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Papers of Note: Feb 8, 2011


Picoliter DNA sequencing chemistry on an electrowetting-based digital microfluidic platform.
Welch ER, Lin YY, Madison A, Fair RB.
Biotechnol J. 2011 Feb;6(2):165-76.

Genome-wide analysis of transcriptional reprogramming in mouse models of acute myeloid leukemia.
Bonadies N, Foster SD, Chan WI, Kvinlaug BT, Spensberger D, et al.
PLoS One. 2011 Jan 28;6(1):e16330.

Genome-wide mapping of Arabidopsis thaliana origins of DNA replication and their associated epigenetic marks.
Costas C, de la Paz Sanchez M, Stroud H, Yu Y, et al.
Nat Struct Mol Biol. 2011 Feb 6. [Epub ahead of print]

Fast DNA sequencing with a graphene-based nanochannel device.
Min SK, Kim WY, Cho Y, Kim KS.
Nat Nanotechnol. 2011 Feb 6. [Epub ahead of print]

Genome size and transposable element content as determined by high-throughput sequencing in maize and Zea luxurians.
Tenaillon MI, Hufford MB, Gaut BS, Ross-Ibarra J.
Genome Biol Evol. 2011 Feb 4. [Epub ahead of print]

Whole-exome sequencing links a variant in DHDDS to retinitis pigmentosa.
Züchner S, Dallman J, Wen R, Beecham G, et al.
Am J Hum Genet. 2011 Feb 2. [Epub ahead of print]

Fluoride-cleavable, fluorescently labelled reversible terminators: synthesis and use in primer extension.
Knapp DC, Serva S, D'Onofrio J, Keller A, et al.
Chemistry. 2011 Feb 3. doi: 10.1002/chem.201001952. [Epub ahead of print]

Mapping copy number variation by population-scale genome sequencing.
Mills RE, Walter K, Stewart C, Handsaker RE, et al.
Nature. 2011 Feb 3;470(7332):59-65.

The ecoresponsive genome of Daphnia pulex.
Colbourne JK, Pfrender ME, Gilbert D, Thomas WK, et al.
Science. 2011 Feb 4;331(6017):555-61.

Structural variation in the chicken genome identified by paired-end next-generation DNA sequencing of reduced representation libraries.
Kerstens HH, Crooijmans RP, Dibbits BW, Vereijken A, et al.
BMC Genomics. 2011 Feb 3;12(1):94.

Deep sequencing to infer HIV-1 co-receptor usage: application to three clinical trials of maraviroc in treatment-experienced patients.
Swenson LC, Mo T, Dong WW, Zhong X, et al.
J Infect Dis. 2011 Jan;203(2):237-45.

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Deep sequencing reveals mixed infection with 2009 pandemic influenza A (H1N1) virus strains and the emergence of oseltamivir resistance.
Ghedin E, Laplante J, Depasse J, Wentworth DE, et al.
J Infect Dis. 2011 Jan;203(2):168-74.

Exome localization of complex disease association signals.
Lehne B, Lewis CM, Schlitt T.
BMC Genomics. 2011 Feb 1;12(1):92.

Whole transcriptome sequencing reveals gene expression and splicing differences in brain regions affected by Alzheimer's disease.
Twine NA, Janitz K, Wilkins MR, Janitz M.
PLoS One. 2011 Jan 21;6(1):e16266.

Sequencing and bioinformatics-based analyses of the microRNA transcriptome in hepatitis B-related hepatocellular carcinoma.
Mizuguchi Y, Mishima T, Yokomuro S, Arima Y, et al.
PLoS One. 2011 Jan 25;6(1):e15304.

The genome of the fire ant Solenopsis invicta.
Wurm Y, Wang J, Riba-Grognuz O, Corona M, et al.
Proc Natl Acad Sci U S A. 2011 Jan 31. [Epub ahead of print]

Draft genome of the red harvester ant Pogonomyrmex barbatus.
Smith CR, Smith CD, Robertson HM, Helmkampf M, et al.
Proc Natl Acad Sci U S A. 2011 Jan 31. [Epub ahead of print]

Widespread establishment and regulatory impact of Alu exons in human genes.
Shen S, Lin L, Cai JJ, Jiang P, et al.
Proc Natl Acad Sci U S A. 2011 Jan 31. [Epub ahead of print]

Draft genome of the globally widespread and invasive Argentine ant (Linepithema humile).
Smith CD, Zimin A, Holt C, Abouheif E, et al.
Proc Natl Acad Sci U S A. 2011 Jan 31. [Epub ahead of print]

The complete mitochondrial genome of an 11,450-year-old Aurochsen (Bos primigenius) from central Italy.
Lari M, Rizzi E, Mona S, Corti G, et al.
BMC Evol Biol. 2011 Jan 31;11(1):32.

ChIPseqR: Analysis of ChIP-seq experiments.
Humburg P, Helliwell CA, Bulger D, Stone G.
BMC Bioinformatics. 2011 Jan 31;12(1):39.

The Scan

Lung Cancer Response to Checkpoint Inhibitors Reflected in Circulating Tumor DNA

In non-small cell lung cancer patients, researchers find in JCO Precision Oncology that survival benefits after immune checkpoint blockade coincide with a dip in ctDNA levels.

Study Reviews Family, Provider Responses to Rapid Whole-Genome Sequencing Follow-up

Investigators identified in the European Journal of Human Genetics variable follow-up practices after rapid whole-genome sequencing.

BMI-Related Variants Show Age-Related Stability in UK Biobank Participants

Researchers followed body mass index variant stability with genomic structural equation modeling and genome-wide association studies of 40- to 72-year olds in PLOS Genetics.

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.