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In Print: Sequencing-Related Papers of Note of the Last Two Weeks


Sequence-based genotyping for marker discovery and co-dominant scoring in germplasm and populations.
Truong HT, Ramos AM, Yalcin F, de Ruiter M, et al.
PLoS One. 2012;7(5):e37565.

Genome-wide genetic changes during modern breeding of maize.
Jiao Y, Zhao H, Ren L, Song W, et al.
Nat Genet. 2012 Jun 3. [Epub ahead of print]

Comparative population genomics of maize domestication and improvement.
Hufford MB, Xu X, van Heerwaarden J, Pyhäjärvi T, et al.
Nat Genet. 2012 Jun 3. [Epub ahead of print]

The tomato genome sequence provides insights into fleshy fruit evolution.
The Tomato Genome Consortium; Kazusa DNA Research Institute, Sato S, Tabata S, et al.
Nature. 2012 May 30;485(7400):635-641.

Nascent-seq indicates widespread cotranscriptional RNA editing in Drosophila.
Rodriguez J, Menet JS, Rosbash M.
Mol Cell. 2012 May 30. [Epub ahead of print]

SNP-ratio mapping (SRM): identifying lethal alleles and mutations in complex genetic backgrounds by next-generation sequencing.
Lindner H, Raissig MT, Sailer C, Shimosato-Asano H, et al.
Genetics. 2012 May 29. [Epub ahead of print]

Amplification-free whole-genome bisulfite sequencing by post-bisulfite adaptor tagging.
Miura F, Enomoto Y, Dairiki R, Ito T.
Nucleic Acids Res. 2012 May 30. [Epub ahead of print]

Fidelity of capture-enrichment for mtDNA genome sequencing: influence of NUMTs.
Li M, Schroeder R, Ko A, Stoneking M.
Nucleic Acids Res. 2012 May 30. [Epub ahead of print]

Reducing sequencing bias of small RNAs.
Sorefan K, Pais H, Hall AE, Kozomara A, et al.
Silence. 2012 May 30;3(1):4.

Limitations of the rhesus macaque draft genome assembly and annotation.
Zhang X, Goodsell J, Norgren RB Jr.
BMC Genomics. 2012 May 30;13(1):206.

Slowing down and stretching DNA with an electrically tunable nanopore in a p-n semiconductor membrane.
Melnikov DV, Leburton JP, Gracheva ME.
Nanotechnology. 2012 Jun 29;23(25):255501.

A novel genome-information content-based statistic for genome-wide association analysis designed for next-generation sequencing data.
Luo L, Zhu Y, Xiong M.
J Comput Biol. 2012 May 31. [Epub ahead of print]

Amplification of GC-rich DNA for high-throughput family-based genetic studies.
Naz S, Fatima A.
Mol Biotechnol. 2012 May 30. [Epub ahead of print]

CEDER: Accurate detection of differentially expressed genes by combining significance of exons using RNA-seq.
Wan L, Sun F.
IEEE/ACM Trans Comput Biol Bioinform. 2012 May 23. [Epub ahead of print]

A shot in the genome: how accurately do shotgun 454 sequences represent a genome?
Meglecz E, Pech N, Gilles A, Martin JF, Gardner MG.
BMC Res Notes. 2012 May 28;5(1):259.

High-throughput sequence analysis of turbot (Scophthalmus maximus) transcriptome using 454-pyrosequencing for the discovery of antiviral immune genes.
Pereiro P, Balseiro P, Romero A, Dios S, et al.
PLoS One. 2012;7(5):e35369.

The UEA sRNA workbench: a suite of tools for analysing and visualising next generation sequencing microRNA and small RNA datasets.
Stocks MB, Moxon S, Mapleson D, Woolfenden HC, et al.
Bioinformatics. 2012 May 24. [Epub ahead of print]

VarioWatch: providing large-scale and comprehensive annotations on human genomic variants in the next generation sequencing era.
Cheng YC, Hsiao FC, Yeh EC, Lin WJ, et al.
Nucleic Acids Res. 2012 May 22. [Epub ahead of print]

Generalized DNA barcode design based on hamming codes.
Bystrykh LV.
PLoS One. 2012;7(5):e36852.

Multiple insert size paired-end sequencing for deconvolution of complex transcriptomes.
Smith LM, Hartmann L, Drewe P, Bohnert R, et al.
RNA Biol. 2012 May 1;9(5).

Gossamer — a resource efficient de novo assembler.
Conway T, Wazny J, Bromage A, Zobel J, Beresford-Smith B.
Bioinformatics. 2012 May 18. [Epub ahead of print]

Inferring direct DNA binding from ChIP-seq.
Bailey TL, Machanick P.
Nucleic Acids Res. 2012 May 18. [Epub ahead of print]

Extremely low-coverage sequencing and imputation increases power for genome-wide association studies.
Pasaniuc B, Rohland N, McLaren PJ, Garimella K, et al.
Nat Genet. 2012 May 20. [Epub ahead of print]

Microbial community structures in different wastewater treatment plants as revealed by 454-pyrosequencing analysis.
Hu M, Wang X, Wen X, Xia Y.
Bioresour Technol. 2012 Apr 26;117C:72-79.

2b-RAD: a simple and flexible method for genome-wide genotyping.
Wang S, Meyer E, McKay JK, Matz MV.
Nat Methods. 2012 May 20. [Epub ahead of print]

miRSeqNovel: An R based workflow for analyzing miRNA sequencing data.
Qian K, Auvinen E, Greco D, Auvinen P.
Mol Cell Probes. 2012 May 17. [Epub ahead of print]

A simple strand-specific RNA-seq library preparation protocol combining the Illumina TruSeq RNA and the dUTP methods.
Sultan M, Dökel S, Amstislavskiy V, Wuttig D, et al.
Biochem Biophys Res Commun. 2012 May 15. [Epub ahead of print]

EXP-PAC: Providing comparative analysis and storage of next generation gene expression data.
Church P, Goscinski A, Lefèvre C.
Genomics. 2012 May 15. [Epub ahead of print]

Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome.
Yu M, Hon GC, Szulwach KE, Song CX, et al.
Cell. 2012 May 16. [Epub ahead of print]
(See our coverage of this article, IS 5/22/2012)

Comprehensive analysis of mRNA methylation reveals enrichment in 3' UTRs and near stop codons.
Meyer KD, Saletore Y, Zumbo P, Elemento O, et al.
Cell. 2012 May 16. [Epub ahead of print]

Exome sequencing generates high quality data in non-target regions.
Guo Y, Long J, He J, Li CI, et al.
BMC Genomics. 2012 May 20;13(1):194.

De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree (Hevea brasiliensis Muell. Arg.).
Li D, Deng Z, Qin B, Liu X, Men Z.
BMC Genomics. 2012 May 18;13(1):192.

The Scan

More Boosters for US

Following US Food and Drug Administration authorization, the Centers for Disease Control and Prevention has endorsed booster doses of the Moderna and Johnson & Johnson SARS-CoV-2 vaccines, the Washington Post writes.

From a Pig

A genetically modified pig kidney was transplanted into a human without triggering an immune response, Reuters reports.

For Privacy's Sake

Wired reports that more US states are passing genetic privacy laws.

Science Paper on How Poaching Drove Evolution in African Elephants

In Science this week: poaching has led to the rapid evolution of tuskless African elephants.