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March's Bioinformatics Papers of Note

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Gonzalez MA, Lebrigio RF, et al.
GEnomes Management Application (GEM.app): A New Software Tool for Large-Scale Collaborative Genome Analysis.
Hum Mutat. 2013 Mar 5. [Epub ahead of print]


Chen J, Fu Y, et al.
Interpretation of genomic variants using a unified biological network approach.
PLoS Comput Biol. Epub 2013 Mar 7.


Baaden M, Chavent M, et al.
Game on, science — how video game technology may help biologists tackle visualization challenges.
PLoS One. Epub 2013 Mar 6.


Alcántara R, Cao H, et al.
The Enzyme Portal: A case study in applying user-centered design methods in bioinformatics.
BMC Bioinformatics. 2013 Mar 20;14(1):103.


Chaudhary K, Gautam A, et al.
CancerDR: Cancer Drug Resistance Database.
Sci Rep. 2013 Mar 13;3:1445.


Alexandrova N, Kaznadzey A, et al.
PSimScan: Algorithm and Utility for Fast Protein Similarity Search.
PLoS One. Epub 2013 Mar 7.


Haslam NJ, Holton TA, et al.
PeptideLocator: prediction of bioactive peptides in protein sequences.
Bioinformatics. 2013 Mar 21. [Epub ahead of print]


Earl D, Haussler D, et al.
HAL: A Hierarchical Format for Storing and Analyzing Multiple Genome Alignments.
Bioinformatics. 2013 Mar 16. [Epub ahead of print]


Bafna V, Kinsella M, Zakov S.
An algorithmic approach for breakage-fusion-bridge detection in tumor genomes.
Proc Natl Acad Sci U S A. 2013 Mar 15. [Epub ahead of print]


Ahrens M, Baba HA, et al.
A practical data processing workflow for multi-OMICS projects.
Biochim Biophys Acta. 2013 Mar 15. [Epub ahead of print]


Goes FS, Leek JT, et al.
SVAw — a web-based application tool for automated surrogate variable analysis of gene expression studies.
Source Code Biol Med. 2013 Mar 11;8(1):8. [Epub ahead of print]


Clark AM, Ekins S, Sarker M.
TB mobile: a mobile app for anti-tuberculosis molecules with known targets.
J Cheminform. 2013 Mar 6;5(1):13. [Epub ahead of print]


Coassin S, Forer L, et al.
SNPflow: A Lightweight Application for the Processing, Storing and Automatic Quality Checking of Genotyping Assays.
PLoS One. Epub 2013 Mar 19.


Chen G, Yang J, et al.
FNphasing: A Novel Fast Heuristic Algorithm for Haplotype Phasing Based on Flow Network Model.
IEEE/ACM Trans Comput Biol Bioinform. 2013 Mar 7. [Epub ahead of print]


Angermann BR, Meier-Schellersheim M, Zhang F.
The Simmune Modeler visual interface for creating signaling net-works based on bi-molecular interactions.
Bioinformatics. 2013 Mar 17. [Epub ahead of print]


Ahsan M, Carlborg O, et al.
PASE: a novel method for functional prediction of amino acid substitutions based on physicochemical properties.
Front Genet. Epub 2013 Mar 6.


Ho BK, Perry AJ
Inmembrane, a bioinformatic workflow for annotation of bacterial cell-surface proteomes.
Source Code Biol Med. 2013 Mar 19;8(1):9.


Li J, Qian L, et al.
Classification of Time Series Gene Expression in Clinical Studies via Integration of Biological Network.
PLoS One. Epub 2013 Mar 13.


Bonfield JK, Mahoney MV.
Compression of FASTQ and SAM Format Sequencing Data.
PLoS One. Epub 2013 Mar 22.


Dilorenzo S, Isaksson A, Mayrhofer M.
Patchwork: allele-specific copy number analysis of whole genome sequenced tumor tissue.
Genome Biol. 2013 Mar 25;14(3):R24.


Filed under

The Scan

Driving Malaria-Carrying Mosquitoes Down

Researchers from the UK and Italy have tested a gene drive for mosquitoes to limit the spread of malaria, NPR reports.

Office Space to Lab Space

The New York Times writes that some empty office spaces are transforming into lab spaces.

Prion Pause to Investigate

Science reports that a moratorium on prion research has been imposed at French public research institutions.

Genome Research Papers on Gut Microbe Antibiotic Response, Single-Cell RNA-Seq Clues to Metabolism, More

In Genome Research this week: gut microbial response to antibiotic treatment, approach to gauge metabolic features from single-cell RNA sequencing, and more.