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In Print: Last Week's Sequencing-Related Papers of Note: Apr 23, 2013


Massively parallel sequencing reveals the complex structure of an irradiated human chromosome on a mouse background in the tc1 model of down syndrome.
Gribble SM, Wiseman FK, Clayton S, et al.
PLoS One. 2013 Apr 15;8(4):e60482.

TherMos: Estimating protein-DNA binding energies from in vivo binding profiles.
Sun W, Hu X, Lim MH, Ng CK, et al.
Nucleic Acids Res. 2013 Apr 16. [Epub ahead of print]

Identification of RNA partners of viral proteins in infected cells.
Komarova AV, Combredet C, Sismeiro O, Dillies MA, et al.
RNA Biol. 2013 Apr 1;10(6).

Evolutionary dynamics of retrotransposons assessed by high throughput sequencing in wild relatives of wheat.
Senerchia N, Wicker T, Felber F, Parisod C.
Genome Biol Evol. 2013 Apr 17. [Epub ahead of print]

Characteristics of cross-hybridization and cross-alignment of expression in pseudo-xenograft samples by RNA-Seq and microarrays.
Valdes C, Seo P, Tsinoremas N, Clarke J.
J Clin Bioinforma. 2013 Apr 18;3(1):8.

The zebrafish reference genome sequence and its relationship to the human genome.
Howe K, Clark MD, Torroja CF, Torrance J, et al.
Nature. 2013 Apr 17. [Epub ahead of print]

A systematic genome-wide analysis of zebrafish protein-coding gene function.
Kettleborough RN, Busch-Nentwich EM, Harvey SA, Dooley CM, et al.
Nature. 2013 Apr 17. [Epub ahead of print]

Quartz-Seq: a highly reproducible and sensitive single-cell RNA-Seq reveals non-genetic gene expression heterogeneity.
Sasagawa Y, Nikaido I, Hayashi T, Danno H, et al.
Genome Biol. 2013 Apr 17;14(4):R31.

Detecting Human Bacterial Pathogens in Wastewater Treatment Plants by High-throughput Shotgun Sequencing Technique.
Cai L, Zhang T.
Environ Sci Technol. 2013 Apr 17. [Epub ahead of print]

A population model for genotyping indels from next-generation sequence data.
Shao H, Bellos E, Yin H, Liu X, et al.
Nucleic Acids Res. 2013 Feb 1;41(3):e46.

Comparative RNA-Seq and Microarray Analysis of Gene Expression Changes in B-Cell Lymphomas of Canis familiaris.
Mooney M, Bond J, Monks N, Eugster E, et al.
PLoS One. 2013 Apr 4;8(4):e61088.

CGAP-Align: A High Performance DNA Short Read Alignment Tool.
Chen Y, Hong J, Cui W, Zaneveld J, et al.
PLoS One. 2013 Apr 11;8(4):e61033.

Revising a Personal Genome by Comparing and Combining Data from Two Different Sequencing Platforms.
Kim D, Kim WY, Lee SY, Lee SY, et al.
PLoS One. 2013 Apr 8;8(4):e60585.

De novo Sequence Assembly and Characterization of Lycoris aurea Transcriptome Using GS FLX Titanium Platform of 454 Pyrosequencing.
Wang R, Xu S, Jiang Y, Jiang J, et al.
PLoS One. 2013 Apr 9;8(4):e60449.

Identification of Optimum Sequencing Depth Especially for De Novo Genome Assembly of Small Genomes Using Next Generation Sequencing Data.
Desai A, Marwah VS, Yadav A, Jha V, et al.
PLoS One. 2013 Apr 12;8(4):e60204.

Reference-Free Population Genomics from Next-Generation Transcriptome Data and the Vertebrate-Invertebrate Gap.
Gayral P, Melo-Ferreira J, Glémin S, Bierne N, et al.
PLoS Genet. 2013 Apr;9(4):e1003457.

Shining a Light on Dark Sequencing: Characterising Errors in Ion Torrent PGM Data.
Bragg LM, Stone G, Butler MK, Hugenholtz P, Tyson GW.
PLoS Comput Biol. 2013 Apr;9(4):e1003031.

