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December's Bioinformatics Papers of Note


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]

Filed under

The Scan

Positive Framing of Genetic Studies Can Spark Mistrust Among Underrepresented Groups

Researchers in Human Genetics and Genomics Advances report that how researchers describe genomic studies may alienate potential participants.

Small Study of Gene Editing to Treat Sickle Cell Disease

In a Novartis-sponsored study in the New England Journal of Medicine, researchers found that a CRISPR-Cas9-based treatment targeting promoters of genes encoding fetal hemoglobin could reduce disease symptoms.

Gut Microbiome Changes Appear in Infants Before They Develop Eczema, Study Finds

Researchers report in mSystems that infants experienced an enrichment in Clostridium sensu stricto 1 and Finegoldia and a depletion of Bacteroides before developing eczema.

Acute Myeloid Leukemia Treatment Specificity Enhanced With Stem Cell Editing

A study in Nature suggests epitope editing in donor stem cells prior to bone marrow transplants can stave off toxicity when targeting acute myeloid leukemia with immunotherapy.