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Papers of Note: Apr 19, 2011


Eukaryotic richness in the abyss: insights from pyrotag sequencing.
Pawlowski J, Christen R, Lecroq B, Bachar D, et al.
PLoS One. 2011 Apr 4;6(4):e18169.

Genome-wide footprints of pig domestication and selection revealed through massive parallel sequencing of pooled DNA.
Amaral AJ, Ferretti L, Megens HJ, Crooijmans RP, et al.
PLoS One. 2011 Apr 4;6(4):e14782.

Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species.
Luo C, Walk ST, Gordon DM, Feldgarden M, et al.
Proc Natl Acad Sci U S A. 2011 Apr 11. [Epub ahead of print]

ECHO: A reference-free short-read error correction algorithm.
Kao WC, Chan AH, Song YS.
Genome Res. 2011 Apr 11. [Epub ahead of print]

Star-shaped polymers for DNA sequencing by capillary electrophoresis.
Gao F, Tie C, Zhang XX, Niu Z, He X, Ma Y.
J Chromatogr A. 2011 Mar 21. [Epub ahead of print]

Next-generation sequencing of transcriptomes: a guide to RNA isolation in nonmodel animals.
Gayral P, Weinert L, Chiari Y, Tsagkogeorga G, et al.
Mol Ecol Resour. 2011 Apr 12. doi: 10.1111/j.1755-0998.2011.03010.x. [Epub ahead of print]

Lipid bilayer coated Al(2)O(3) nanopore sensors: towards a hybrid biological solid-state nanopore.
Venkatesan BM, Polans J, Comer J, Sridhar S, et al.
Biomed Microdevices. 2011 Apr 13. [Epub ahead of print]

SOLiDzipper: a high speed encoding method for the next-generation sequencing data.
Jeon YJ, Park SH, Ahn SM, Hwang HJ.
Evol Bioinform Online. 2011 Mar 10;7:1-6.

High-throughput sequencing of complete human mtDNA genomes from the Caucasus and West Asia: high diversity and demographic inferences.
Schönberg A, Theunert C, Li M, Stoneking M, Nasidze I.
Eur J Hum Genet. 2011 Apr 13. [Epub ahead of print]

Assessing the benefits of using mate-pairs to resolve repeats in de novo short-read prokaryotic assemblies.
Wetzel J, Kingsford C, Pop M.
BMC Bioinformatics. 2011 Apr 13;12(1):95.

Accurate and exact CNV identification from targeted high-throughput sequence data.
Nord AS, Lee M, King MC, Walsh T.
BMC Genomics. 2011 Apr 12;12(1):184.

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Identifying insertion mutations by whole-genome sequencing.
Smith HE.
Biotechniques. 2011 Feb;50(2):96-7.

Enhanced translocation of poly(dt)(45) through an α-hemolysin nanopore by binding with antibody.
Ying YL, Li DW, Li Y, Lee JS, Long YT.
Chem Commun (Camb) . 2011 Apr 14. [Epub ahead of print]

DNA extraction from paraffin embedded material for genetic and epigenetic analyses.
Pikor LA, Enfield KS, Cameron H, Lam WL.
Vis Exp. 2011 Mar 26;(49). pii: 2763. doi: 10.3791/2763.

A method for counting PCR template molecules with application to next-generation sequencing.
Casbon JA, Osborne RJ, Brenner S, Lichtenstein CP.
Nucleic Acids Res. 2011 Apr 13. [Epub ahead of print]

Second-generation sequencing supply an effective way to screen RNAi targets in large scale for potential application in pest insect control.
Wang Y, Zhang H, Li H, Miao X.
PLoS One. 2011 Apr 11;6(4):e18644.

Bismark: A flexible aligner and methylation caller for bisulfite-seq applications.
Krueger F, Andrews SR.
Bioinformatics. 2011 Apr 14. [Epub ahead of print]

De novo assembly and transcriptome analysis of five major tissues of Jatropha curcas L. using GS FLX titanium platform of 454 pyrosequencing.
Natarajan P, Parani M.
BMC Genomics. 2011 Apr 15;12(1):191.

A single-cell sequencing approach to the classification of large, vacuolated sulfur bacteria.
Salman V, Amann R, Girnth AC, Polerecky L, et al.
Syst Appl Microbiol. 2011 Apr 15. [Epub ahead of print]

Hybrid capture and next-generation sequencing identify viral integration sites from formalin-fixed, paraffin-embedded tissue.
Duncavage EJ, Magrini V, Becker N, Armstrong JR, et al.
J Mol Diagn. 2011 May;13(3):325-33.

Assessing pooled BAC and whole genome shotgun strategies for assembly of complex genomes.
Haiminen N, Feltus FA, Parida L.
BMC Genomics. 2011 Apr 15;12(1):194.

Transverse conductance of DNA nucleotides in a graphene nanogap from first principles.
Prasongkit J, Grigoriev A, Pathak B, Ahuja R, Scheicher RH.
Nano Lett. 2011 Apr 15. [Epub ahead of print]

The Scan

UK Pilot Study Suggests Digital Pathway May Expand BRCA Testing in Breast Cancer

A randomized pilot study in the Journal of Medical Genetics points to similar outcomes for breast cancer patients receiving germline BRCA testing through fully digital or partially digital testing pathways.

Survey Sees Genetic Literacy on the Rise, Though Further Education Needed

Survey participants appear to have higher genetic familiarity, knowledge, and skills compared to 2013, though 'room for improvement' remains, an AJHG paper finds.

Study Reveals Molecular, Clinical Features in Colorectal Cancer Cases Involving Multiple Primary Tumors

Researchers compare mismatch repair, microsatellite instability, and tumor mutation burden patterns in synchronous multiple- or single primary colorectal cancers.

FarGen Phase One Sequences Exomes of Nearly 500 From Faroe Islands

The analysis in the European Journal of Human Genetics finds few rare variants and limited geographic structure among Faroese individuals.