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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

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.

Study Reveals Potential Sex-Specific Role for Noncoding RNA in Depression

A long, noncoding RNA called FEDORA appears to be a sex-specific regulator of major depressive disorder, affecting more women, researchers report in Science Advances.

New mRNA Vaccines Offer Hope for Fighting Malaria

A George Washington University-led team has developed mRNA vaccines for malaria that appear to provide protection in mice, as they report in NPJ Vaccines.

Unique Germline Variants Found Among Black Prostate Cancer Patients

Through an exome sequencing study appearing in JCO Precision Oncology, researchers have found unique pathogenic or likely pathogenic variants within a cohort of Black prostate cancer patients.