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In Print: Last Week's Sequencing-Related Papers of Note: Feb 28, 2012


Winnowing DNA for rare sequences: highly specific sequence and methylation based enrichment.
Thompson JD, Shibahara G, Rajan S, Pel J, Marziali A.
PLoS One. 2012;7(2):e31597.

nMETR: Technique for facile recovery of hypomethylation genomic tags.
Baskaev K, Garazha A, Gaifullin N, Suntsova MV, et al.
Gene. 2012 Feb 13. [Epub ahead of print]

Modeling RNA degradation for RNA-seq with applications.
Wan L, Yan X, Chen T, Sun F.
Biostatistics. 2012 Feb 21. [Epub ahead of print]

Genoviewer, a SAM/BAM viewer tool.
Laczik M, Tukacs E, Uzonyi B, Domokos B, et al.
Bioinformation. 2012;8(2):107-9.

Transcriptome characterization and sequencing-based identification of salt-responsive genes in Millettia pinnata, a semi-mangrove plant.
Huang J, Lu X, Yan H, Chen S, et al.
DNA Res. 2012 Feb 19. [Epub ahead of print]

High-throughput sequencing-based gene profiling on multi-staged fruit development of date palm (Phoenix dactylifera, L.) .
Yin Y, Zhang X, Fang Y, Pan L, et al.
Plant Mol Biol. 2012 Feb 21. [Epub ahead of print]

Identifying insecticide resistance genes in mosquito by combining AFLP genome scans and 454 pyrosequencing.
Paris M, Despres L.
Mol Ecol. 2012 Feb 20. [Epub ahead of print]

Rapid microsatellite identification from Illumina paired-end genomic sequencing in two birds and a snake.
Castoe TA, Poole AW, de Koning AP, Jones KL, et al.
PLoS One. 2012;7(2):e30953.

Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample.
Luo C, Tsementzi D, Kyrpides N, Read T, Konstantinidis KT.
PLoS One. 2012;7(2):e30087.

Transcriptomic analysis of rice (Oryza sativa) developing embryos using the RNA-seq technique.
Xu H, Gao Y, Wang J.
PLoS One. 2012;7(2):e30646.

Transcriptome analysis of the model protozoan, Tetrahymena thermophila, using deep RNA sequencing.
Xiong J, Lu X, Zhou Z, Chang Y, Yuan D, et al.
PLoS One. 2012;7(2):e30630.

Whole genome resequencing reveals natural target site preferences of transposable elements in Drosophila melanogaster.
Linheiro RS, Bergman CM.
PLoS One. 2012;7(2):e30008.

Signal analysis for genome wide maps of histone modifications measured by ChIP-seq.
Beck D, Brandl MB, Boelen L, Unnikrishnan A, Pimanda JE.
Bioinformatics. 2012 Feb 17. [Epub ahead of print]

RNA-seq Atlas - A reference database for gene expression profiling in normal tissue by next generation sequencing.
Krupp M, Marquardt JU, Sahin U, Galle PR, et al.
Bioinformatics. 2012 Feb 17. [Epub ahead of print]

GMD: Measuring the distance between histograms with applications on high-throughput sequencing reads.
Zhao X, Sandelin A.
Bioinformatics. 2012 Feb 17. [Epub ahead of print]

Homology-independent discovery of replicating pathogenic circular RNAs by deep sequencing and a new computational algorithm.
Wu Q, Wang Y, Cao M, Pantaleo V, et al.
Proc Natl Acad Sci U S A. 2012 Feb 15. [Epub ahead of print]

A differential sequencing-based analysis of the C. elegans noncoding transcriptome.
Xiao T, Wang Y, Luo H, Liu L, et al.
RNA. 2012 Feb 16. [Epub ahead of print]

Widespread occurrence of 5-methylcytosine in human coding and non-coding RNA.
Squires JE, Patel HR, Nousch M, Sibbritt T, et al.
Nucleic Acids Res. 2012 Feb 16. [Epub ahead of print]

Comparison of alignment software for genome-wide bisulphite sequence data.
Chatterjee A, Stockwell PA, Rodger EJ, Morison IM.
Nucleic Acids Res. 2012 Feb 16. [Epub ahead of print]

Profiling of the metabolically active community from a production-scale biogas plant by means of high-throughput metatranscriptome sequencing.
Zakrzewski M, Goesmann A, Jaenicke S, Jünemann S, et al.
J Biotechnol. 2012 Feb 8. [Epub ahead of print]

Spatial organization of the mouse genome and its role in recurrent chromosomal translocations.
Zhang Y, McCord RP, Ho YJ, Lajoie BR, et al.
Cell. 2012 Feb 15. [Epub ahead of print]

Genome sequencing and analysis of the tasmanian devil and its transmissible cancer.
Murchison EP, Schulz-Trieglaff OB, Ning Z, Alexandrov LB, et al.
Cell. 2012 Feb 17;148(4):780-91.

Whole-genome sequencing and genetic variant analysis of a Quarter horse mare.
Doan R, Cohen ND, Sawyer J, Ghaffari N, et al.
BMC Genomics. 2012 Feb 17;13(1):78.

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Science Papers Examine State of Human Genomic Research, Single-Cell Protein Quantification

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