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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

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Unfair Targeting

Technology Review writes that a new report says the US has been unfairly targeting Chinese and Chinese-American individuals in economic espionage cases.

Limited Rapid Testing

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Genome Research Papers on IPAFinder, Structural Variant Expression Effects, Single-Cell RNA-Seq Markers

In Genome Research this week: IPAFinder method to detect intronic polyadenylation, influence of structural variants on gene expression, and more.