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In Print: Last Week's Sequencing-Related Papers of Note: Aug 7, 2012

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Shaping of human germline IgH repertoires revealed by deep sequencing.
Larimore K, McCormick MW, Robins HS, Greenberg PD.
J Immunol. 2012 Aug 3. [Epub ahead of print]


Plasmodium cynomolgi genome sequences provide insight into Plasmodium vivax and the monkey malaria clade.
Tachibana SI, Sullivan SA, Kawai S, Nakamura S, et al.
Nat Genet. 2012 Aug 5. [Epub ahead of print]


The malaria parasite Plasmodium vivax exhibits greater genetic diversity than Plasmodium falciparum.
Neafsey DE, Galinsky K, Jiang RH, Young L, et al.
Nat Genet. 2012 Aug 5. [Epub ahead of print]


Pacific Biosciences sequencing technology for genotyping and variation discovery in human data.
Carneiro MO, Russ C, Ross MG, Gabriel S, et al..
BMC Genomics. 2012 Aug 5;13(1):375.


Cell-type specificity of ChIP-predicted transcription factor binding sites.
Håndstad T, Rye M, Mocnik R, Drabløs F, Sætrom P.
BMC Genomics. 2012 Aug 3;13(1):372.


RNA-sequencing as useful screening tool in the combat against the misuse of anabolic agents.
Riedmaier I, Benes V, Blake J, Bretschneider N, et al.
Anal Chem. 2012 Jul 13. [Epub ahead of print]


Synthetic spike-in standards improve run-specific systematic error analysis for DNA and RNA sequencing.
Zook JM, Samarov D, McDaniel J, Sen SK, Salit M.
PLoS One. 2012;7(7):e41356.


Sequencing intractable DNA to close microbial genomes.
Hurt RA Jr, Brown SD, Podar M, Palumbo AV, Elias DA.
PLoS One. 2012;7(7):e41295.


Defining the core Arabidopsis thaliana root microbiome.
Lundberg DS, Lebeis SL, Paredes SH, Yourstone S, et al.
Nature. 2012 Aug 2;488(7409):86-90.


Analysis of the epigenetic status of telomeres by using ChIP-seq data.
Vaquero-Sedas MI, Luo C, Vega-Palas MA.
Nucleic Acids Res. 2012 Aug 1. [Epub ahead of print]


A fast collapsed data method for estimating haplotype frequencies from pooled genotype data with applications to the study of rare variants.
Kuk AY, Li X, Xu J.
Stat Med. 2012 Aug 1. [Epub ahead of print]


Detection of ultra-rare mutations by next-generation sequencing.
Schmitt MW, Kennedy SR, Salk JJ, Fox EJ, et al.
Proc Natl Acad Sci U S A. 2012 Aug 1. [Epub ahead of print]


Trapping DNA near a solid-state nanopore.
Vlassarev DM, Golovchenko JA.
Biophys J. 2012 Jul 18;103(2):352-6.


Quantitative RNA-seq analysis in non-model species: assessing transcriptome assemblies as a scaffold and the utility of evolutionary divergent genomic reference species.
Hornett EA, Wheat CW.
BMC Genomics. 2012 Aug 1;13(1):361.


Sequencing the miRNAs in maternal plasma from women before and after parturition.
Pan M, Ge Q, Li H, Yang Q, et al.
J Nanosci Nanotechnol. 2012 May;12(5):4035-43.


PRISM: Pair read informed split read mapping for base-pair level detection of insertion, deletion and structural variants.
Jiang Y, Wang Y, Brudno M.
Bioinformatics. 2012 Jul 31. [Epub ahead of print]


Microbial 16S rRNA ion tag and community metagenome sequencing using the Ion Torrent (PGM) platform.
Whiteley AS, Jenkins S, Waite I, Kresoje N, et al.
J Microbiol Methods. 2012 Jul 28. [Epub ahead of print]


Metagenomic taxonomic classification using extreme learning machines.
Rasheed Z, Rangwala H.
J Bioinform Comput Biol. 2012 Oct;10(5):1250015.


Empirical validation of pooled whole genome population re-sequencing in Drosophila melanogaster.
Zhu Y, Bergland AO, González J, Petrov DA.
PLoS One. 2012;7(7):e41901.


The "most wanted" taxa from the human microbiome for whole genome sequencing.
Fodor AA, Desantis TZ, Wylie KM, Badger JH, et al.
PLoS One. 2012;7(7):e41294.


An effort to use human-based exome capture methods to analyze chimpanzee and macaque exomes.
Jin X, He M, Ferguson B, Meng Y, et al.
PLoS One. 2012;7(7):e40637.


Identification of miRNA signatures during the differentiation of hESCs into retinal pigment epithelial cells.
Hu G, Huang K, Yu J, Gopalakrishna-Pillai S, et al.
PLoS One. 2012;7(7):e37224.


easyRNASeq: a bioconductor package for processing RNA-seq data.
Delhomme N, Padioleau I, Furlong EE, Steinmetz L.
Bioinformatics. 2012 Jul 30. [Epub ahead of print]


Scaling metagenome sequence assembly with probabilistic de Bruijn graphs.
Pell J, Hintze A, Canino-Koning R, Howe A, et al.
Proc Natl Acad Sci U S A. 2012 Jul 30. [Epub ahead of print]


Construction of a stability landscape of the CH3 domain of human IgG1 by combining directed evolution with high throughput sequencing.
Traxlmayr MW, Hasenhindl C, Hackl M, Stadlmayr G, et al.
J Mol Biol. 2012 Jul 27. [Epub ahead of print]


Comprehensive microRNA profiling in B-cells of human centenarians by massively parallel sequencing.
Gombar S, Jung HJ, Dong F, Calder B, et al.
BMC Genomics. 2012 Jul 31;13(1):353.


Estimation of sequencing error rates in short reads.
Wang XV, Blades N, Ding J, Sultana R, Parmigiani G.
BMC Bioinformatics. 2012 Jul 30;13(1):185.

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