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In Print: Last Week's Sequencing-Related Papers of Note: Sep 18, 2012


Systematic analysis of small RNAs associated with human mitochondria by deep sequencing: detailed analysis of mitochondrial associated miRNA.
Sripada L, Tomar D, Prajapati P, Singh R, et al.
PLoS One. 2012;7(9):e44873.

Chromatin conformation governs T-cell receptor Jβ gene segment usage.
Ndifon W, Gal H, Shifrut E, Aharoni R, et al.
Proc Natl Acad Sci U S A. 2012 Sep 10. [Epub ahead of print]

Precise control of the size and noise of solid-state nanopores using high electric fields.
Beamish E, Kwok H, Tabard-Cossa V, Godin M.
Nanotechnology. 2012 Sep 14;23(40):405301.

The bench scientist's guide to statistical analysis of RNA-seq data.
Yendrek CR, Ainsworth EA, Thimmapuram J.
BMC Res Notes. 2012 Sep 14;5(1):506.

SPInDel: a multifunctional workbench for species identification using insertion/deletion variants.
Carneiro J, Pereira F, Amorim A.
Mol Ecol Resour. 2012 Sep 15. [Epub ahead of print]

Application of circular consensus sequencing and network analysis to characterize the bovine IgG repertoire.
Larsen PA, Smith TP.
BMC Immunol. 2012 Sep 14;13(1):52.

The Saccharomyces cerevisiae W303-K6001 cross-platform genome sequence: insights into ancestry and physiology of a laboratory mutt.
Ralser M, Kuhl H, Ralser M, Werber M, et al.
Open Biol. 2012 Aug;2(8):120093.

Extra-binomial variation approach for analysis of pooled DNA sequencing data.
Yang X, Todd JA, Clayton D, Wallace C.

Bioinformatics. 2012 Sep 12. [Epub ahead of print]

VarB: A Variation Browsing and analysis tool for variants derived from next-generation sequencing data.
Preston MD, Manske M, Horner N, Assefa S, et al.
Bioinformatics. 2012 Sep 13. [Epub ahead of print]

GapMis: a tool for pairwise sequence alignment with a single gap.
Flouri T, Frousios K, Iliopoulos CS, Park K, et al.
Recent Pat DNA Gene Seq. 2012 Sep 10. [Epub ahead of print]

De novo assembly of highly diverse viral populations.
Yang X, Charlebois P, Gnerre S, Coole MG, et al.
BMC Genomics. 2012 Sep 13;13(1):475. [Epub ahead of print]

oPOSSUM-3: advanced analysis of regulatory motif over-representation across genes or ChIP-seq datasets.
Kwon AT, Arenillas DJ, Hunt RW, Wasserman WW.
G3 (Bethesda) . 2012 Sep;2(9):987-1002. Epub 2012 Sep 1.

Exploring the shallow end; estimating information content in transcriptomics studies.
Kliebenstein DJ.
Front Plant Sci. 2012;3:213. Epub 2012 Sep 10.

A high-throughput method for Illumina RNA-seq library preparation.
Kumar R, Ichihashi Y, Kimura S, Chitwood DH, et al.
Front Plant Sci. 2012;3:202. Epub 2012 Aug 28.

Challenges and opportunities in estimating viral genetic diversity from next-generation sequencing data.
Beerenwinkel N, Günthard HF, Roth V, Metzner KJ.
Front Microbiol. 2012;3:329. Epub 2012 Sep 11.

SOAPindel: efficient identification of indels from short paired reads.
Li S, Li R, Li H, Lu J, et al.
Genome Res. 2012 Sep 12. [Epub ahead of print]

Development of InDel markers for Brassica rapa based on whole-genome re-sequencing.
Liu B, Wang Y, Zhai W, Deng J, et al.
Theor Appl Genet. 2012 Sep 13. [Epub ahead of print]

RNA-Seq reveals complex genetic response to deepwater horizon oil release in Fundulus grandis.
Garcia TI, Shen Y, Crawford D, Oleksiak MF, et al.
BMC Genomics. 2012 Sep 12;13(1):474. [Epub ahead of print]

Whole transcriptome analyses of six thoroughbred horses before and after exercise using RNA-Seq.
Park KD, Park J, Ko J, Kim BC, et al.
BMC Genomics. 2012 Sep 12;13(1):473. [Epub ahead of print]

Highly improved homopolymer aware nucleotide-protein alignments with 454 data.
Lysholm F.
BMC Bioinformatics. 2012 Sep 12;13(1):230. [Epub ahead of print]

Whole genome sequencing of field isolates provides robust characterization of genetic diversity in Plasmodium vivax.
Chan ER, Menard D, David PH, Ratsimbasoa A, et al.
PLoS Negl Trop Dis. 2012 Sep;6(9):e1811. Epub 2012 Sep 6.

Comparative transcriptome analyses of deltamethrin-resistant and -susceptible Anopheles gambiae mosquitoes from Kenya by RNA-seq.
Bonizzoni M, Afrane Y, Dunn WA, Atieli FK, et al.
PLoS One. 2012;7(9):e44607. Epub 2012 Sep 7.

Groundtruthing next-gen sequencing for microbial ecology-biases and errors in community structure estimates from PCR amplicon pyrosequencing.
Lee CK, Herbold CW, Polson SW, Wommack KE, et al.
PLoS One. 2012;7(9):e44224. Epub 2012 Sep 6.

Improved variation calling via an iterative backbone remapping and local assembly method for bacterial genomes.
Tae H, Settlage RE, Shallom S, Bavarva JH, et al.
Genomics. 2012 Aug 10. [Epub ahead of print]

3-D simulation of nanopore structure for DNA sequencing.
Park JM, Pak YE, Chun H, Lee JH.
J Nanosci Nanotechnol. 2012 Jul;12(7):5160-3.

Coverage theories for metagenomic DNA sequencing based on a generalization of Stevens' theorem.
Wendl MC, Kota K, Weinstock GM, Mitreva M.
J Math Biol. 2012 Sep 11. [Epub ahead of print]

From next-generation sequencing alignments to accurate comparison and validation of single-nucleotide variants: the pibase software.
Forster M, Forster P, Elsharawy A, Hemmrich G, et al.
Nucleic Acids Res. 2012 Sep 10. [Epub ahead of print]

A comprehensive comparison of RNA-seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae.
Nookaew I, Papini M, Pornputtpong N, Scalcinati G, et al.
Nucleic Acids Res. 2012 Sep 10. [Epub ahead of print]

FadE: whole genome methylation analysis for multiple sequencing platforms.
Souaiaia T, Zhang Z, Chen T.
Nucleic Acids Res. 2012 Sep 10. [Epub ahead of print]

Improving the limit of detection for Sanger sequencing: a comparison of methodologies for KRAS variant detection.
Davidson CJ, Zeringer E, Champion KJ, Gauthier MP, et al.
Biotechniques. 2012 Sep;53(3):182-8.

Simultaneous SNP identification and assessment of allele-specific bias from ChIP-seq data.
Ni Y, Hall AW, Battenhouse A, Iyer VR.
BMC Genet. 2012 Sep 10;13(1):79. [Epub ahead of print]

Large-area anodized alumina nanopore arrays assisted by soft ultraviolet nanoimprint prepatterning.
Ng SM, Wong HF, Lau HK, Leung CW.
J Nanosci Nanotechnol. 2012 Aug;12(8):6315-20.

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.