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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.

The Scan

Dropped Charges

The US Justice Department has dropped visa fraud charges against five Chinese researchers, according to the Wall Street Journal.

More Kids

The Associated Press says Moderna is expanding its SARS-CoV-2 vaccine study to included additional children and may include even younger children.

PNAS Papers on Rat Clues to Human Migration, Thyroid Cancer, PolyG-DS

In PNAS this week: ancient rat genome analysis gives hints to human migrations, WDR77 gene mutations in thyroid cancer, and more.

Purnell Choppin Dies

Purnell Choppin, a virologist who led the Howard Hughes Medical Institute, has died at 91, according to the Washington Post.