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Papers of Note: Apr 26, 2011


Next-generation sequencing to generate interactome datasets.
Yu H, Tardivo L, Tam S, Weiner E, et al.
Nat Methods. 2011 Apr 24. [Epub ahead of print]:

Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection.
Ford CB, Lin PL, Chase MR, Shah RR, et al.
Nat Genet. 2011 Apr 24. [Epub ahead of print]

miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments.
Hackenberg M, Rodríguez-Ezpeleta N, Aransay AM.
Nucleic Acids Res. 2011 Apr 22. [Epub ahead of print]

A multiplex RNA-seq strategy to profile poly(A(+)) RNA: Application to analysis of transcription response and 3' end formation.
Fox-Walsh K, Davis-Turak J, Zhou Y, Li H, Fu XD.
Genomics. 2011 Apr 15. [Epub ahead of print]

A novel method for determining microflora composition using dynamic phylogenetic analysis of 16S ribosomal RNA deep sequencing data.
Chan ER, Hester J, Kalady M, Xiao H, Li X, Serre D.
Genomics. 2011 Apr 15. [Epub ahead of print]

An incremental mean first passage analysis for a quasistatic model of polymer translocation through a nanopore.
de Haan HW, Slater GW.
J Chem Phys. 2011 Apr 21;134(15):154905.

Detection of recurrent rearrangement breakpoints from copy number data.
Ritz A, Paris PL, Ittmann MM, Collins C, Raphael BJ.
BMC Bioinformatics. 2011 Apr 21;12(1):114.

Enterotypes of the human gut microbiome.
Arumugam M, Raes J, Pelletier E, Le Paslier D, et al.
Nature. 2011 Apr 20. [Epub ahead of print]

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FR-HIT, a very fast program to recruit metagenomic reads to homologous reference genomes.
Niu B, Zhu Z, Fu L, Wu S, Li W.
Bioinformatics. 2011 Apr 19. [Epub ahead of print]

Efficient algorithms for tandem copy number variation reconstruction in repeat-rich regions.
He D, Hormozdiari F, Furlotte N, Eskin E.
Bioinformatics. 2011 Apr 19. [Epub ahead of print]

Population genetics in non-model organisms: II. Natural selection in marginal habitats revealed by deep sequencing on dual platforms.
Zhou R, Ling S, Zhao W, Osada N, et al.
Mol Biol Evol. 2011 Apr 18. [Epub ahead of print]

MiRPara: a SVM-based software tool for prediction of most probable microRNA coding regions in genome scale sequences.
Wu Y, Wei B, Liu H, Li T, Rayner S.
BMC Bioinformatics. 2011 Apr 19;12(1):107.

Estimation of alternative splicing isoform frequencies from RNA-seq data.
Nicolae M, Mangul S, Mandoiu II, Zelikovsky A.
Algorithms Mol Biol. 2011 Apr 19;6(1):9.

ENGINES: exploring single nucleotide variation in entire human genomes.
Amigo J, Salas A, Phillips C.
BMC Bioinformatics. 2011 Apr 19;12(1):105.

The Scan

Ancient Greek Army Ancestry Highlights Mercenary Role in Historical Migrations

By profiling genomic patterns in 5th century samples from in and around Himera, researchers saw diverse ancestry in Greek army representatives in the region, as they report in PNAS.

Estonian Biobank Team Digs into Results Return Strategies, Experiences

Researchers in the European Journal of Human Genetics outline a procedure developed for individual return of results for the population biobank, along with participant experiences conveyed in survey data.

Rare Recessive Disease Insights Found in Individual Genomes

Researchers predict in Genome Medicine cross-population deletions and autosomal recessive disease impacts by analyzing recurrent nonallelic homologous recombination-related deletions.

Genetic Tests Lead to Potential Prognostic Variants in Dutch Children With Dilated Cardiomyopathy

Researchers in Circulation: Genomic and Precision Medicine found that the presence of pathogenic or likely pathogenic variants was linked to increased risk of death and poorer outcomes in children with pediatric dilated cardiomyopathy.