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December's Bioinformatics Papers of Note

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Note: In addition to the below listing, papers for Nucleic Acids Research's annual database issue are available here.

Avillach P, Bauer-Mehren A, et al.
The EU-ADR Web Platform: delivering advanced pharmacovigilance tools.
Pharmacoepidemiol Drug Saf. 2012 Dec 4.


Argoud-Puy G, Bairoch A, et al.
neXtProt: Organizing Protein Knowledge in the Context of Human Proteome Projects.
J Proteome Res. 2012 Dec 3. [Epub ahead of print]


Chung Sham P, Jun Li M, et al.
A fast and accurate SNP detection algorithm for next-generation sequencing data.
Nat Commun. 2012 Dec 4;3:1258.


Boyle J, Csordas A, et al.
Hydra: a scalable proteomic search engine which utilizes the Hadoop distributed computing framework.
BMC Bioinformatics. 2012 Dec 5;13(1):324.


Alexeev DG, Altukhov IA, et al.
MALINA: a web service for visual analytics of human gut microbiota whole-genome metagenomic reads.
Source Code Biol Med. 2012 Dec 7;7(1):13.


Chen X, Mao X, et al.
CINPER: An Interactive Web System for Pathway Prediction for Prokaryotes.
PLoS One. Epub 2012 Dec 7.


Booth JG, Bustamante CD, Eilertson KE.
SnIPRE: Selection Inference Using a Poisson Random Effects Model.
PLoS Comput Biol. Epub 2012 Dec 6.


Budczies J, Denkert C, et al.
Cutoff finder: a comprehensive and straightforward web application enabling rapid biomarker cutoff optimization.
PLoS One. Epub 2012 Dec 14.


Reed JL, Tervo CJ.
FOCAL: an experimental design tool for systematizing metabolic discoveries and model development.
Genome Biol. 2012 Dec 13;13(12):R116.


Beck T, Brookes AJ, et al.
Semantically enabling a genome-wide association study database.
J Biomed Semantics. 2012 Dec 17;3(1):9.


Lopes P, Oliveira JL.
COEUS: "semantic web in a box" for biomedical applications.
J Biomed Semantics. 2012 Dec 17;3(1):11.


Cheng W, Fu D, et al.
A framework for annotating human genome in disease context.
PLoS One. Epub 2012 Dec 10.


Blakesley RR, Brooks S, et al.
Pan-PCR, a computational method for designing bacterial-typing assays based on whole genome sequence data.
J Clin Microbiol. 2012 Dec 19. [Epub ahead of print]


Büchel F, Eichner J, et al.
InCroMAP: Integrated analysis of Cross-platform MicroArray and Pathway data.
Bioinformatics. 2012 Dec 20. [Epub ahead of print]


Barrett JH, Boehnke M, et al.
SNP Prioritization Using a Bayesian Probability of Association.
Genet Epidemiol. 2012 Dec 26. [Epub ahead of print]


Berger J, Gontarz PM, Wong CF.
SRmapper: A Fast and Sensitive Genome-Hashing Alignment Tool.
Bioinformatics. 2012 Dec 24. [Epub ahead of print]


Antinori P, Dayon L, et al.
EasyProt - an easy-to-use graphical platform for proteomics data analysis.
J Proteomics. 2012 Dec 28. [Epub ahead of print]


Brudno M, Donmez N.
SCARPA: Scaffolding Reads with Practical Algorithms.
Bioinformatics. 2012 Dec 29. [Epub ahead of print]


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