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.