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In Print: Oct 28, 2011

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Bioinformatics Tool-Related Papers of Note, October 2011


An J, Jones SJ, Li YY.
A computational approach to finding novel targets for existing drugs.
PLoS Comput Biol. 2011 Sep;7(9):e1002139.


Ayres DL, Darling A, Zwickl DJ, et al.
BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics.
Syst Biol. 2011 Oct 1. [Epub ahead of print]


Schmidtke P, Bidon-Chanal A, Luque FJ, Barril X.
MDpocket: open source cavity detection and characterization on molecular dynamics trajectories.
Bioinformatics. 2011 Oct 3. [Epub ahead of print]


Engreitz JM, Chen R, Morgan AA, Dudley JT, Mallelwar R, Butte AJ.
ProfileChaser: searching microarray repositories based on genome-wide patterns of differential expression.
Bioinformatics. 2011 Oct 3. [Epub ahead of print]


Weng MP, Liao BY.
DroPhEA: Drosophila phenotype enrichment analysis for insect functional genomics.
Bioinformatics. 2011 Oct 5. [Epub ahead of print]


Pantano L, Estivill X, Marti E.
A non-biased framework for the annotation and classification of the non-miRNA small RNA transcriptome.
Bioinformatics. 2011 Oct 5. [Epub ahead of print]


Thompson P, McNaught J, Montemagni S, et al.
The BioLexicon: a large-scale terminological resource for biomedical text mining.
BMC Bioinformatics. 2011 Oct 12;12(1):397.


Cumbie JS, Kimbrel JA, Di Y, et al.
GENE-Counter: A computational pipeline for the analysis of RNA-seq data for gene expression differences.
PLoS One. 2011;6(10):e25279.


Zytnicki M, Quesneville H.
S-MART, a software toolbox to aid RNA-seq data analysis.
PLoS One. 2011;6(10):e25988.


Mordelet F, Vert JP.
ProDiGe: PRioritization Of Disease Genes with multitask machine learning from positive and unlabeled examples.
BMC Bioinformatics. 2011 Oct 6;12(1):389.


Liu Z, Hsiao W, Cantarel BL, Drábek EF, Fraser-Liggett C.
Sparse distance based learning for simultaneous multiclass classification and feature selection of metagenomic data.
Bioinformatics. 2011 Oct 7. [Epub ahead of print]


Yanovsky V.
ReCoil — an algorithm for compression of extremely large datasets of DNA data.
Algorithms Mol Biol. 2011 Oct 11;6(1):23.


Yosef N, Zalckvar E, Rubinstein AD, et al.
ANAT: a tool for constructing and analyzing functional protein networks.
Sci Signal. 2011 Oct 25;4(196):pl1.


Hendrix W, Rocha AM, Padmanabhan K, Choudhary A, Scott K, Mihelcic JR, Samatova NF.
DENSE: efficient and prior knowledge-driven discovery of phenotype-associated protein functional modules.
BMC Syst Biol. 2011 Oct 24;5(1):172.
The Scan

Not Immediately Told

The US National Institutes of Health tells lawmakers that one of its grantees did not immediately report that it had developed a more infectious coronavirus, Science says.

Seems Effective in Kids

The Associated Press reports that the Pfizer-BioNTech SARS-CoV-2 vaccine for children appears to be highly effective at preventing symptomatic disease.

Intelligence Warning on Bioeconomy Threats

US intelligence warns over China's focus on technologies and data related to the bioeconomy, the New York Times reports.

PLOS Papers on Campylobacteriosis Sources, Inherited Retinal Dystrophies, Liver Cancer Prognosis

In PLOS this week: approach to uncover source of Campylobacteriosis, genetic risk factors for inherited retinal dystrophies, and more.