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In Print: Last Week's Sequencing-Related Papers of Note: Jan 24, 2012


A comparison of statistical methods for detecting differentially expressed genes from RNA-seq data.
Kvam VM, Liu P, Si Y.
Am J Bot. 2012 Jan 20. [Epub ahead of print]

The dynamics and persistence of Dead Sea microbial populations as shown by high throughput sequencing of ribosomal RNA.
Rhodes ME, Oren A, House CH.
Appl Environ Microbiol. 2012 Jan 20. [Epub ahead of print]

Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture.
Rohland N, Reich D.
Genome Res. 2012 Jan 20. [Epub ahead of print]

The primary transcriptome of barley chloroplasts: numerous noncoding RNAs and the dominating role of the plastid-encoded RNA polymerase.
Zhelyazkova P, Sharma CM, Förstner KU, Liere K, et al.
Plant Cell. 2012 Jan 20. [Epub ahead of print]

Genome sequencing reveals agronomically important loci in rice using MutMap.
Abe A, Kosugi S, Yoshida K, Natsume S, et al.
Nat Biotechnol. 2012 Jan 22. [Epub ahead of print]

Maternal and paternal genomes contribute equally to the transcriptome of early plant embryos.
Nodine MD, Bartel DP.
Nature. 2012 Jan 22. [Epub ahead of print]

MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-seq data.
Shen S, Won Park J, Huang J, Dittmar KA, et al.
Nucleic Acids Res. 2012 Jan 20. [Epub ahead of print]

Revealing stable processing products from ribosome-associated small RNAs by deep-sequencing data analysis.
Zywicki M, Bakowska-Zywicka K, Polacek N.
Nucleic Acids Res. 2012 Jan 20. [Epub ahead of print]

A computational pipeline to discover highly phylogenetically informative genes in sequenced genomes: application to Saccharomyces cerevisiae natural strains.
Ramazzotti M, Berná L, Stefanini I, Cavalieri D.
Nucleic Acids Res. 2012 Jan 20. [Epub ahead of print]

Gene-centric metagenomics analysis of feline intestinal microbiome using 454 Junior pyrosequencing.
Tun HM, Brar MS, Khin N, Jun L, et al.
J Microbiol Methods. 2012 Jan 12. [Epub ahead of print]

Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation.
Li G, Ruan X, Auerbach RK, Sandhu KS, et al.
Cell. 2012 Jan 20;148(1-2):84-98.

Transcriptome sequencing of Salmonella enterica serovar Enteritidis under desiccation and starvation stress in peanut oil.
Deng X, Li Z, Zhang W.
Food Microbiol. 2012 May;30(1):311-5.

Bacterial community analysis during fermentation of ten representative kinds of kimchi with barcoded pyrosequencing.
Park EJ, Chun J, Cha CJ, Park WS, et al.
Food Microbiol. 2012 May;30(1):197-204.

Recombination mapping using Boolean logic and high-density SNP genotyping for exome sequence filtering.
Markello TC, Han T, Carlson-Donohoe H, Ahaghotu C, et al.
Mol Genet Metab. 2011 Dec 23. [Epub ahead of print]

A powerful test for multiple rare variants association studies that incorporates sequencing qualities.
Daye ZJ, Li H, Wei Z.
Nucleic Acids Res. 2012 Jan 19. [Epub ahead of print]

Label-free electrical detection of pyrophosphate generated from DNA polymerase reactions on field-effect devices.
Credo GM, Su X, Wu K, Elibol OH, et al.
Analyst. 2012 Jan 19. [Epub ahead of print]

Using formaldehyde-assisted isolation of regulatory elements (FAIRE) to isolate active regulatory DNA.
Simon JM, Giresi PG, Davis IJ, Lieb JD.
Nat Protoc. 2012 Jan 19;7(2):256-267.

A systematically improved high quality genome and transcriptome of the human blood fluke Schistosoma mansoni.
Protasio AV, Tsai IJ, Babbage A, Nichol S, et al.
PLoS Negl Trop Dis. 2012 Jan;6(1):e1455.

Two-stage clustering (TSC): a pipeline for selecting operational taxonomic units for the high-throughput sequencing of PCR amplicons.
Jiang XT, Zhang H, Sheng HF, Wang Y, et al.
PLoS One. 2012;7(1):e30230.

Transcriptome-based differentiation of closely-related miscanthus lines.
Chouvarine P, Cooksey AM, McCarthy FM, Ray DA, et al.
PLoS One. 2012;7(1):e29850.

Generation of long insert pairs using a Cre-LoxP inverse PCR approach.
Peng Z, Zhao Z, Nath N, Froula JL, et al.
PLoS One. 2012;7(1):e29437.

SNP calling using genotype model selection on high-throughput sequencing data.
Yo u N, Murillo G, Su X, Zeng X, et al.
Bioinformatics. 2012 Jan 16. [Epub ahead of print]

BamView: visualizing and interpretation of next-generation sequencing read alignments.
Carver T, Harris SR, Otto TD, Berriman M, et al.
Brief Bioinform. 2012 Jan 16. [Epub ahead of print]

Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression.
Vining KJ, Pomraning KR, Wilhelm LJ, Priest HD, et al.
BMC Genomics. 2012 Jan 17;13(1):27.

Ecology of the microbiome of the infected root canal system: a comparison between apical and coronal root segments.
Ozok AR, Persoon IF, Huse SM, Keijser BJ, et al.
Int Endod J. 2012 Jan 17. [Epub ahead of print]

Carnivore diet analysis based on next-generation sequencing: application to the leopard cat (Prionailurus bengalensis) in Pakistan.
Shehzad W, Riaz T, Nawaz MA, Miquel C, et al.
Mol Ecol. 2012 Jan 17. [Epub ahead of print]

Tracking earthworm communities from soil DNA.
Bienert F, DE Danieli S, Miquel C, Coissac E, et al.
Mol Ecol. 2012 Jan 17. [Epub ahead of print]

AnnTools: A comprehensive and versatile annotation toolkit for genomic variants.
Makarov V, O'Grady T, Cai G, Lihm J, et al.
Bioinformatics. 2012 Jan 18. [Epub ahead of print]

FX: an RNA-seq analysis tool on the cloud.
Hong D, Rhie A, Park SS, Lee J, et al.
Bioinformatics. 2012 Jan 17. [Epub ahead of print]

Electronic fingerprints of DNA bases on graphene.
Ahmed T, Kilina SV, Das T, Haraldsen JT, et al.
Nano Lett. 2012 Jan 18. [Epub ahead of print]

The Scan

Transcriptomic, Epigenetic Study Appears to Explain Anti-Viral Effects of TB Vaccine

Researchers report in Science Advances on an interferon signature and long-term shifts in monocyte cell DNA methylation in Bacille Calmette-Guérin-vaccinated infant samples.

DNA Storage Method Taps Into Gene Editing Technology

With a dual-plasmid system informed by gene editing, researchers re-wrote DNA sequences in E. coli to store Charles Dickens prose over hundreds of generations, as they recount in Science Advances.

Researchers Model Microbiome Dynamics in Effort to Understand Chronic Human Conditions

Investigators demonstrate in PLOS Computational Biology a computational method for following microbiome dynamics in the absence of longitudinally collected samples.

New Study Highlights Role of Genetics in ADHD

Researchers report in Nature Genetics on differences in genetic architecture between ADHD affecting children versus ADHD that persists into adulthood or is diagnosed in adults.