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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.

The Scan

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.

Study Reveals Potential Sex-Specific Role for Noncoding RNA in Depression

A long, noncoding RNA called FEDORA appears to be a sex-specific regulator of major depressive disorder, affecting more women, researchers report in Science Advances.

New mRNA Vaccines Offer Hope for Fighting Malaria

A George Washington University-led team has developed mRNA vaccines for malaria that appear to provide protection in mice, as they report in NPJ Vaccines.

Unique Germline Variants Found Among Black Prostate Cancer Patients

Through an exome sequencing study appearing in JCO Precision Oncology, researchers have found unique pathogenic or likely pathogenic variants within a cohort of Black prostate cancer patients.