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In Print: Last Week's Sequencing-Related Papers of Note: Dec 6, 2011


Comparative analysis of human protein-coding and noncoding RNAs between brain and 10 mixed cell lines by RNA-seq.
Chen G, Yin K, Shi L, Fang Y, et al.
PLoS One. 2011;6(11):e28318.

Systematic comparison of three methods for fragmentation of long-range PCR products for next generation sequencing.
Knierim E, Lucke B, Schwarz JM, Schuelke M, Seelow D.
PLoS One. 2011;6(11):e28240.

Transcriptome-wide discovery of circular RNAs in Archaea.
Danan M, Schwartz S, Edelheit S, Sorek R.
Nucleic Acids Res. 2011 Dec 2. [Epub ahead of print]

GReEn: a tool for efficient compression of genome resequencing data.
Pinho AJ, Pratas D, Garcia SP.
Nucleic Acids Res. 2011 Dec 1. [Epub ahead of print]

Integrated annotation and analysis of genetic variants from next-generation sequencing studies with variant tools.
San Lucas FA, Wang G, Scheet P, Peng B.
Bioinformatics. 2011 Dec 2. [Epub ahead of print]

Sparse linear modeling of next-generation mRNA sequencing (RNA-seq) data for isoform discovery and abundance estimation.
Li JJ, Jiang CR, Brown JB, Huang H, Bickel PJ.
Proc Natl Acad Sci U S A. 2011 Dec 1. [Epub ahead of print]

GCAT-SEEKquence: Genome Consortium for Active Teaching of undergraduates through increased faculty access to next-generation sequencing data.
Buonaccorsi VP, Boyle MD, Grove D, Praul C, et al.
CBE Life Sci Educ. 2011 Winter;10(4):342-5.

Low-pass genomewide sequencing and variant inference using identity-by-descent in an isolated human population.
Gusev A, Shah MJ, Kenny EE, Ramachandran A, et al.
Genetics. 2011 Nov 30. [Epub ahead of print]

Characterizing the citrus cultivar Carrizo genome through 454 shotgun sequencing.
Belknap WR, Wang Y, Huo N, Wu J, et al.
Genome. 2011 Dec 1. [Epub ahead of print]

Influence of DNA extraction and PCR amplification on studies of soil fungal communities based on amplicon sequencing.
Xu L, Ravnskov S, Larsen J, Nicolaisen M.
Can J Microbiol. 2011 Dec 1. [Epub ahead of print]

Revealing the missing expressed genes beyond the human reference genome by RNA-seq.
Chen G, Li R, Shi L, Qi J, et al.
BMC Genomics. 2011 Dec 2;12(1):590.

Microbial biogeography of public restroom surfaces.
Flores GE, Bates ST, Knights D, Lauber CL, et al.
PLoS One. 2011;6(11):e28132.

Novel tools for conservation genomics: comparing two high-throughput approaches for SNP discovery in the transcriptome of the European hake.
Milano I, Babbucci M, Panitz F, Ogden R, et al.
PLoS One. 2011;6(11):e28008.

Global mapping of H3K4me1 and H3K4me3 reveals the chromatin state-based cell type-specific gene regulation in human Treg cells.
Tian Y, Jia Z, Wang J, Huang Z, et al.
PLoS One. 2011;6(11):e27770.

MetaBinG: using GPUs to accelerate metagenomic sequence classification.
Jia P, Xuan L, Liu L, Wei C.
PLoS One. 2011;6(11):e25353.

Genome-wide identification and annotation of HIF-1α binding sites in two cell lines using massively parallel sequencing.
Tanimoto K, Tsuchihara K, Kanai A, Arauchi T, et al.
Hugo J. 2010 Dec;4(1-4):35-48.

Illumina mate-paired DNA sequencing-library preparation using Cre-Lox recombination.
Van Nieuwerburgh F, Thompson RC, Ledesma J, Deforce D, et al.
Nucleic Acids Res. 2011 Nov 29. [Epub ahead of print]

The allele distribution in next-generation sequencing data sets is accurately described as the result of a stochastic branching process.
Heinrich V, Stange J, Dickhaus T, Imkeller P, et al.
Nucleic Acids Res. 2011 Nov 29. [Epub ahead of print]

Finding consistent patterns: A nonparametric approach for identifying differential expression in RNA-seq data.
Li J, Tibshirani R.
Stat Methods Med Res. 2011 Nov 28. [Epub ahead of print]

An evolutionarily and ecologically focused strategy for genome sequencing efforts.
Barribeau SM, Gerardo NM.
Heredity. 2011 Nov 30. [Epub ahead of print]

An efficient procedure for plant organellar genome assembly, based on whole genome data from the 454 GS FLX sequencing platform.
Zhang T, Zhang X, Hu S, Yu J.
Plant Methods. 2011 Nov 29;7(1):38.

The entomopathogenic bacterial endosymbionts Xenorhabdus and Photorhabdus: convergent lifestyles from divergent genomes.
Chaston JM, Suen G, Tucker SL, Andersen AW, et al.
PLoS One. 2011;6(11):e27909.

Construction and analysis of an integrated regulatory network derived from high-throughput sequencing data.
Cheng C, Yan KK, Hwang W, Qian J, et al.
PLoS Comput Biol. 2011 Nov;7(11):e1002190.

Genome-wide antisense transcription drives mRNA processing in bacteria.
Lasa I, Toledo-Arana A, Dobin A, Villanueva M, et al.
Proc Natl Acad Sci U S A. 2011 Nov 28. [Epub ahead of print]

Complex microbiome underlying secondary and primary metabolism in the tunicate-Prochloron symbiosis.
Donia MS, Fricke WF, Partensky F, Cox J, et al.
Proc Natl Acad Sci U S A. 2011 Nov 28. [Epub ahead of print]

Cell walls of developing wheat (Triticum aestivum L.) starchy endosperm: comparison of composition and RNA seq transcriptome.
Pellny TK, Lovegrove A, Freeman J, Tosi P, et al.
Plant Physiol. 2011 Nov 28. [Epub ahead of print]

Direct imaging of DNA motif sequences with encoded nanoparticles.
Fernandez RE, Mastrangelo CH.
N Biotechnol. 2011 Nov 18. [Epub ahead of print]

Transposase mediated construction of RNA-seq libraries.
Gertz J, Varley KE, Davis NS, Baas BJ, et al.
Genome Res. 2011 Nov 29. [Epub ahead of print]

The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.