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In Print: Last Week's Sequencing-Related Papers of Note: Aug 14, 2012


A rapid method for combined analysis of common and rare variants at the level of a region, gene, or pathway.
Curtis D.
Adv Appl Bioinform Chem. 2012;5:1-9.

Barcoded cDNA library preparation for small RNA profiling by next-generation sequencing.
Hafner M, Renwick N, Farazi TA, Mihailovi A, et al.
Methods. 2012 Aug 7. [Epub ahead of print]

Microfluidic PCR combined with pyrosequencing identify allelic variants with phenotypic associations in targeted Salmonella genes.
Yue M, Schmieder R, Edwards RA, Rankin SC, Schifferli DM.
Appl Environ Microbiol. 2012 Aug 10. [Epub ahead of print]

Discovery and characterization of new transcripts from RNA-seq data in mouse CD4(+) T cells.
Hutchins AP, Poulain S, Fujii H, Miranda-Saavedra D.
Genomics. 2012 Aug 4. [Epub ahead of print]

Normalization of ChIP-seq data with control.
Liang K, Keles S.
BMC Bioinformatics. 2012 Aug 10;13(1):199.

Optimization of Bartonella henselae multilocus sequence typing scheme using single-nucleotide polymorphism analysis of SOLiD sequence data.
Zhao F, Chaloner G, Darby A, Song XP, et al.
Chin Med J (Engl). 2012 Jul;125(13):2284-8.

SAP-A sequence mapping and analyzing program for long sequence reads alignment and accurate variants discovery.
Sun Z, Tian W.
PLoS One. 2012;7(8):e42887.

Mis-assembled "segmental duplications" in two versions of the Bos taurus genome.
Zimin AV, Kelley DR, Roberts M, Marçais G, et al.
PLoS One. 2012;7(8):e42680.

Soil bacterial diversity screening using single 16S rRNA gene V regions coupled with multi-million read generating sequencing technologies.
Vasileiadis S, Puglisi E, Arena M, Cappa F, et al.
PLoS One. 2012;7(8):e42671.

Genome-wide detection of spontaneous chromosomal rearrangements in bacteria.
Sun S, Ke R, Hughes D, Nilsson M, Andersson DI.
PLoS One. 2012;7(8):e42639.

Discovery of genes related to insecticide resistance in Bactrocera dorsalis by functional genomic analysis of a de novo assembled transcriptome.
Hsu JC, Chien TY, Hu CC, Chen MJ, et al.
PLoS One. 2012;7(8):e40950.

Copy-number-aware differential analysis of quantitative DNA sequencing data.
Robinson MD, Strbenac D, Stirzaker C, Statham AL, et al.
Genome Res. 2012 Aug 9. [Epub ahead of print]

A solid quality-control analysis of AB SOLiD short-read sequencing data.
Castellana S, Romani M, Valente EM, Mazza T.
Brief Bioinform. 2012 Aug 9. [Epub ahead of print]

Application of next generation sequencing to human gene fusion detection: computational tools, features and perspectives.
Wang Q, Xia J, Jia P, Pao W, Zhao Z.
Brief Bioinform. 2012 Aug 9. [Epub ahead of print]

Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples.
Wagner GP, Kin K, Lynch VJ.
Theory Biosci. 2012 Aug 8. [Epub ahead of print]

SIMPLEX: cloud-enabled pipeline for the comprehensive analysis of exome sequencing data.
Fischer M, Snajder R, Pabinger S, Dander A, et al.
PLoS One. 2012;7(8):e41948.

Bacterial community shift in treated periodontitis patients revealed by Ion Torrent 16S rRNA gene amplicon sequencing.
Jünemann S, Prior K, Szczepanowski R, Harks I, et al.
PLoS One. 2012;7(8):e41606.

Deep panning: steps towards probing the IgOme.
Ryvkin A, Ashkenazy H, Smelyanski L, Kaplan G, et al.
PLoS One. 2012;7(8):e41469.

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.