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Papers of Note: Aug 24, 2010


ChIP-seq and functional analysis of the SOX2 gene in colorectal cancers.
Fang X, Yu W, Li L, Shao J, et al.
OMICS. 2010 Aug;14(4):369-84.

Complete genome sequence of Staphylococcus aureus strain JKD6159, a unique Australian clone of ST93-IV community methicillin-resistant Staphylococcus aureus.
Chua K, Seemann T, Harrison PF, Davies JK, et al.
J Bacteriol. 2010 Aug 20. [Epub ahead of print]

A new dominant peroxiredoxin allele identified by whole-genome re-sequencing of random mutagenized yeast causes oxidant-resistance and premature aging.
Timmermann B, Jarolim S, Rußmayer H, Kerick M, et al.
Aging (Albany NY). 2010 Aug 13. [Epub ahead of print]

Whole-exome sequencing identifies recessive WDR62 mutations in severe brain malformations.
Bilgüvar K, Oztürk AK, Louvi A, Kwan KY, et al.
Nature. 2010 Aug 22. [Epub ahead of print]

ChIP-seq identification of weakly conserved heart enhancers.
Blow MJ, McCulley DJ, Li Z, Zhang T, et al.
Nat Genet. 2010 Aug 22. [Epub ahead of print]

One-way traffic of a viral motor channel for double-stranded DNA translocation.
Jing P, Haque F, Shu D, Montemagno C, Guo P.
Nano Lett. 2010 Aug 19. [Epub ahead of print]

Detection of nucleic acids with graphene nanopores: ab initio characterization of a novel sequencing device.
Nelson T, Zhang B, Prezhdo OV.
Nano Lett. 2010 Aug 19. [Epub ahead of print]

Understanding human genetic variation in the era of high-throughput sequencing.
Knight JC.
EMBO Rep. 2010 Aug 20. [Epub ahead of print]

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Use of cancer-specific genomic rearrangements to quantify disease burden in plasma from patients with solid tumors.
McBride DJ, Orpana AK, Sotiriou C, Joensuu H, et al.
Genes Chromosomes Cancer. 2010 Aug 19. [Epub ahead of print]

Identification by whole genome resequencing of gene defect responsible for severe hypercholesterolemia.
Rios J, Stein E, Shendure J, Hobbs HH, Cohen JC.
Hum Mol Genet. 2010 Aug 18. [Epub ahead of print]

Graphene as a subnanometre trans-electrode membrane.
Garaj S, Hubbard W, Reina A, Kong J, Branton D, Golovchenko JA.
Nature. 2010 Aug 18. [Epub ahead of print]

rSW-seq: Algorithm for detection of copy number alterations in deep sequencing data.
Kim TM, Luquette LJ, Xi R, Park PJ.
BMC Bioinformatics. 2010 Aug 18;11(1):432

Oral bacterial genome sequencing using the high-throughput Roche Genome Sequencer FLX System.
Heng NC, Stanton JA.
Methods Mol Biol. 2010;666:197-218.

An approach to evaluate the reliability of hybridization-based and sequencing-based gene expression profiling technologies.
Yang DY, Wang XL, Deng PJ, Zhou XY, et al.
Biotechnol Prog. 2010 Jun 1. [Epub ahead of print]

SICTIN: Rapid footprinting of massively parallel sequencing data.
Enroth S, Andersson R, Wadelius C, Komorowski J.
BioData Min. 2010 Aug 13;3(1):4

Genetic validation of whole-transcriptome sequencing for mapping expression affected by cis-regulatory variation.
Babak T, Garrett-Engele P, Armour CD, Raymond CK, et al.
BMC Genomics. 2010 Aug 13;11(1):473

Exome sequencing identifies MLL2 mutations as a cause of Kabuki syndrome.
Ng SB, Bigham AW, Buckingham KJ, Hannibal MC, et al.
Nat Genet. 2010 Aug 15. [Epub ahead of print]

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Comprehensive comparative analysis of strand-specific RNA sequencing methods.
Levin JZ, Yassour M, Adiconis X, Nusbaum C, et al.
Nat Methods. 2010 Aug 15. [Epub ahead of print]

Quantitative selection of DNA aptamers through microfluidic selection and high-throughput sequencing.
Cho M, Xiao Y, Nie J, Stewart R, et al.
Proc Natl Acad Sci U S A. 2010 Aug 12. [Epub ahead of print]

DNA translocation through graphene nanopores.
Merchant CA, Healy K, Wanunu M, Ray V, et al.
Nano Lett. 2010 Aug 11;10(8):2915-21.

A complete DNA sequence map of the ovine Major Histocompatibility Complex.
Gao J, Liu K, Liu H, Blair HT, Li G, Chen C, Tan P, Ma RZ.
BMC Genomics. 2010 Aug 10;11(1):466

Identification of rare alleles and their carriers using compressed se(que)nsing.
Shental N, Amir A, Zuk O.
Nucleic Acids Res. 2010 Aug 10. [Epub ahead of print]

High-throughput SuperSAGE for digital gene expression analysis of multiple samples using next generation sequencing.
Matsumura H, Yoshida K, Luo S, Kimura E, et al.
PLoS One. 2010 Aug 6;5(8). pii: e12010.

SNP discovery by high-throughput sequencing in soybean.
Wu X, Ren C, Joshi T, Vuong T, Xu D, Nguyen HT.
BMC Genomics. 2010 Aug 11;11(1):469

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.