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Papers of Note: Oct 26, 2010


Whole-genome sequencing and comprehensive variant analysis of a Japanese individual using massively parallel sequencing.
Fujimoto A, Nakagawa H, Hosono N, Nakano K, et al.
Nat Genet. 2010 Oct 24. [Epub ahead of print]

Genome-wide patterns of genetic variation among elite maize inbred lines.
Lai J, Li R, Xu X, Jin W, et al.
Nat Genet. 2010 Oct 24. [Epub ahead of print]

GAMES identifies and annotates mutations in next-generation sequencing projects.
Sana ME, Iascone M, Marchetti D, Palatini J, et al.
Bioinformatics. 2010 Oct 22. [Epub ahead of print]

Deep cap analysis of gene expression.
Kurosawa J, Nishiyori H, Hayashizaki Y.
Methods Mol Biol. 2011;687:147-63.

High-throughput SuperSAGE.
Matsumura H, Yoshida K, Luo S, Krüger DH, et al.
Methods Mol Biol. 2011;687:135-46.

Sequencing of difficult DNA regions by SAM sequencing.
Mitchelson KR.
Methods Mol Biol. 2011;687:75-88.

SmashCell: A software framework for the analysis of single-cell amplified genome sequences.
Harrington ED, Arumugam M, Raes J, Bork P, Relman DA.
Bioinformatics. 2010 Oct 21. [Epub ahead of print]

CNAseg — a novel framework for identification of copy number changes in cancer from second-generation sequencing data.
Ivakhno S, Royce T, Cox AJ, Evers DJ, et al.
Bioinformatics. 2010 Oct 21. [Epub ahead of print]

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NGSmethDB: a database for next-generation sequencing single-cytosine-resolution DNA methylation data.
Hackenberg M, Barturen G, Oliver JL.
Nucleic Acids Res. 2010 Oct 21. [Epub ahead of print]

FusionSeq: a modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data.
Sboner A, Habegger L, Pflueger D, Terry S, et al.
Genome Biol. 2010 Oct 21;11(10):R104. [Epub ahead of print]

Reduction of non-insert sequence reads by dimer eliminator LNA oligonucleotide for small RNA deep sequencing.
Kawano M, Kawazu C, Lizio M, Kawaji H, et al.
Biotechniques. 2010 Oct;49(4):751-5.

BIPES, a cost-effective high-throughput method for assessing microbial diversity.
Zhou HW, Li DF, Tam NF, Jiang XT, et al.
ISME J. 2010 Oct 21. [Epub ahead of print]

Genome-wide identification of human microRNAs located in leukemia-associated genomic alterations.
Starczynowski DT, Morin R, McPherson A, Lam J, et al.
Blood. 2010 Oct 20. [Epub ahead of print]

Ray: Simultaneous assembly of reads from a mix of high-throughput sequencing technologies.
Boisvert S, Laviolette F, Corbeil J.
Comput Biol. 2010 Oct 20. [Epub ahead of print]

MethylViewer: computational analysis and editing for bisulfite sequencing and methyltransferase accessibility protocol for individual templates (MAPit) projects.
Pardo CE, Carr IM, Hoffman CJ, Darst RP, et al.
Nucleic Acids Res. 2010 Oct 19. [Epub ahead of print]

The Scan

Driving Malaria-Carrying Mosquitoes Down

Researchers from the UK and Italy have tested a gene drive for mosquitoes to limit the spread of malaria, NPR reports.

Office Space to Lab Space

The New York Times writes that some empty office spaces are transforming into lab spaces.

Prion Pause to Investigate

Science reports that a moratorium on prion research has been imposed at French public research institutions.

Genome Research Papers on Gut Microbe Antibiotic Response, Single-Cell RNA-Seq Clues to Metabolism, More

In Genome Research this week: gut microbial response to antibiotic treatment, approach to gauge metabolic features from single-cell RNA sequencing, and more.