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March's Bioinformatics Papers of Note


Gonzalez MA, Lebrigio RF, et al.
GEnomes Management Application ( 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.

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The Scan

Transcriptomic, Epigenetic Study Appears to Explain Anti-Viral Effects of TB Vaccine

Researchers report in Science Advances on an interferon signature and long-term shifts in monocyte cell DNA methylation in Bacille Calmette-Guérin-vaccinated infant samples.

DNA Storage Method Taps Into Gene Editing Technology

With a dual-plasmid system informed by gene editing, researchers re-wrote DNA sequences in E. coli to store Charles Dickens prose over hundreds of generations, as they recount in Science Advances.

Researchers Model Microbiome Dynamics in Effort to Understand Chronic Human Conditions

Investigators demonstrate in PLOS Computational Biology a computational method for following microbiome dynamics in the absence of longitudinally collected samples.

New Study Highlights Role of Genetics in ADHD

Researchers report in Nature Genetics on differences in genetic architecture between ADHD affecting children versus ADHD that persists into adulthood or is diagnosed in adults.