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In Print: Last Week's Sequencing-Related Papers of Note: Oct 29, 2012


Identifying transcriptional miRNA biomarkers by integrating high-throughput sequencing and real-time PCR data.
Rahmann S, Martin M, Schulte JH, Köster J, et al.
Methods. 2012 Oct 22. [Epub ahead of print]

Comparison of 454 pyrosequencing methods for characterizing the major histocompatibility complex of nonmodel species and the advantages of ultra deep coverage.
Oomen RA, Gillett RM, Kyle CJ.
Mol Ecol Resour. 2012 Oct 24. [Epub ahead of print]

GapFiller: a de novo assembly approach to fill the gap within paired reads.
Nadalin F, Vezzi F, Policriti A.
BMC Bioinformatics. 2012;13 Suppl 14:S8.

ENU-induced phenovariance in mice: inferences from 587 mutations.
Arnold CN, Barnes MJ, Berger M, Blasius AL, Brandl K, et al.
BMC Res Notes. 2012 Oct 24;5(1):577.

Local assemblies of paired-end reduced representation libraries sequenced with the Illumina Genome Analyzer in maize.
Deschamps S, Nannapaneni K, Zhang Y, Hayes K.
Int J Plant Genomics. 2012;2012:360598.

Modeling kinetic rate variation in third generation DNA sequencing data to detect putative modifications to DNA bases.
Schadt E, Banerjee O, Fang G, Feng Z, et al.
Genome Res. 2012 Oct 23. [Epub ahead of print]

Genotype calling and phasing using next-generation sequencing reads and a haplotype scaffold.
Menelaou A, Marchini J.
Bioinformatics. 2012 Oct 23. [Epub ahead of print]

Discovering chimeric transcripts in paired-end RNA-seq data by using EricScript.
Benelli M, Pescucci C, Marseglia G, Severgnini M, et al.
Bioinformatics. 2012 Oct 23. [Epub ahead of print]

Toward an understanding of changes in diversity associated with fecal microbiome transplantation based on 16S rRNA gene deep sequencing.
Shahinas D, Silverman M, Sittler T, Chiu C, et al.
MBio. 2012 Oct 23;3(5).

Beyond Streptococcus mutans: dental caries onset linked to multiple species by 16S rRNA community analysis.
Gross EL, Beall CJ, Kutsch SR, Firestone ND, et al.
PLoS One. 2012;7(10):e47722.

De novo assembly, characterization and functional annotation of pineapple fruit transcriptome through massively parallel sequencing.
Ong WD, Voo LY, Kumar VS.
PLoS One. 2012;7(10):e46937.

Genotype of a historic strain of Mycobacterium tuberculosis.
Bouwman AS, Kennedy SL, Müller R, Stephens RH, et al.
Proc Natl Acad Sci U S A. 2012 Oct 22. [Epub ahead of print]

Accurate human microsatellite genotypes from high-throughput resequencing data using informed error profiles.
Highnam G, Franck C, Martin A, Stephens C, et al.
Nucleic Acids Res. 2012 Oct 22. [Epub ahead of print]

The Scan

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.

Team Presents Cattle Genotype-Tissue Expression Atlas

Using RNA sequences representing thousands of cattle samples, researchers looked at relationships between cattle genotype and tissue expression in Nature Genetics.

Researchers Map Recombination in Khoe-San Population

With whole-genome sequences for dozens of individuals from the Nama population, researchers saw in Genome Biology fine-scale recombination patterns that clustered outside of other populations.

Myotonic Dystrophy Repeat Detected in Family Genome Sequencing Analysis

While sequencing individuals from a multi-generation family, researchers identified a myotonic dystrophy type 2-related short tandem repeat in the European Journal of Human Genetics.