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In Print: Last Week's Sequencing-Related Papers of Note: May 7, 2013


Artifactual pyrosequencing reads in multiple-displacement-amplified sediment metagenomes from the Red Sea.
Wang Y, Lee OO, Yang JK, Li TG, Qian PY.
Peerj. 2013 Apr 30;1:e69.

CNVrd, a read-depth algorithm for assigning copy-number at the FCGR locus: population-specific tagging of copy number variation at FCGR3B.
Nguyen HT, Merriman TR, Black MA.
PLoS One. 2013 Apr 30;8(4):e63219.

High quality methylome-wide investigations through next-generation sequencing of DNA from a single archived dry blood spot.
Aberg KA, Xie LY, Nerella S, Copeland WE, et al.
Epigenetics. 2013 Apr 18;8(5).

DNA sequencing using electrical conductance measurements of a DNA polymerase.
Chen YS, Lee CH, Hung MY, Pan HA, et al.
Nat Nanotechnol. 2013 May 5. [Epub ahead of print]

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data.
Chin CS, Alexander DH, Marks P, Klammer AA, et al.
Nat Methods. 2013 May 5. [Epub ahead of print]

Identification of somatic mutations in cancer through Bayesian-based analysis of sequenced genome pairs.
Christoforides A, Carpten JD, Weiss GJ, Demeure MJ, et al.
BMC Genomics. 2013 May 4;14(1):302.

Sequence-based SNP genotyping in durum wheat.
van Poecke RM, Maccaferri M, Tang J, Truong HT, et al.
Plant Biotechnol J. 2013 May 3. [Epub ahead of print]

Effects of GC bias in next-generation-sequencing data on de novo genome assembly.
Chen YC, Liu T, Yu CH, Chiang TY, Hwang CC.
PLoS One. 2013 Apr 29;8(4):e62856.

Simultaneous transcriptome analysis of sorghum and bipolaris sorghicola by using RNA-seq in combination with de novo transcriptome assembly.
Yazawa T, Kawahigashi H, Matsumoto T, Mizuno H.
PLoS One. 2013 Apr 30;8(4):e62460.

Parallel tagged next-generation sequencing on pooled samples — a new approach for population genetics in ecology and conservation.
Zavodna M, Grueber CE, Gemmell NJ.
PLoS One. 2013 Apr 18;8(4):e61471.

On the power and the systematic biases of the detection of chromosomal inversions by paired-end genome sequencing.
Lucas Lledó JI, Cáceres M.
PLoS One. 2013 Apr 23;8(4):e61292.

Mouse oocyte methylomes at base resolution reveal genome-wide accumulation of non-CpG methylation and role of DNA methyltransferases.
Shirane K, Toh H, Kobayashi H, Miura F, et al.
PLoS Genet. 2013 Apr;9(4):e1003439.

The transcription start site landscape of C. elegans.
Saito TL, Hashimoto SI, Gu SG, Morton JJ, et al.
Genome Res. 2013 May 1. [Epub ahead of print]

Enhancer transcripts mark active estrogen receptor binding sites.
Hah N, Murakami S, Nagari A, Danko C, Kraus WL.
Genome Res. 2013 May 1. [Epub ahead of print]

Rare variant association testing under low-coverage sequencing.
Navon O, Sul JH, Han B, Conde L, et al.
Genetics. 2013 May 1. [Epub ahead of print]

Single ion channel recordings with CMOS-anchored lipid membranes.
Rosenstein JK, Ramakrishnan S, Roseman J, Shepard K.
Nano Lett. 2013 May 1. [Epub ahead of print]

CNV-TV: A robust method to discover copy number variation from short sequencing reads.
Duan J, Zhang JG, Deng HW, Wang YP.
BMC Bioinformatics. 2013 May 2;14(1):150.

