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Papers of Note: Jun 7, 2011


Single-tube linear DNA amplification (LinDA) for robust ChIP-seq.
Shankaranarayanan P, Mendoza-Parra MA, Walia M, Wang L, et al.
Nat Methods. 2011 Jun 5. [Epub ahead of print]

Modeling and automation of sequencing-based characterization of RNA structure.
Aviran S, Trapnell C, Lucks JB, Mortimer SA, et al.
Proc Natl Acad Sci U S A. 2011 Jun 3. [Epub ahead of print]

Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-seq).
Lucks JB, Mortimer SA, Trapnell C, Luo S, et al.
Proc Natl Acad Sci U S A. 2011 Jun 3. [Epub ahead of print]

The passage of homopolymeric RNA through small solid-state nanopores.
van den Hout M, Skinner GM, Klijnhout S, Krudde V, Dekker NH.
Small. 2011 Jun 3. doi: 10.1002/smll.201100265. [Epub ahead of print]

Comparative analyses by sequencing of transcriptomes during skeletal muscle development between pig breeds differing in muscle growth rate and fatness.
Zhao X, Mo D, Li A, Gong W, et al.
PLoS One. 2011;6(5):e19774.

Deep sequencing reveals novel microRNAs and regulation of microRNA expression during cell senescence.
Dhahbi JM, Atamna H, Boffelli D, Magis W, et al.
PLoS One. 2011;6(5):e20509.

Human aging and somatic point mutations in mtDNA: A comparative study of generational differences (grandparents and grandchildren).
do Rosário Marinho AN, de Moraes MR, Santos S, Ribeiro-Dos-Santos A.
Genet Mol Biol. 2011 Jan;34(1):31-4.

Comparative studies of de novo assembly tools for next-generation sequencing technologies.
Lin Y, Li J, Shen H, Zhang L, et al.
Bioinformatics. 2011 Jun 2. [Epub ahead of print]

Aligning short reads to reference alignments and trees.
Berger SA, Stamatakis A.
Bioinformatics. 2011 Jun 2. [Epub ahead of print]

A memory-efficient data structure representing exact-match overlap graphs with application for next generation DNA assembly.
Dinh H, Rajasekaran S.
Bioinformatics. 2011 Jun 2. [Epub ahead of print]

Coverage tradeoffs and power estimation in the design of whole-genome sequencing experiments for detecting association.
Shen Y, Song R, Pe'er I.
Bioinformatics. 2011 Jun 2. [Epub ahead of print]

ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using next generation sequence.
Blanca JM, Pascual L, Ziarsolo P, Nuez F, Canizares J.
BMC Genomics. 2011 Jun 2;12(1):285.

Sequencing and comparative genome analysis of two pathogenic Streptococcus gallolyticus subspecies: genome plasticity, adaptation and virulence.
Lin IH, Liu TT, Teng YT, Wu HL, et al.
PLoS One. 2011;6(5):e20519.

Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data.
Zhang C, Darnell RB.
Nat Biotechnol. 2011 Jun 1. [Epub ahead of print]

Application of two-part statistics for comparison of sequence variant counts.
Wagner BD, Robertson CE, Harris JK.
PLoS One. 2011;6(5):e20296.

Going deeper: metagenome of a hadopelagic microbial community.
Eloe EA, Fadrosh DW, Novotny M, Zeigler Allen L, et al.
PLoS One. 2011;6(5):e20388.

A reduced representation approach to population genetic analyses and applications to human evolution.
Luca F, Hudson RR, Witonsky DB, Di Rienzo A.
Genome Res. 2011 May 31. [Epub ahead of print]

Potential forensic application of DNA methylation profiling to body fluid identification.
Lee HY, Park MJ, Choi A, An JH, et al.
Int J Legal Med. 2011 Apr 6. [Epub ahead of print]

Acyclic identification of aptamers for human alpha-thrombin using over-represented libraries and deep sequencing.
Kupakuwana GV, Crill JE 2nd, McPike MP, Borer PN.
PLoS One. 2011;6(5):e19395.

Rapid screening of complex DNA samples by single-molecule amplification and sequencing.
Huang J, Zheng Z, Andersson AF, Engstrand L, Ye W.
PLoS One. 2011;6(5):e19723.

Evaluating the fidelity of de novo short read metagenomic assembly using simulated data.
Pignatelli M, Moya A.
PLoS One. 2011;6(5):e19984.

SVA: software for annotating and visualizing sequenced human genomes.
Ge D, Ruzzo EK, Shianna KV, He M, et al.
Bioinformatics. 2011 May 29. [Epub ahead of print]

Looking ultra deep: Short identical sequences and transcriptional slippage.
Ritz K, van Schaik BD, Jakobs ME, Aronica E, et al.
Genomics. 2011 May 23. [Epub ahead of print]

Moving pictures of the human microbiome.
Caporaso JG, Lauber CL, Costello EK, Berg-Lyons D, et al.
Genome Biol. 2011 May 30;12(5):R50.

The Scan

Cell Atlas of Human Lung Development Gives View of Developing Airway

Researchers have generated a cell atlas of human lung development, which they report in Cell.

Study Finds Costs of Genome Sequencing May Limit Utility in Routine Care

Researchers report in the European Journal of Human Genetics that genome sequencing for rare disease diagnoses currently has similar benefits as less expensive exome analysis.

Study Suggests Nursing Mother's Diet Can Impact Offspring's Gut Microbiome

A new Cell Host and Microbe paper finds that mice whose mothers were fed a low-fiber diet during nursing experience lasting microbiota dysbiosis and increased obesity.

Study Links Genetic Risk for ADHD With Alzheimer's Disease

A higher polygenic risk score for attention-deficit/hyperactivity disorder is also linked to cognitive decline and Alzheimer's disease, a new study in Molecular Psychiatry finds.