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In Print: Last Week's Sequencing-Related Papers of Note: Nov 15, 2011


Embryonic stem cell-based mapping of developmental transcriptional programs.
Mazzoni EO, Mahony S, Iacovino M, Morrison CA, et al.
Nat Methods. 2011 Nov 13. [Epub ahead of print]

Targeted RNA sequencing reveals the deep complexity of the human transcriptome.
Mercer TR, Gerhardt DJ, Dinger ME, Crawford J, et al.
Nat Biotechnol. 2011 Nov 13. [Epub ahead of print]

Slowing and controlling the translocation of DNA in a solid-state nanopore.
Luan B, Stolovitzky G, Martyna G.
Nanoscale. 2011 Nov 14. [Epub ahead of print]

Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions.
Schmidtke C, Findeiß S, Sharma CM, Kuhfuß J, et al.
Nucleic Acids Res. 2011 Nov 12. [Epub ahead of print]

Global DNA demethylation during mouse erythropoiesis in vivo.
Shearstone JR, Pop R, Bock C, Boyle P, et al.
Science. 2011 Nov 11;334(6057):799-802.

Optical mapping and sequencing of the Escherichia coli KO11 genome reveal extensive chromosomal rearrangements, and multiple tandem copies of the Zymomonas mobilis pdc and adhB genes.

Turner PC, Yomano LP, Jarboe LR, York SW, et al.
J Ind Microbiol Biotechnol. 2011 Nov 11. [Epub ahead of print]

Use of low-coverage, large-insert, short-read data for rapid and accurate generation of enhanced-quality draft Pseudomonas genome sequences.
O'Brien HE, Gong Y, Fung P, Wang PW, Guttman DS.
PLoS One. 2011;6(11):e27199.

The statistics of bulk segregant analysis using next generation sequencing.
Magwene PM, Willis JH, Kelly JK.
PLoS Comput Biol. 2011 Nov;7(11):e1002255.

Using Poisson mixed-effects model to quantify transcript-level gene expression in RNA-seq.
Hu M, Zhu Y, Taylor JM, Liu JS, Qin Z.
Bioinformatics. 2011 Nov 8. [Epub ahead of print]

NARWHAL, a primary analysis pipeline for NGS data.
Brouwer RW, van den Hout MC, Grosveld FG, van Ijcken WF.
Bioinformatics. 2011 Nov 8. [Epub ahead of print]

Fast and cost-effective mining of microsatellite markers using NGS technology: an example of a Korean water deer Hydropotes inermis argyropus.
Yu JN, Won C, Jun J, Lim Y, Kwak M.
PLoS One. 2011;6(11):e26933.

Segtor: rapid annotation of genomic coordinates and single nucleotide variations using segment trees.
Renaud G, Neves P, Folador EL, Ferreira CG, Passetti F.
PLoS One. 2011;6(11):e26715.

Comparative approach to capture bacterial diversity of coastal waters.
Na H, Kim OS, Yoon SH, Kim Y, Chun J.
J Microbiol. 2011 Oct;49(5):729-40.

Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems.
Minoche AE, Dohm JC, Himmelbauer H.
Genome Biol. 2011 Nov 8;12(11):R112.

Exploring the gonad transcriptome of two extreme male pigs with RNA-seq.
Esteve-Codina A, Kofler R, Palmieri N, Bussotti G, et al.
BMC Genomics. 2011 Nov 8;12(1):552.

Characterizing and controlling the motion of ssDNA in a solid-state nanopore.
Luan B, Martyna G, Stolovitzky G.
Biophys J. 2011 Nov 2;101(9):2214-22.

Copy number variation detection in whole-genome sequencing data using the Bayesian information criterion.
Xi R, Hadjipanayis AG, Luquette LJ, Kim TM, et al.
Proc Natl Acad Sci U S A. 2011 Nov 7. [Epub ahead of print]

A cross-sample statistical model for SNP detection in short-read sequencing data.
Muralidharan O, Natsoulis G, Bell J, Newburger D, et al.
Nucleic Acids Res. 2011 Nov 7. [Epub ahead of print]

Single read and paired end mRNA-seq Illumina libraries from 10 nanograms total RNA.
Sengupta S, Bolin JM, Ruotti V, Nguyen BK, et al.
J Vis Exp. 2011 Oct 27;(56). pii: 3340.

Next-generation sequencing reveals phylogeographic structure and a species tree for recent bird divergences.
McCormack JE, Maley JM, Hird SM, Derryberry EP, et al.
Mol Phylogenet Evol. 2011 Oct 31. [Epub ahead of print]

The Scan

And For Adolescents

The US Food and Drug Administration has authorized the Pfizer-BioNTech SARS-CoV-2 vaccine for children between the ages of 12 and 15 years old.

Also of Concern to WHO

The Wall Street Journal reports that the World Health Organization has classified the SARS-CoV-2 variant B.1.617 as a "variant of concern."

Test for Them All

The New York Times reports on the development of combined tests for SARS-CoV-2 and other viruses like influenza.

PNAS Papers on Oral Microbiome Evolution, Snake Toxins, Transcription Factor Binding

In PNAS this week: evolution of oral microbiomes among hominids, comparative genomic analysis of snake toxins, and more.