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Papers of Note: Dec 21, 2010


Picoliter DNA sequencing chemistry on an electrowetting-based digital microfluidic platform.
Welch ER, Lin YY, Madison A, Fair RB.
Biotechnol J. 2010 Dec 17. [Epub ahead of print]

Haplotype-resolved genome sequencing of a Gujarati Indian individual.
Kitzman JO, Mackenzie AP, Adey A, Hiatt JB, et al.
Nat Biotechnol. 2010 Dec 19. [Epub ahead of print]

Identifying cancer driver genes in tumor genome sequencing studies.
Youn A, Simon R.
Bioinformatics. 2010 Dec 17. [Epub ahead of print]

Using non-uniform read distribution models to improve isoform expression inference in RNA-seq.
Wu Z, Wang X, Zhang X.
Bioinformatics. 2010 Dec 17. [Epub ahead of print]

Inaugural article: Completely phased genome sequencing through chromosome sorting.
Yang H, Chen X, Wong WH.
Proc Natl Acad Sci U S A. 2010 Dec 15. [Epub ahead of print]

Detection of quasispecies variants predicted to use CXCR4 by ultra-deep pyrosequencing during early HIV infection.
Abbate I, Vlassi C, Rozera G, Bruselles A, et al.
AIDS. 2010 Dec 14. [Epub ahead of print]

MethVisual — visualization and exploratory statistical analysis of DNA methylation profiles from bisulfite sequencing.
Zackay A, Steinhoff C.
BMC Res Notes. 2010 Dec 15;3(1):337.

The genetic landscape of the childhood cancer medulloblastoma.
Parsons DW, Li M, Zhang X, Jones S, et al.
Science. 2010 Dec 16. [Epub ahead of print]

Multiplex target enrichment using DNA indexing for ultra-high throughput SNP detection.
Kenny EM, Cormican P, Gilks WP, Gates AS, et al.
DNA Res. 2010 Dec 16. [Epub ahead of print]

Discrimination of methylcytosine from hydroxymethylcytosine in DNA molecules.
Wanunu M, Cohen-Karni D, Johnson RR, Fields L, et al.
Am Chem Soc. 2010 Dec 14. [Epub ahead of print]

Isoform abundance inference provides a more accurate estimation of gene expression levels in RNA-seq.
Wang X, Wu Z, Zhang X.
J Bioinform Comput Biol. 2010 Dec;8(supp01):177-192.

Efficient double fragmentation ChIP-seq provides nucleotide resolution protein-DNA binding profiles.
Mokry M, Hatzis P, de Bruijn E, Koster J, et al.
PLoS One. 2010 Nov 30;5(11):e15092.

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Characterization of the small RNA transcriptomes of androgen dependent and independent prostate cancer cell line by deep sequencing.
Xu G, Wu J, Zhou L, Chen B, et al.
PLoS One. 2010 Nov 30;5(11):e15519.

Dehydration and ionic conductance quantization in nanopores.
Zwolak M, Wilson J, Di Ventra M.
J Phys Condens Matter. 2010 Nov 17;22(45). pii: 454126.

Resequencing of positional candidates identifies low frequency IL23R coding variants protecting against inflammatory bowel disease.
Momozawa Y, Mni M, Nakamura K, Coppieters W, et al.
Nat Genet. 2010 Dec 12. [Epub ahead of print]

Maternal plasma DNA sequencing reveals the genome-wide genetic and mutational profile of the fetus.
Lo YM, Chan KC, Sun H, Chen EZ, et al.
Sci Transl Med. 2010 Dec 8;2(61):61ra91.

High-throughput sequencing of complete human mtDNA genomes from the Philippines.
Gunnarsdóttir ED, Li M, Bauchet M, Finstermeier K, Stoneking M.
Genome Res. 2010 Dec 8. [Epub ahead of print]

Copy number and targeted mutational analysis reveals novel somatic events in metastatic prostate tumors.
Robbins CM, Tembe WA, Baker A, Sinari S, et al.
Genome Res. 2010 Dec 8. [Epub ahead of print]

Molecular diagnosis for heterogeneous genetic diseases with targeted high-throughput DNA sequencing applied to retinitis pigmentosa.
Simpson DA, Clark GR, Alexander S, Silvestri G, Willoughby CE.
J Med Genet. 2010 Dec 8. [Epub ahead of print]

Exome sequencing reveals VCP mutations as a cause of familial ALS.
Johnson JO, Mandrioli J, Benatar M, Abramzon Y, et al.
Neuron. 2010 Dec 9;68(5):857-864.

Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition.
Adey A, Morrison HG, No Last Name A, Xun X, et al.
Genome Biol. 2010 Dec 8;11(12):R119.

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.