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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

Self-Reported Hearing Loss in Older Adults Begins Very Early in Life, Study Says

A JAMA Otolaryngology — Head & Neck Surgery study says polygenic risk scores associated with hearing loss in older adults is also associated with hearing decline in younger groups.

Genome-Wide Analysis Sheds Light on Genetics of ADHD

A genome-wide association study meta-analysis of attention-deficit hyperactivity disorder appearing in Nature Genetics links 76 genes to risk of having the disorder.

MicroRNA Cotargeting Linked to Lupus

A mouse-based study appearing in BMC Biology implicates two microRNAs with overlapping target sites in lupus.

Enzyme Involved in Lipid Metabolism Linked to Mutational Signatures

In Nature Genetics, a Wellcome Sanger Institute-led team found that APOBEC1 may contribute to the development of the SBS2 and SBS13 mutational signatures in the small intestine.