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August's Bioinformatics Papers of Note


Goldberg JM, Griggs AD, et al.
Kinannote, a computer program to identify and classify members of the eukaryotic protein kinase superfamily.
Bioinformatics. 2013 Aug 13. [Epub ahead of print]

Anderson JR, Bachmeyer KM, et al.
A novel algorithm for simplification of complex gene classifiers in cancer.
Cancer Res. 2013 Aug 2. [Epub ahead of print]

Aboyoun P, Carey VJ, et al.
Software for computing and annotating genomic ranges.
PLoS Comput Biol. Epub 2013 Aug 8.

Matlock M, Swamidass SJ, Zaretzki J.
Scaffold Network Generator: A Tool for Mining Molecular Structures.
Bioinformatics. 2013 Aug 5. [Epub ahead of print]

Yau C.
OncoSNP-SEQ: a statistical approach for the identification of somatic copy number alterations from next-generation sequencing of cancer genomes.
Bioinformatics. 2013 Aug 7. [Epub ahead of print]

Good BM, Loguercio S, Su AI.
Dizeez: an online game for human gene-disease annotation.
PLoS One. 2013 Aug 7

Chiu YF, Fang YH
A Novel Support Vector Machine-Based Approach for Rare Variant Detection.
PLoS One. 2013 Aug 7

Cabanski CR, Hayes DN, et al.
BlackOPs: increasing confidence in variant detection through mappability filtering.
Nucleic Acids Res. 2013 Aug 8. [Epub ahead of print]

Aleksic J, Hu F,et al.
metabolicMine: an integrated genomics, genetics and proteomics data warehouse for common metabolic disease research.
Database (Oxford) 2013 Aug 9.

Abecasis AB, Alves RJ,et al.
inTB - a data integration platform for molecular and clinical epidemiological analysis of tuberculosis.
BMC Bioinformatics. 2013 Aug 30;14(1):264. [Epub ahead of print]

Hauser M, Mayer CE, Söding J.
kClust: fast and sensitive clustering of large protein sequence databases.
BMC Bioinformatics. 2013 Aug 15;14(1):248. [Epub ahead of print]

Bains N, Ballouz S, et al.
Gentrepid V2.0: a web server for candidate disease gene prediction.
BMC Bioinformatics. 2013 Aug 16;14(1):249. [Epub ahead of print]

Covert MW, Karr JR, Lee R.
WholeCellViz: data visualization for whole-cell models.
BMC Bioinformatics. 2013 Aug 21

Allison B, Combs S, et al.
Computational design of protein-small molecule interfaces.
J Struct Biol. 2013 Aug 17. [Epub ahead of print]

Novo FJ, Ortiz de Mendíbil I, et al.
Oncofuse: a computational framework for the prediction of the oncogenic potential of gene fusions.
Bioinformatics. 2013 Aug 24. [Epub ahead of print]

Callister SJ, Conlan S, et al.
SPOCS: software for predicting and visualizing orthology/paralogy relationships among genomes.
Bioinformatics. 2013 Aug 27. [Epub ahead of print]

Biggin PC, Vohra S
Mutationmapper: a tool to aid the mapping of protein mutation data.
PLoS One. 2013 Aug 9.

Danek A, Deorowicz S, Grabowski S
Genome compression: a novel approach for large collections.
Bioinformatics. 2013 Aug 29. [Epub ahead of print]

Bhattacharya A, Cui Y, Ziebarth JD.
Bayesian Network Webserver: a comprehensive tool for biological network modeling.
Bioinformatics. 2013 Aug 28. [Epub ahead of print]

Rescheneder P, Sedlazeck FJ, von Haeseler A.
NextGenMap: fast and accurate read mapping in highly polymorphic genomes.
Bioinformatics. 2013 Aug 30. [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.