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Papers of Note: Jul 5, 2011


Extensive genomic and transcriptional diversity identified through massively parallel DNA and RNA sequencing of eighteen Korean individuals.
Ju YS, Kim JI, Kim S, Hong D, et al.
Nat Genet. 2011 Jul 3. doi: 10.1038/ng.872. [Epub ahead of print]

Simple and efficient synthesis of 5' pre-adenylated DNA using thermostable RNA ligase.
Zhelkovsky AM, McReynolds LA.
Nucleic Acids Res. 2011 Jun 30. [Epub ahead of print]

MethylCoder: Software pipeline for bisulfite-treated sequences.
Pedersen B, Hsieh TF, Ibarra C, Fischer RL.
Bioinformatics. 2011 Jun 30. [Epub ahead of print]

TOTALRECALLER: Improved accuracy and performance via integrated alignment & base-calling.
Menges F, Narzisi G, Mishra B.
Bioinformatics. 2011 Jun 30. [Epub ahead of print]

Origins and consequences of velocity fluctuations during DNA passage through a nanopore.
Lu B, Albertorio F, Hoogerheide DP, Golovchenko JA.
Biophys J. 2011 Jul 6;101(1):70-9.

Linear amplification for deep sequencing.
Hoeijmakers WA, Bártfai R, Françoijs KJ, Stunnenberg HG.
Nat Protoc. 2011 Jun 23;6(7):1026-36.

The genome of the leaf-cutting ant Acromyrmex echinatior suggests key adaptations to advanced social life and fungus farming.
Nygaard S, Zhang G, Schiøtt M, Li C, et al.
Genome Res. 2011 Jun 30. [Epub ahead of print]

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CANGS DB: a stand-alone web-based database tool for processing, managing and analyzing 454 data in biodiversity studies.
Pandey RV, Nolte V, Boenigk J, Schlotterer C.
BMC Res Notes. 2011 Jun 30;4(1):227.

Saliva microbiomes distinguish caries-active from healthy human populations.
Yang F, Zeng X, Ning K, Liu KL, et al.
ISME J. 2011 Jun 30. doi: 10.1038/ismej.2011.71. [Epub ahead of print]

The oral metagenome in health and disease.
Belda-Ferre P, Alcaraz LD, Cabrera-Rubio R, Romero H, et al.
ISME J. 2011 Jun 30. doi: 10.1038/ismej.2011.85. [Epub ahead of print]

High-throughput single-cell sequencing identifies photoheterotrophs and chemoautotrophs in freshwater bacterioplankton.
Martinez-Garcia M, Swan BK, Poulton NJ, Gomez ML, et al.
ISME J. 2011 Jun 30. doi: 10.1038/ismej.2011.84. [Epub ahead of print]

De novo metagenomic assembly reveals abundant novel major lineage of Archaea in hypersaline microbial communities.
Narasingarao P, Podell S, Ugalde JA, Brochier-Armanet C, et al.
ISME J. 2011 Jun 30. doi: 10.1038/ismej.2011.78. [Epub ahead of print]

SeqGene: a comprehensive software solution for mining exome- and transcriptome-sequencing data.
Deng X.
BMC Bioinformatics. 2011 Jun 29;12(1):267.

MicroRNA preparations from individual monogenean Gyrodactylus salaries — a comparison of six commercially available totalRNA extraction kits.
Fromm B, Harris PD, Bachmann L.
BMC Res Notes. 2011 Jun 29;4(1):217.

Alternative transcription exceeds alternative splicing in generating the transcriptome diversity of cerebellar development.
Pal S, Gupta R, Kim H, Wickramasinghe P, et al.
Genome Res. 2011 Jun 28. [Epub ahead of print]

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Paired-end RAD-seq for de novo assembly and marker design without available reference.
Willing EM, Hoffmann M, Klein JD, Weigel D, Dreyer C.
Bioinformatics. 2011 Jun 27. [Epub ahead of print]

Shrinking of solid-state nanopores by direct thermal heating.
Asghar W, Ilyas A, Billo JA, Iqbal SM.
Nanoscale Res Lett. 2011 May 4;6(1):372.

The genomic standards consortium.
Field D, Amaral-Zettler L, Cochrane G, Cole JR, et al.
PLoS Biol. 2011 Jun;9(6):e1001088. Epub 2011 Jun 21.

Electrokinetic particle translocation through a nanopore containing a floating electrode.
Zhang M, Ai Y, Sharma A, Joo SW, et al.
Electrophoresis. 2011 Jun 24. doi: 10.1002/elps.201100050. [Epub ahead of print]

Unzipping of double-stranded DNA in engineered α-hemolysin pores.
Liu A, Zhao Q, Krishantha DM, Guan X.
J Phys Chem Lett. 2011 Jun 12;2(12):1372-1376.

Genetic diversity and population structure of the endangered marsupial Sarcophilus harrisii (Tasmanian devil).
Miller W, Hayes VM, Ratan A, Petersen DC, et al.
Proc Natl Acad Sci U S A. 2011 Jun 27. [Epub ahead of print]

MicroRNA-seq reveals cocaine-regulated expression of striatal microRNAs.
Eipper-Mains JE, Kiraly DD, Palakodeti D, Mains RE, et al.
RNA. 2011 Jun 27. [Epub ahead of print]

Tight control of mycotoxin biosynthesis gene expression in Aspergillus flavus by temperature as revealed by RNA-seq.
Yu J, Fedorova ND, Montalbano BG, Bhatnagar D, et al.
FEMS Microbiol Lett. 2011 Jun 24. doi: 10.1111/j.1574-6968.2011.02345.x. [Epub ahead of print]

The Scan

Team Tracks Down Potential Blood Plasma Markers Linked to Heart Failure in Atrial Fibrillation Patients

Researchers in BMC Genomics found 10 differentially expressed proteins or metabolites that marked atrial fibrillation with heart failure cases.

Study Points to Synonymous Mutation Effects on E. Coli Enzyme Activity

Researchers in Nature Chemistry saw signs of enzyme activity shifts in the presence of synonymous mutations in a multiscale modeling analysis of three Escherichia coli genes.

Team Outlines Paternal Sample-Free Single-Gene Approach for Non-Invasive Prenatal Screening

With data for nearly 9,200 pregnant individuals, researchers in Genetics in Medicine demonstrate the feasibility of their carrier screening and reflex single-gene non-invasive prenatal screening approach.

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.