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In Print: Last Week's Sequencing-Related Papers of Note: Jan 31, 2012


Performance comparison and evaluation of software tools for microRNA deep-sequencing data analysis.
Li Y, Zhang Z, Liu F, Vongsangnak W, et al.
Nucleic Acids Res. 2012 Jan 28. [Epub ahead of print]

R-SAP: a multi-threading computational pipeline for the characterization of high-throughput RNA-sequencing data.
Mittal VK, McDonald JF.
Nucleic Acids Res. 2012 Jan 28. [Epub ahead of print]

Differential expression analysis of multifactor RNA-seq experiments with respect to biological variation.
McCarthy DJ, Chen Y, Smyth GK.
Nucleic Acids Res. 2012 Jan 28. [Epub ahead of print]

Scanning-probe microscopy: probing access resistance of solid-state nanopores with a scanning-probe microscope tip.
Hyun C, Rollings R, Li J.
Small. 2012 Feb 6;8(3):384.

Chromosome-scale selective sweeps shape Caenorhabditis elegans genomic diversity.
Andersen EC, Gerke JP, Shapiro JA, Crissman JR, et al.
Nat Genet. 2012 Jan 29. [Epub ahead of print]

Removing technical variability in RNA-seq data using conditional quantile normalization.
Hansen KD, Irizarry RA, Wu Z.
Biostatistics. 2012 Jan 27. [Epub ahead of print]

A new approach to bias correction in RNA-seq.
Jones DC, Ruzzo WL, Peng X, Katze MG.
Bioinformatics. 2012 Jan 28. [Epub ahead of print]

The transcriptome analysis and comparison explorer — T-ACE: a platform-independent, graphical tool to process large RNA-seq data sets of non-model organisms.
Philipp EE, Kraemer L, Mountfort D, Schilhabel M, et al.
Bioinformatics. 2012 Jan 27. [Epub ahead of print]

Genotype calling from next generation sequencing data using haplotype information of reads.
Zhi D, Wu J, Liu N, Zhang K.
Bioinformatics. 2012 Jan 27. [Epub ahead of print]
[PubMed - as supplied by publisher]

A de novo transcriptome assembly of Lucilia sericata (Diptera: Calliphoridae) with predicted alternative splices, single nucleotide polymorphisms and transcript expression estimates.
Sze SH, Dunham JP, Carey B, Chang PL, et al.
Insect Mol Biol. 2012 Jan 29. [Epub ahead of print]

Deep-sequencing of endothelial cells exposed to hypoxia reveals the complexity of known and novel microRNAs.
Voellenkle C, van Rooij J, Guffanti A, Brini E, et al.
RNA. 2012 Jan 26. [Epub ahead of print]

Combining SNP discovery from next-generation sequencing data with bulked segregant analysis (BSA) to fine-map genes in polyploid wheat.
Trick M, Adamski NM, Mugford SG, Jiang CC, et al.
BMC Plant Biol. 2012 Jan 26;12(1):14.

Transcriptome analysis of silver carp (Hypophthalmichthys molitrix) by paired-end RNA sequencing.
Fu B, He S.
DNA Res. 2012 Jan 24. [Epub ahead of print]

Milk microbiome signatures of subclinical mastitis-affected cattle analyzed by shotgun sequencing.
Bhatt VD, Ahir VB, Koringa PG, Jakhesara SJ, et al.
J Appl Microbiol. 2012 Jan 25. [Epub ahead of print]

Transcriptional profiling of bovine milk using RNA sequencing.
Wickramasinghe S, Rincon G, Islas-Trejo A, Medrano JF.
BMC Genomics. 2012 Jan 25;13(1):45.

Pair-barcode high-throughput sequencing for large-scale multiplexed sample analysis.
Tu J, Ge Q, Wang S, Wang L, et al.
BMC Genomics. 2012 Jan 25;13(1):43.

Fast computation and applications of genome mappability.
Derrien T, Estellé J, Marco Sola S, Knowles DG, et al.
PLoS One. 2012;7(1):e30377.

High-resolution analysis of cytosine methylation in ancient DNA.
Llamas B, Holland ML, Chen K, Cropley JE, et al.
PLoS One. 2012;7(1):e30226.

Isoform diversity and regulation in peripheral and central neurons revealed through RNA-seq.
Lerch JK, Kuo F, Motti D, Morris R, et al.
PLoS One. 2012;7(1):e30417.

Rapid sequencing of the bamboo mitochondrial genome using Illumina technology and parallel episodic evolution of organelle genomes in grasses.
Ma PF, Guo ZH, Li DZ.
PLoS One. 2012;7(1):e30297.

Manifold learning for human population structure studies.
Siu H, Jin L, Xiong M.
PLoS One. 2012;7(1):e29901.

De novo sequencing and a comprehensive analysis of purple sweet potato (Impomoea batatas L.) transcriptome.
Xie F, Burklew CE, Yang Y, Liu M, et al.
Planta. 2012 Jan 21. [Epub ahead of print]