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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

Germline-Targeting HIV Vaccine Shows Promise in Phase I Trial

A National Institutes of Health-led team reports in Science that a broadly neutralizing antibody HIV vaccine induced bnAb precursors in 97 percent of those given the vaccine.

Study Uncovers Genetic Mutation in Childhood Glaucoma

A study in the Journal of Clinical Investigation ties a heterozygous missense variant in thrombospondin 1 to childhood glaucoma.

Gene Co-Expression Database for Humans, Model Organisms Gets Update

GeneFriends has been updated to include gene and transcript co-expression networks based on RNA-seq data from 46,475 human and 34,322 mouse samples, a new paper in Nucleic Acids Research says.

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.