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Papers of Note: May 31, 2011


Global gene disruption in human cells to assign genes to phenotypes by deep sequencing.
Carette JE, Guimaraes CP, Wuethrich I, et al.
Nat Biotechnol. 2011 May 29. [Epub ahead of print]

De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera).
Al-Dous EK, George B, Al-Mahmoud ME, et al.
Nat Biotechnol. 2011 May 29. [Epub ahead of print]

Computational methods for transcriptome annotation and quantification using RNA-seq.
Garber M, Grabherr MG, Guttman M, Trapnell C.
Nat Methods. 2011 Jun;8(6):469-77.

DARIO: a ncRNA detection and analysis tool for next-generation sequencing experiments.
Fasold M, Langenberger D, Binder H, Stadler PF, Hoffmann S.
Nucleic Acids Res. 2011 May 27. [Epub ahead of print]

Illuminator, a desktop program for mutation detection using short-read clonal sequencing.
Carr IM, Morgan JE, Diggle CP, et al.
Genomics. 2011 May 19. [Epub ahead of print]

Rapid hybrid de novo assembly of a microbial genome using only short reads: Corynebacterium pseudotuberculosis I19 as a case study.
Cerdeira LT, Carneiro AR, Ramos RT, et al.
J Microbiol Methods. 2011 May 18. [Epub ahead of print]

Profiling the venom gland transcriptomes of Costa Rican snakes by 454 pyrosequencing.
Durban J, Juarez P, Angulo Y, et al.
BMC Genomics. 2011 May 23;12(1):259.

High-throughput SNP discovery and genotyping in durum wheat (Triticum durum Desf.) .
Trebbi D, Maccaferri M, de Heer P, et al.
Theor Appl Genet. 2011 May 25. [Epub ahead of print]

Comparison of sequence reads obtained from three next-generation sequencing platforms.
Suzuki S, Ono N, Furusawa C, Ying BW, Yomo T.
PLoS One. 2011;6(5):e19534.

The rocks and shallows of deep RNA sequencing: Examples in the Vibrio cholerae RNome.
Raabe CA, Hoe CH, Randau G, Brosius J, Tang TH, Rozhdestvensky TS.
RNA. 2011 May 24. [Epub ahead of print]

PRI-CAT: a web-tool for the analysis, storage and visualization of plant ChIP-seq experiments.
Muiño JM, Hoogstraat M, van Ham RC, van Dijk AD.
Nucleic Acids Res. 2011 May 24. [Epub ahead of print]

An efficient and rapid protocol for plant nuclear DNA preparation suitable for next generation sequencing methods.
Carrier G, Santoni S, Rodier-Goud M, et al.
Am J Bot. 2011 Jan;98(1):e13-5.

rnaSeqMap: a Bioconductor package for RNA sequencing data exploration.
Lesniewska A, Okoniewski MJ.
BMC Bioinformatics. 2011 May 25;12(1):200.

Optimum designs for next-generation sequencing to discover rare variants for common complex disease.
Shi G, Rao DC.
Genet Epidemiol. 2011 May 26. [Epub ahead of print]

The origin of dips for the graphene-based DNA sequencing device.
Cho Y, Min SK, Kim WY, Kim KS.
Phys Chem Chem Phys. 2011 May 26. [Epub ahead of print]

A novel and well-defined benchmarking method for second generation read mapping.
Holtgrewe M, Emde AK, Weese D, Reinert K.
BMC Bioinformatics. 2011 May 26;12(1):210.

Assessment of replicate bias in 454 pyrosequencing and a multi-purpose read-filtering tool.
Mariette J, Noirot C, Klopp C.
BMC Res Notes. 2011 May 26;4(1):149.

The Scan

Study Finds Few FDA Post-Market Regulatory Actions Backed by Research, Public Assessments

A Yale University-led team examines in The BMJ safety signals from the US FDA Adverse Event Reporting System and whether they led to regulatory action.

Duke University Team Develops Programmable RNA Tool for Cell Editing

Researchers have developed an RNA-based editing tool that can target specific cells, as they describe in Nature.

Novel Gene Editing Approach for Treating Cystic Fibrosis

Researchers in Science Advances report on their development of a non-nuclease-based gene editing approach they hope to apply to treat cystic fibrosis.

Study Tracks Responses in Patients Pursuing Polygenic Risk Score Profiling

Using interviews, researchers in the European Journal of Human Genetics qualitatively assess individuals' motivations for, and experiences with, direct-to-consumer polygenic risk score testing.