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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

And For Adolescents

The US Food and Drug Administration has authorized the Pfizer-BioNTech SARS-CoV-2 vaccine for children between the ages of 12 and 15 years old.

Also of Concern to WHO

The Wall Street Journal reports that the World Health Organization has classified the SARS-CoV-2 variant B.1.617 as a "variant of concern."

Test for Them All

The New York Times reports on the development of combined tests for SARS-CoV-2 and other viruses like influenza.

PNAS Papers on Oral Microbiome Evolution, Snake Toxins, Transcription Factor Binding

In PNAS this week: evolution of oral microbiomes among hominids, comparative genomic analysis of snake toxins, and more.