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Papers of Note: Jul 20, 2010


454 pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases.
Tedersoo L, Nilsson RH, Abarenkov K, Jairus T, et al.
New Phytol. 2010 Jul 15. [Epub ahead of print]

A simple method to confirm and size deletion, duplication, and insertion mutations detected by sequence analysis.
Hjelm LN, Chin EL, Hegde MR, Coffee BW, Bean LJ.
J Mol Diagn. 2010 Jul 15. [Epub ahead of print]

BigWig and BigBed: enabling browsing of large distributed data sets.
Kent WJ, Zweig AS, Barber G, Hinrichs AS, Karolchik D.
Bioinformatics. 2010 Jul 17. [Epub ahead of print]

SVDetect: a tool to identify genomic structural variations from paired-end and mate-pair sequencing data.
Zeitouni B, Boeva V, Janoueix-Lerosey I, Loeillet S, et al.
Bioinformatics. 2010 Aug 1;26(15):1895-6.

Amplification-free digital gene expression profiling from minute cell quantities.
Ozsolak F , Ting DT, Wittner BS, Brannigan BW, Paul S, et al.
Nat Methods. 2010 Jul 18. [Epub ahead of print]

Graph-based clustering and characterization of repetitive sequences in next-generation sequencing data.
Novak P, Neumann P, Macas J.
BMC Bioinformatics. 2010 Jul 15;11(1):378. [Epub ahead of print]

ANDES: Statistical tools for the ANalyses of DEep Sequencing.
Li K, Venter E, Yooseph S, Stockwell TB, et al.
BMC Res Notes. 2010 Jul 15;3(1):199. [Epub ahead of print]

Read length and repeat resolution: exploring prokaryote genomes using next-generation sequencing technologies.
Cahill MJ, Köser CU, Ross NE, Archer JA.
PLoS One. 2010 Jul 12;5(7):e11518.

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Bisulfite patch PCR enables multiplexed sequencing of promoter methylation across cancer samples.
Varley KE, Mitra RD.
Genome Res. 2010 Jul 13. [Epub ahead of print]

Evaluation of algorithm performance in ChIP-seq peak detection.
Wilbanks EG, Facciotti MT.
PLoS One. 2010 Jul 8;5(7):e11471.

The effects of alignment quality, distance calculation method, sequence filtering, and region on the analysis of 16S rRNA gene-based studies.
Schloss PD.
PLoS Comput Biol. 2010 Jul 8;6(7):e1000844.

Dynamics of HIV-1 quasispecies during antiviral treatment dissected using ultra-deep pyrosequencing.
Hedskog C, Mild M, Jernberg J, Sherwood E, et al.
PLoS One. 2010 Jul 7;5(7):e11345.

Directed evolution of DNA polymerases for next-generation sequencing.
Leconte AM, Patel MP, Sass LE, McInerney P, et al.
Angew Chem Int Ed Engl. 2010 Jul 13. [Epub ahead of print]

SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments.
Burdick DB, Cavnor CC, Handcock J, Killcoyne S, et al.
BMC Bioinformatics. 2010 Jul 14;11(1):377. [Epub ahead of print]

Semi-automated library preparation for high-throughput DNA sequencing platforms.
Farias-Hesson E, Erikson J, Atkins A, Shen P, et al.
J Biomed Biotechnol. 2010;2010:617469. Epub 2010 Jun 8.

Using deep RNA sequencing for the structural annotation of the Laccaria bicolor mycorrhizal transcriptome.
Larsen PE, Trivedi G, Sreedasyam A, Lu V, et al.
PLoS One. 2010 Jul 6;5(7):e9780.

A comparison of several algorithms for the single individual SNP haplotyping reconstruction problem.
Geraci F.
Bioinformatics. 2010 Jul 11. [Epub ahead of print]

Index-free de novo assembly and deconvolution of mixed mitochondrial genomes.
McComish BJ, Hills SF, Biggs PJ, Penny D.
Genome Biol Evol. 2010 Jul 12;2:410-24. Print 2010.

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Whirlwind Decade of CRISPR

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PNAS Papers on Blue Cone Monochromacy Structural Variants, HIV-1 Mutant, T-ALL

In PNAS this week: structural variants linked to blue cone monochromacy, HIV-1 variants affecting the matrix protein p17, and more.