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Papers of Note: Aug 2, 2011


Dissecting the genome of the polyploid crop oilseed rape by transcriptome sequencing.
Bancroft I, Morgan C, Fraser F, Higgins J, et al.
Nat Biotechnol. 2011 Jul 31. [Epub ahead of print]

True single-molecule DNA sequencin g of a Pleistocene horse bone.
Orlando L, Ginolhac A, Raghavan M, Vilstrup J, et al.
Genome Res. 2011 Jul 29. [Epub ahead of print]

Gee Fu: a sequence version and web-services database tool for genomic assembly, genome feature and NGS data.
Ramirez-Gonzalez R, Caccamo M, Maclean D.
Bioinformatics. 2011 Jul 29. [Epub ahead of print]

ContEst: Estimating cross-contamination of human samples in next generation sequencing data.
Cibulskis K, McKenna A, Fennell T, Banks E, et al.
Bioinformatics. 2011 Jul 29. [Epub ahead of print]

Efficiently identifying genome-wide changes with next-generation sequencing data.
Huang W, Umbach DM, Vincent Jordan N, Abell AN, et al.
Nucleic Acids Res. 2011 Jul 29. [Epub ahead of print]

A massively parallel sequencing approach uncovers ancient origins and high genetic variability of endangered Przewalski's horses.
Goto H, Ryder OA, Fisher AR, Schultz B, et al.
Genome Biol Evol. 2011 Jul 29. [Epub ahead of print]

A whole-genome analysis of premature termination codons.
Cirulli ET, Heinzen EL, Dietrich FS, Shianna KV, et al.
Genomics. 2011 Jul 22. [Epub ahead of print]

Addressing challenges in the production and analysis of Illumina sequencing data.
Kircher M, Heyn P, Kelso J.
BMC Genomics. 2011 Jul 29;12(1):382.

Dynamics of ion migration in nanopores and the effect of DNA-ion interaction.
Cui S.
J Phys Chem B. 2011 Jul 29. [Epub ahead of print]

Structural alterations from multiple displacement amplification of a human genome revealed by mate-pair sequencing.
Jiao X, Rosenlund M, Hooper SD, Tellgren-Roth C, et al.
PLoS One. 2011;6(7):e22250.

ExpressionPlot: A web-based framework for analysis of RNA-seq and microarray gene expression data.
Friedman BA, Maniatis T.
Genome Biol. 2011 Jul 28;12(7):R69.

Prospective genomic characterization of the German enterohemorrhagic Escherichia coli O104:H4 outbreak by rapid next generation sequencing technology.
Mellmann A, Harmsen D, Cummings CA, Zentz EB, et al.
PLoS One. 2011;6(7):e22751.

Performance of ultra-deep pyrosequencing in analysis of HIV-1 pol gene variation.
Mild M, Hedskog C, Jernberg J, Albert J.
PLoS One. 2011;6(7):e22741.

Transgenomic capture and sequencing of primate exomes reveals new targets of positive selection.
George RD, McVicker G, Diederich R, Ng SB, et al.
Genome Res. 2011 Jul 27. [Epub ahead of print]

RseqFlow: Workflows for RNA-seq data analysis.
Wang Y, Mehta G, Mayani R, Lu J, et al.
Bioinformatics. 2011 Jul 27. [Epub ahead of print]

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Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate genes.
Feltus FA, Saski CA, Mockaitis K, Haiminen N, et al.
BMC Genomics. 2011 Jul 27;12(1):379.

Origins of the E. coli strain causing an outbreak of hemolytic-uremic syndrome in Germany.
Rasko DA, Webster DR, Sahl JW, Bashir A, et al.
N Engl J Med. 2011 Jul 27. [Epub ahead of print]

Open-source genomic analysis of shiga-toxin-producing E. coli O104:H4.
Rohde H, Qin J, Cui Y, Li D, et al.
N Engl J Med. 2011 Jul 27. [Epub ahead of print]

The lifestyle of the segmented filamentous bacterium: a non-culturable gut-associated immunostimulating microbe inferred by whole-genome sequencing.
Kuwahara T, Ogura Y, Oshima K, Kurokawa K, et al.
DNA Res. 2011 Jul 26. [Epub ahead of print]

Comparative high-throughput transcriptome sequencing and development of SiESTa, the silene EST annotation database.
Blavet N, Charif D, Oger-Desfeux C, Marais GA, Widmer A.
BMC Genomics. 2011 Jul 26;12(1):376.

Museum genomics: low-cost and high-accuracy genetic data from historical specimens.
Rowe KC, Singhal S, Macmanes MD, Ayroles JF, et al.
Mol Ecol Resour. 2011 Jul 25. [Epub ahead of print]

Ultra-deep sequencing of foraminiferal microbarcodes unveils hidden richness of early monothalamous lineages in deep-sea sediments.
Lecroq B, Lejzerowicz F, Bachar D, Christen R, et al.
Proc Natl Acad Sci U S A. 2011 Jul 25. [Epub ahead of print]

Identification of genomic indels and structural variations using split reads.
Zhang ZD, Du J, Lam H, Abyzov A, et al.
BMC Genomics. 2011 Jul 25;12(1):375.

Targeted enrichment beyond the consensus coding DNA sequence exome reveals exons with higher variant densities.
Bainbridge MN, Wang M, Wu YQ, Newsham I, et al.
Genome Biol. 2011 Jul 25;12(7):R68.

ZINBA integrates local covariates with DNA-seq data to identify broad and narrow regions of enrichment, even within amplified genomic regions.
Rashid N, Giresi PG, Ibrahim JG, Sun W, Lieb JD.
Genome Biol. 2011 Jul 25;12(7):R67.

An integrated strategy for identification of both sharp and broad peaks from next-generation sequencing data.
Peng W, Zhao K.
Genome Biol. 2011 Jul 25;12(7):120.

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.