Combinatorial Pooling Enables Selective Sequencing of the Barley Gene Space.
Lonardi S, Duma D, Alpert M, Cordero F, et al.
PLoS Comput Biol. 2013 Apr;9(4):e1003010.

Improving mammalian genome scaffolding using large insert mate-pair next-generation sequencing.
van Heesch S, Kloosterman WP, Lansu N, Ruzius FP, et al.
BMC Genomics. 2013 Apr 16;14(1):257.

A Sequence-Based Variation Map of Zebrafish.
Patowary A, Purkanti R, Singh M, Chauhan R, et al.
Zebrafish. 2013 Mar;10(1):15-20.

Quantifying sequence proportions in a DNA-based diet study using Ion Torrent amplicon sequencing: which counts count?
Deagle BE, Thomas AC, Shaffer AK, Trites AW, Jarman SN.
Mol Ecol Resour. 2013 Apr 17. [Epub ahead of print]

Shrinkage estimation of dispersion in Negative Binomial models for RNA-seq experiments with small sample size.
Yu D, Huber W, Vitek O.
Bioinformatics. 2013 Apr 14. [Epub ahead of print]

Exome-based Analysis for RNA Epigenome Sequencing Data.
Meng J, Cui X, Rao M, Chen Y, Huang Y.
Bioinformatics. 2013 Apr 14. [Epub ahead of print]

Analyzing Genome Coverage Profiles with Applications to Quality Control in Metagenomics.
Lindner MS, Kollock M, Zickmann F, Renard BY.
Bioinformatics. 2013 Apr 14. [Epub ahead of print]

Laser capture microdissection-reduced representation bisulfite sequencing (LCM-RRBS) maps changes in DNA methylation associated with gonadectomy-induced adrenocortical neoplasia in the mouse.
Schillebeeckx M, Schrade A, Löbs AK, Pihlajoki M, et al.
Nucleic Acids Res. 2013 Apr 15. [Epub ahead of print]

Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification.
Zhou X, Li Y, Liu S, Yang Q, et al.
Gigascience. 2013 Mar 27;2(1):4.

AXIOME: automated exploration of microbial diversity.
Lynch MDj, Masella AP, Hall MW, Bartram AK, Neufeld JD.
Gigascience. 2013 Mar 13;2(1):3.

Massively-parallel sequencing of genes on a single chromosome: a comparison of solution hybrid selection and flow sorting.
Teer JK, Johnston JJ, Anzick SL, Pineda M, et al.
BMC Genomics. 2013 Apr 15;14(1):253.

Dynamic and electronic transport properties of DNA translocation through graphene nanopores.
Avdoshenko SM, Nozaki D, Gomes da Rocha C, Gonzalez J, et al.
Nano Lett. 2013 Apr 15. [Epub ahead of print]

Base calling for high-throughput short-read sequencing: dynamic programming solutions.
Das S, Vikalo H.
BMC Bioinformatics. 2013 Apr 15;14(1):129.

Time Series Expression Analyses Using RNA-seq: A Statistical Approach.
Oh S, Song S, Grabowski G, Zhao H, Noonan JP.
Biomed Res Int. 2013;2013:203681.

A 454 Survey Reveals the Community Composition and Core Microbiome of the Common Bed Bug (Cimex lectularius) across an Urban Landscape.
Meriweather M, Matthews S, Rio R, Baucom RS.
PLoS One. 2013 Apr 9;8(4):e61465.

Accurate detection of differential RNA processing.
Drewe P, Stegle O, Hartmann L, Kahles A, et al.
Nucleic Acids Res. 2013 Apr 12. [Epub ahead of print]

Mass spectrometry and next-generation sequencing reveal an abundant and rapidly evolving abalone sperm protein.
Palmer MR, McDowall MH, Stewart L, Ouaddi A, et al.
Mol Reprod Dev. 2013 Apr 13. [Epub ahead of print]

Transcriptomic analysis of cultured whale skin cells exposed to hexavalent chromium [Cr(VI)].
Pabuwal V, Boswell M, Pasquali A, Wise SS, et al.
Aquat Toxicol. 2013 Mar 20;134-135C:74-81.