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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]

The Scan

Study Finds Few FDA Post-Market Regulatory Actions Backed by Research, Public Assessments

A Yale University-led team examines in The BMJ safety signals from the US FDA Adverse Event Reporting System and whether they led to regulatory action.

Duke University Team Develops Programmable RNA Tool for Cell Editing

Researchers have developed an RNA-based editing tool that can target specific cells, as they describe in Nature.

Novel Gene Editing Approach for Treating Cystic Fibrosis

Researchers in Science Advances report on their development of a non-nuclease-based gene editing approach they hope to apply to treat cystic fibrosis.

Study Tracks Responses in Patients Pursuing Polygenic Risk Score Profiling

Using interviews, researchers in the European Journal of Human Genetics qualitatively assess individuals' motivations for, and experiences with, direct-to-consumer polygenic risk score testing.