peterson ES, McCue LA, Schrimpe-Rutledge AC, Jensen JL, et al.
BMC Genomics. 2012 Apr 5;13(1):131.

Exploring the switchgrass transcriptome using second-generation sequencing technology.
Wang Y, Zeng X, Iyer NJ, Bryant DW, et al.
PLoS One. 2012;7(3):e34225.

Reconstructing viral genomes from the environment using fosmid clones: the case of haloviruses.
Garcia-Heredia I, Martin-Cuadrado AB, Mojica FJ, Santos F, et al.
PLoS One. 2012;7(3):e33802.

A combined approach of high-throughput sequencing and degradome analysis reveals tissue specific expression of microRNAs and their targets in cucumber.
Mao W, Li Z, Xia X, Li Y, Yu J.
PLoS One. 2012;7(3):e33040.

Critical evaluation of imprinted gene expression by RNA-seq: a new perspective.
Deveale B, van der Kooy D, Babak T.
PLoS Genet. 2012 Mar;8(3):e1002600.

A normalization strategy for comparing tag count data.
Kadota K, Nishiyama T, Shimizu K.
Algorithms Mol Biol. 2012 Apr 5;7(1):5.

Deep sequencing the circadian and diurnal transcriptome of Drosophila brain.
Hughes ME, Grant GR, Paquin C, Qian J, Nitabach MN.
Genome Res. 2012 Apr 3. [Epub ahead of print]

Allele discovery of ten candidate drought-response genes in Austrian oak using a systematically informatics approach based on 454 amplicon sequencing.
Homolka A, Eder T, Kopecky D, Berenyi M, et al.
BMC Res Notes. 2012 Apr 3;5(1):175.

Genome sequence and transcriptome analysis of the radioresistant bacterium Deinococcus gobiensis: insights into the extreme environmental adaptations.
Yuan M, Chen M, Zhang W, Lu W, et al.
PLoS One. 2012;7(3):e34458.

Next-generation phylogeography: a targeted approach for multilocus sequencing of non-model organisms.
Puritz JB, Addison JA, Toonen RJ.
PLoS One. 2012;7(3):e34241.

De-novo assembly and analysis of the heterozygous triploid genome of the wine spoilage yeast Dekkera bruxellensis AWRI1499.
Curtin CD, Borneman AR, Chambers PJ, Pretorius IS.
PLoS One. 2012;7(3):e33840.

A genome-wide identification analysis of small regulatory RNAs in Mycobacterium tuberculosis by RNA-seq and conservation analysis.
Pellin D, Miotto P, Ambrosi A, Cirillo DM, Di Serio C.
PLoS One. 2012;7(3):e32723.

CONTRA: copy number analysis for targeted resequencing.
Li J, Lupat R, Amarasinghe KC, Thompson ER, et al.
Bioinformatics. 2012 Apr 2. [Epub ahead of print]

Genome analysis of the domestic dog (Korean Jindo) by massively parallel sequencing.
Kim RN, Kim DS, Choi SH, Yoon BH, et al.
DNA Res. 2012 Apr 3. [Epub ahead of print]

The Scan

Myotonic Dystrophy Repeat Detected in Family Genome Sequencing Analysis

While sequencing individuals from a multi-generation family, researchers identified a myotonic dystrophy type 2-related short tandem repeat in the European Journal of Human Genetics.

TB Resistance Insights Gleaned From Genome Sequence, Antimicrobial Response Assays

Researchers in PLOS Biology explore M. tuberculosis resistance with a combination of sequencing and assays looking at the minimum inhibitory concentrations of 13 drugs.

Mendelian Disease Genes Prioritized Using Tissue-Specific Expression Clues

Mendelian gene candidates could be flagged for further functional analyses based on tissue-specific transcriptome and proteome profiles, a new Journal of Human Genetics paper says.

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.