Bacterial community profiling of milk samples as a means to understand culture-negative bovine clinical mastitis.
Kuehn JS, Gorden PJ, Munro D, Rong R, et al.
PLoS One. 2013 Apr 25;8(4):e61959.

QualitySNPng: a user-friendly SNP detection and visualization tool.
Nijveen H, van Kaauwen M, Esselink DG, Hoegen B, Vosman B.
Nucleic Acids Res. 2013 Apr 30. [Epub ahead of print]

Virome profiling of bats from myanmar by metagenomic analysis of tissue samples reveals more novel mammalian viruses.
He B, Li Z, Yang F, Zheng J, et al.
PLoS One. 2013 Apr 22;8(4):e61950.

RNA-seq profiling reveals novel hepatic gene expression pattern in aflatoxin B1 treated rats.
Merrick BA, Phadke DP, Auerbach SS, Mav D, et al.
PLoS One. 2013 Apr 22;8(4):e61768.

Phyloseq: an R package for reproducible interactive analysis and graphics of microbiome census data.
McMurdie PJ, Holmes S.
PLoS One. 2013 Apr 22;8(4):e61217.

CMS: a web-based system for visualization and analysis of genome-wide methylation data of human cancers.
Gu F, Doderer MS, Huang YW, Roa JC, et al.
PLoS One. 2013 Apr 22;8(4):e60980.

Non-polyadenylated transcription in embryonic stem cells reveals novel non-coding RNA related to pluripotency and differentiation.
Livyatan I, Harikumar A, Nissim-Rafinia M, Duttagupta R, et al.
Nucleic Acids Res. 2013 Apr 29. [Epub ahead of print]

Single-cell paired-end genome sequencing reveals structural variation per cell cycle.
Voet T, Kumar P, Van Loo P, Cooke SL, et al.
Nucleic Acids Res. 2013 Apr 29. [Epub ahead of print]

RUbioSeq: a suite of parallelized pipelines to automate exome variation and bisulfite-seq analyses.
Rubio-Camarillo M, Gómez-López G, Fernández JM, Valencia A, Pisano DG.
Bioinformatics. 2013 Apr 28. [Epub ahead of print]

Discovery and mass spectrometric analysis of novel splice-junction peptides using RNA-seq.
Sheynkman GM, Shortreed MR, Frey BL, Smith LM.
Mol Cell Proteomics. 2013 Apr 29. [Epub ahead of print]

Generation of high quality chromatin immunoprecipitation DNA template for high-throughput sequencing (ChIP-seq).
Deliard S, Zhao J, Xia Q, Grant SF.
J Vis Exp. 2013 Apr 19;(74).

Exploring the sampling universe of RNA-seq.
Tauber S, von Haeseler A.
Stat Appl Genet Mol Biol. 2013 Apr 16:1-14. [Epub ahead of print]

ContigScape: a Cytoscape plugin facilitating microbial genome gap closing.
Tang B, Wang Q, Yang M, Xie F, et al.
BMC Genomics. 2013 Apr 30;14(1):289. [Epub ahead of print]

The Scan

Myotonic Dystrophy Repeat Detected in Family Genome Sequencing Analysis

While sequencing individuals from a multi-generation family, researchers identified a myotonic dystrophy type 2-related short tandem repeat in the European Journal of Human Genetics.

TB Resistance Insights Gleaned From Genome Sequence, Antimicrobial Response Assays

Researchers in PLOS Biology explore M. tuberculosis resistance with a combination of sequencing and assays looking at the minimum inhibitory concentrations of 13 drugs.

Mendelian Disease Genes Prioritized Using Tissue-Specific Expression Clues

Mendelian gene candidates could be flagged for further functional analyses based on tissue-specific transcriptome and proteome profiles, a new Journal of Human Genetics paper says.

Single-Cell Sequencing Points to Embryo Mosaicism

Mosaicism may affect preimplantation genetic tests for aneuploidy, a single-cell sequencing-based analysis of almost three dozen embryos in PLOS Genetics finds.