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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

Self-Reported Hearing Loss in Older Adults Begins Very Early in Life, Study Says

A JAMA Otolaryngology — Head & Neck Surgery study says polygenic risk scores associated with hearing loss in older adults is also associated with hearing decline in younger groups.

Genome-Wide Analysis Sheds Light on Genetics of ADHD

A genome-wide association study meta-analysis of attention-deficit hyperactivity disorder appearing in Nature Genetics links 76 genes to risk of having the disorder.

MicroRNA Cotargeting Linked to Lupus

A mouse-based study appearing in BMC Biology implicates two microRNAs with overlapping target sites in lupus.

Enzyme Involved in Lipid Metabolism Linked to Mutational Signatures

In Nature Genetics, a Wellcome Sanger Institute-led team found that APOBEC1 may contribute to the development of the SBS2 and SBS13 mutational signatures in the small intestine.