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In Print: Last Week's Sequencing-Related Papers of Note: Jul 24, 2012


MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads.
Namiki T, Hachiya T, Tanaka H, Sakakibara Y.
Nucleic Acids Res. 2012 Jul 19. [Epub ahead of print]

Deep sequencing of RNA from immune cell-derived vesicles uncovers the selective incorporation of small non-coding RNA biotypes with potential regulatory functions.
Nolte-'t Hoen EN, Buermans HP, Waasdorp M, Stoorvogel W, et al.
Nucleic Acids Res. 2012 Jul 19. [Epub ahead of print]

Joint genotype calling with array and sequence data.
O'Connell J, Marchini J.
Genet Epidemiol. 2012 Jul 20. [Epub ahead of print]

Direct sequencing of Arabidopsis thaliana RNA reveals patterns of cleavage and polyadenylation.
Sherstnev A, Duc C, Cole C, Zacharaki V, et al.
Nat Struct Mol Biol. 2012 Jul 22. [Epub ahead of print]

Denaturation mapping of Saccharomyces cerevisiae.
Welch RL, Sladek R, Dewar K, Reisner WW.
Lab Chip. 2012 Jul 23. [Epub ahead of print]

SpliceSeq: a resource for analysis and visualization of RNA-seq data on alternative splicing and its functional impacts.
Ryan MC, Cleland J, Kim R, Wong WC, Weinstein JN.
Bioinformatics. 2012 Jul 20. [Epub ahead of print]

Genome-wide single-cell analysis of recombination activity and de novo mutation rates in human sperm.
Wang J, Fan HC, Behr B, Quake SR.
Cell. 2012 Jul 20;150(2):402-12.
(See our coverage of this paper here.)

Transcript dynamics of proinflammatory genes revealed by sequence analysis of subcellular RNA fractions.
Bhatt DM, Pandya-Jones A, Tong AJ, Barozzi I, et al.
Cell. 2012 Jul 20;150(2):279-90.

Breakdown of phylogenetic signal: a survey of microsatellite densities in 454 shotgun sequences from 154 non model eukaryote species.
Meglécz E, Nève G, Biffin E, Gardner MG.
PLoS One. 2012;7(7):e40861.

Quantifying uniformity of mapped reads.
Hower V, Starfield R, Roberts A, Pachter L.
Bioinformatics. 2012 Jul 18. [Epub ahead of print]

Fast and accurate read alignment for resequencing.
Mu JC, Jiang H, Kiani A, Mohiyuddin M, et al.
Bioinformatics. 2012 Jul 18. [Epub ahead of print]

Analysis of context-dependent errors for Illumina sequencing.
Abnizova I, Leonard S, Skelly T, Brown A, et al.
J Bioinform Comput Biol. 2012 Apr;10(2):1241005.

Optimization of de novo transcriptome assembly from high-throughput short read sequencing data improves functional annotation for non-model organisms.
Haznedaroglu BZ, Reeves D, Rismani-Yazdi H, Peccia J.
BMC Bioinformatics. 2012 Jul 18;13(1):170.

Electrokinetic ion and fluid transport in nanopores functionalized by polyelectrolyte brushes.
Yeh LH, Zhang M, Hu N, Joo SW, et al.
Nanoscale. 2012 Jul 17. [Epub ahead of print]

Paired-end sequencing of fosmid libraries by Illumina.
Williams LJ, Tabbaa DG, Li N, Berlin AM, et al.
Genome Res. 2012 Jul 16. [Epub ahead of print]

Slim-Filter: an interactive windows-based application for Illumina Genome Analyzer data assessment and manipulation.
Golovko G, Khanipov K, Rojas M, Martinez-Alcántara A, et al.
BMC Bioinformatics. 2012 Jul 16;13(1):166.

Testing the limits of 454 pyrotag sequencing: reproducibility, quantitative assessment and comparison to T-RFLP fingerprinting of aquifer microbes.
Pilloni G, Granitsiotis MS, Engel M, Lueders T.
PLoS One. 2012;7(7):e40467.

Genome-wide detection of genes targeted by non-Ig somatic hypermutation in lymphoma.
Jiang Y, Soong TD, Wang L, Melnick AM, Elemento O.
PLoS One. 2012;7(7):e40332.

Efficiency and power as a function of sequence coverage, SNP array density, and imputation.
Flannick J, Korn JM, Fontanillas P, Grant GB, et al.
PLoS Comput Biol. 2012 Jul;8(7):e1002604.

Application of next-generation sequencing for rapid marker development in molecular plant breeding: a case study on anthracnose disease resistance in Lupinus angustifolius L.
Yang H, Tao Y, Zheng Z, Li C, et al.
BMC Genomics. 2012 Jul 17;13(1):318.

Measurement of the docking time of a DNA molecule onto a solid-state nanopore.
Kowalczyk SW, Dekker C.
Nano Lett. 2012 Jul 17. [Epub ahead of print]

Human gut microbiome viewed across age and geography.
Yatsunenko T, Rey FE, Manary MJ, Trehan I, et al.
Nature. 2012 May 9;486(7402):222-7.

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.