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In Print: Last Week's Sequencing-Related Papers of Note: Sep 25, 2012


PEG-labeled nucleotides and nanopore detection for single molecule DNA sequencing by synthesis.
Kumar S, Tao C, Chien M, Hellner B, et al.
Sci Rep. 2012;2:684.

A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data.
Wu H, Wang C, Wu Z.
Biostatistics. 2012 Sep 22. [Epub ahead of print]

Estimating the human mutation rate using autozygosity in a founder population.
Campbell CD, Chong JX, Malig M, Ko A, et al.
Nat Genet. 2012 Sep 23. [Epub ahead of print]

Next-generation phylogenomics using a target restricted assembly method.
Johnson KP, Walden KK, Robertson HM.
Mol Phylogenet Evol. 2012 Sep 18. [Epub ahead of print]

Reprogramming of DNA methylation in pollen guides epigenetic inheritance via small RNA.
Calarco JP, Borges F, Donoghue MT, Van Ex F, et al.
Cell. 2012 Sep 19. [Epub ahead of print]

Challenges and strategies in transcriptome assembly and differential gene expression quantification. A comprehensive in silico assessment of RNA-seq experiments.
Vijay N, Poelstra JW, Künstner A, Wolf JB.
Mol Ecol. 2012 Sep 24. [Epub ahead of print]

The oyster genome reveals stress adaptation and complexity of shell formation.
Zhang G, Fang X, Guo X, Li L, et al.
Nature. 2012 Sep 19. [Epub ahead of print]

SNP calling by sequencing pooled samples.
Raineri E, Ferretti L, Esteve-Codina A, Heath S, et al.
BMC Bioinformatics. 2012 Sep 20;13(1):239.

Tools to kill: Genome of one of the most destructive plant pathogenic fungi Macrophomina phaseolina.
Islam MS, Haque MS, Islam MM, Emdad EM, et al.
BMC Genomics. 2012 Sep 19;13(1):493.

A cost-effective method for Illumina small RNA-seq library preparation using T4 RNA ligase 1 adenylated adapters.
Chen YR, Zheng Y, Liu B, Zhong S, et al.
Plant Methods. 2012 Sep 20;8(1):41.

Accurate variant detection across non-amplified and whole genome amplified DNA using targeted next generation sequencing.
Elsharawy A, Warner J, Olson J, Forster M, et al.
BMC Genomics. 2012 Sep 20;13(1):500.

Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by whole-genome sequencing.
Lee H, Popodi E, Tang H, Foster PL.
Proc Natl Acad Sci U S A. 2012 Sep 18. [Epub ahead of print]

Functional transcriptomics of a migrating cell in Caenorhabditis elegans.
Schwarz EM, Kato M, Sternberg PW.
Proc Natl Acad Sci U S A. 2012 Sep 18. [Epub ahead of print]

Recognizing nucleosides with transverse electronic transport via perpendicular direction of base planes for DNA sequencing.
Yang B, Dong R, Yan X, Shi Q.
Nanoscale Res Lett. 2012 Sep 19;7(1):512.

Transcriptome-scale homoeolog-specific transcript assemblies of bread wheat.
Schreiber AW, Hayden MJ, Forrest KL, Kong SL, et al.
BMC Genomics. 2012 Sep 19;13(1):492.

Mapping single molecule sequencing reads using Basic Local Alignment with Successive Refinement (BLASR): theory and application.
Chaisson MJ, Tesler G.
BMC Bioinformatics. 2012 Sep 19;13(1):238.

Bayesian analysis of RNA sequencing data by estimating multiple shrinkage priors.
Van De Wiel MA, Leday GG, Pardo L, Rue H, et al.
Biostatistics. 2012 Sep 17. [Epub ahead of print]

A comprehensive evaluation of normalization methods for Illumina high-throughput RNA sequencing data analysis.
Dillies MA, Rau A, Aubert J, Hennequet-Antier C, et al.
Brief Bioinform. 2012 Sep 17. [Epub ahead of print]

Computer and statistical analysis of transcription factor binding and chromatin modifications by ChIP-seq data in embryonic stem cell.
Orlov Y, Xu H, Afonnikov D, Lim B, et al.
J Integr Bioinform. 2012 Sep 18;9(2):211.

A genome-wide survey for prion-regulated miRNAs associated with cholesterol homeostasis.
Montag J, Brameier M, Schmädicke AC, Gilch S, et al.
BMC Genomics. 2012 Sep 17;13(1):486.

Efficient experimental design and analysis strategies for the detection of differential expression using RNA-sequencing.
Robles JA, Qureshi SE, Stephen SJ, Wilson SR, et al.
BMC Genomics. 2012 Sep 17;13(1):484.

High-throughput sequencing of black pepper root transcriptome.
Gordo SM, Pinheiro DG, Moreira EC, Rodrigues SM, et al.
BMC Plant Biol. 2012 Sep 17;12(1):168.

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