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Last Week's Sequencing-Related Papers of Note: Sep 20, 2011


Efficient de novo assembly of single-cell bacterial genomes from short-read data sets.
Chitsaz H, Yee-Greenbaum JL, Tesler G, Lombardo MJ, et al.
Nat Biotechnol. 2011 Sep 18. [Epub ahead of print] (See our coverage of this paper in this week's issue here)

Assemblathon 1: A competitive assessment of de novo short read assembly methods.
Earl DA, Bradnam K, St John J, Darling A, et al.
Genome Res. 2011 Sep 16. [Epub ahead of print]

Updated genome assembly and annotation of Paenibacillus larvae, the agent of American foulbrood disease of honey bees.
Chan QW, Cornman RS, Birol I, Liao NY, et al.
BMC Genomics. 2011 Sep 16;12(1):450.

Massively parallel rRNA gene sequencing exacerbates the potential for biased community diversity comparisons due to variable library sizes.
Gihring TM, Green SJ, Schadt CW.
Environ Microbiol. 2011 Sep 19. [Epub ahead of print]

Exome sequencing: the expert view.
Biesecker LG, Shianna KV, Mullikin JC.
Genome Biol. 2011 Sep 14;12(9):128.

Expanding whole exome resequencing into non-human primates.
Vallender EJ.
Genome Biol. 2011 Sep 14;12(9):R87.

Mutation discovery in mice by whole exome sequencing.
Fairfield H, Gilbert GJ, Barter M, Corrigan RR, et al.
Genome Biol. 2011 Sep 14;12(9):R86.

Meta-barcoding of 'dirt' DNA from soil reflects vertebrate biodiversity.
Andersen K, Bird KL, Rasmussen M, Haile J, et al.
Mol Ecol. 2011 Sep 14. doi: 10.1111/j.1365-294X.2011.05261.x. [Epub ahead of print]

Solexa sequencing of novel and differentially expressed microRNAs in testicular and ovarian tissues in Holstein cattle.
Huang J, Ju Z, Li Q, Hou Q, et al.
Int J Biol Sci. 2011;7(7):1016-26.

Testing hypotheses on the rate of molecular evolution in relation to gene expression using microRNAs.
Shen Y, Lv Y, Huang L, Liu W, et al.
Proc Natl Acad Sci U S A. 2011 Sep 12. [Epub ahead of print]

On the suitability of short reads of 16S rRNA for phylogeny-based analyses in environmental surveys.
Jeraldo P, Chia N, Goldenfeld N.
Environ Microbiol. 2011 Sep 13. [Epub ahead of print]

Evaluation of methods for de novo genome assembly from high-throughput sequencing reads reveals dependencies that affect the quality of the results.
Haiminen N, Kuhn DN, Parida L, Rigoutsos I.
PLoS One. 2011;6(9):e24182.

A fully Bayesian hidden Ising model for ChIP-seq data analysis.
Mo Q.
Biostatistics. 2011 Sep 13. [Epub ahead of print]

Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome.
Saintenac C, Jiang D, Akhunov ED.
Genome Biol. 2011 Sep 14;12(9):R88.

The Scan

Octopus Brain Complexity Linked to MicroRNA Expansions

Investigators saw microRNA gene expansions coinciding with complex brains when they analyzed certain cephalopod transcriptomes, as they report in Science Advances.

Study Tracks Outcomes in Children Born to Zika Virus-Infected Mothers

By following pregnancy outcomes for women with RT-PCR-confirmed Zika virus infections, researchers saw in Lancet Regional Health congenital abnormalities in roughly one-third of live-born children.

Team Presents Benchmark Study of RNA Classification Tools

With more than 135 transcriptomic datasets, researchers tested two dozen coding and non-coding RNA classification tools, establishing a set of potentially misclassified transcripts, as they report in Nucleic Acids Research.

Breast Cancer Risk Related to Pathogenic BRCA1 Mutation May Be Modified by Repeats

Several variable number tandem repeats appear to impact breast cancer risk and age at diagnosis in almost 350 individuals carrying a risky Ashkenazi Jewish BRCA1 founder mutation.