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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

Genetic Risk Factors for Hypertension Can Help Identify Those at Risk for Cardiovascular Disease

Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.

Circulating Tumor DNA Linked to Post-Treatment Relapse in Breast Cancer

Post-treatment detection of circulating tumor DNA may identify breast cancer patients who are more likely to relapse, a new JCO Precision Oncology study finds.

Genetics Influence Level of Depression Tied to Trauma Exposure, Study Finds

Researchers examine the interplay of trauma, genetics, and major depressive disorder in JAMA Psychiatry.

UCLA Team Reports Cost-Effective Liquid Biopsy Approach for Cancer Detection

The researchers report in Nature Communications that their liquid biopsy approach has high specificity in detecting all- and early-stage cancers.