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

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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]

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