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Papers of Note: Sep 28, 2010


Replication of individual DNA molecules under electronic control using a protein nanopore.
Olasagasti F, Lieberman KR, Benner S, Cherf GM, et al.
Nat Nanotechnol. 2010 Sep 26. [Epub ahead of print]

High Redundancy Draft Sequencing of 15 Clinical and Environmental Burkholderia strains.
Mukhopadhyay S, Thomason MP, Lentz S, Nolan N, et al.
J Bacteriol. 2010 Sep 24. [Epub ahead of print]

Re-sequencing the Mycobacterium avium subsp. paratuberculosis K10 genome: improved annotation and revised genome sequence.
Wynne JW, Seemann T, Bulach D, Coutts SA, Talaat AM, Michalski WP.
J Bacteriol. 2010 Sep 24. [Epub ahead of print]

BMPER Mutation in Diaphanospondylodysostosis Identified by Ancestral Autozygosity Mapping and Targeted High-Throughput Sequencing.
Funari VA, Krakow D, Nevarez L, Chen Z, Funari TL, Vatanavicharn N, Wilcox WR, Rimoin DL, Nelson SF, Cohn DH.
Am J Hum Genet. 2010 Sep 22. [Epub ahead of print]

Base-By-Base Ratcheting of Single Stranded DNA through a Solid-State Nanopore.
Luan B, Peng H, Polonsky S, Rossnagel S, Stolovitzky G, Martyna G.
Phys Rev Lett. 2010 Jun 11;104(23):238103.

Polymer translocation into a fluidic channel through a nanopore.
Luo K, Metzler R.
Phys Rev E Stat Nonlin Soft Matter Phys. 2010 Aug;82(2-1):021922.

Biological databases at DNA Data Bank of Japan in the era of next-generation sequencing technologies.
Kodama Y, Kaminuma E, Saruhashi S, Ikeo K, et al.
Adv Exp Med Biol. 2010;680:125-135.

Host imprints on bacterial genomes — rapid, divergent evolution in individual patients.
Zdziarski J, Brzuszkiewicz E, Wullt B, Liesegang H, et al.
PLoS Pathog. 2010 Aug 26;6(8). pii: e1001078.

Identification of the bovine arachnomelia mutation by massively parallel sequencing implicates sulfite oxidase (SUOX) in bone development.
Drögemüller C, Tetens J, Sigurdsson S, Gentile A, et al.
PLoS Genet. 2010 Aug 26;6(8). pii: e1001079.

Genomic characterization of Campylobacter jejuni strain M1.
Friis C, Wassenaar TM, Javed MA, Snipen L, et al.
PLoS One. 2010 Aug 26;5(8). pii: e12253.

Evaluation of second-generation sequencing of 19 dilated cardiomyopathy genes for clinical applications.
Gowrisankar S, Lerner-Ellis JP, Cox S, White ET, et al.
J Mol Diagn. 2010 Sep 23. [Epub ahead of print]

A comparison of RNA-seq and high-density exon array for detecting differential gene expression between closely related species.
Liu S, Lin L, Jiang P, Wang D, Xing Y.
Nucleic Acids Res. 2010 Sep 22. [Epub ahead of print]

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SOLiD pyrosequencing of four Vibrio vulnificus genomes enables comparative genomic analysis and identification of candidate clade-specific virulence genes.
Gulig PA, de Crecy-Lagard V, Wright AC, Walts B, et al.
BMC Genomics. 2010 Sep 24;11(1):512.

Characterization of Epstein-Barr virus miRNAome in nasopharyngeal carcinoma by deep sequencing.
Chen SJ, Chen GH, Chen YH, Liu CY, et al.
PLoS One. 2010 Sep 20;5(9). pii: e12745.

Identification of disease-causing mutations in autosomal dominant retinitis pigmentosa (adRP) using next-generation DNA sequencing.
Bowne SJ, Sullivan LS, Koboldt DC, Ding L, et al.
Invest Ophthalmol Vis Sci. 2010 Sep 22. [Epub ahead of print]

The complete chloroplast genome sequence of date palm (Phoenix dactylifera L.).
Yang M, Zhang X, Liu G, Yin Y, et al.
PLoS One. 2010 Sep 15;5(9). pii: e12762.

MetMap enables genome-scale methyltyping for determining methylation states in populations.
Singer M, Boffelli D, Dhahbi J, Schönhuth A, et al.
PLoS Comput Biol. 2010 Aug 19;6(8). pii: e1000888.

Accurate reconstruction for DNA sequencing by hybridization based on a constructive heuristic.
Ch en Y, Hu J.
IEEE/ACM Trans Comput Biol Bioinform. 2010 Sep 8. [Epub ahead of print]

Use of barcoded pyrosequencing and shared OTUs to determine sources of fecal bacteria in watersheds.
Unno T, Jang J, Han D, Kim JH, et al.
Environ Sci Technol. 2010 Sep 20. [Epub ahead of print]

Whole genome re-sequencing identifies a mutation in an ABC transporter (mdr2) in a Plasmodium chabaudi clone with altered susceptibility to antifolate drugs.
Martinelli A, Henriques G, Cravo P, Hunt P.
Int J Parasitol. 2010 Sep 18. [Epub ahead of print]

New class of gene-termini-associated human RNAs suggests a novel RNA copying mechanism.
Kapranov P, Ozsolak F, Kim SW, Foissac S, et al.
Nature. 2010 Jul 29;466(7306):642-6.
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.