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April's Bioinformatics Papers of Note


Aladjem MI, Fried JY, et al.
PathVisio-Faceted Search: An Exploration Tool for Multi-Dimensional Navigation of Large Pathways.
Bioinformatics. 2013 Apr 1. [Epub ahead of print]

Chen CK, Ruf S, et al.
TRACER: a resource to study the regulatory architecture of the mousegenome.
BMC Genomics. 2013 Apr 2.

Ning K, Su X, et al.
QC-Chain: Fast and Holistic Quality Control Method for Next-Generation Sequencing Data.
PLoS One. Epub 2013 Apr 2.

Liao Y, Smyth GK, Shi W.
The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote.
Nucleic Acids Res. 2013 Apr 4. [Epub ahead of print]

Ackermann J, Einloft J, et al.
MonaLisa - visualization and analysis of functional modules in biochemical networks.
Bioinformatics. 2013 Apr 5. [Epub ahead of print]

Harris BR, Kao HY, et al.
tmVar: A text mining approach for extracting sequence variants in biomedical literature.
Bioinformatics. 2013 Apr 5. [Epub ahead of print]

Balado F, Haughton D.
BioCode: Two biologically compatible Algorithms for embedding data in non-coding and coding regions of DNA.
BMC Bioinformatics. 2013 Apr 9;14(1):121. [Epub ahead of print]

Albrecht M, Doncheva NT, Kacprowski T.
NetworkPrioritizer: a versatile tool for network-based prioritization of candidate disease genes or other molecules.
Bioinformatics. 2013 Apr 17. [Epub ahead of print]

Chen Y, Chen R, et al.
CGAP-Align: A High Performance DNA Short Read Alignment Tool.
PLoS One. 2013 Apr 11

Chaudhary K, Chauhan JS, et al.
Computational approach for designing tumor homing peptides.
Sci Rep. 2013 Apr 5;3:1607. doi: 10.1038/srep01607.

Bedard PL, Brown AM, et al.
Clinical genomics information management software linking cancergenome sequence and clinical decisions.
Genomics. 2013 Apr 17. [Epub ahead of print]

Barakat M, Ortet P, Whitworth DE.
P2RP: a web-based framework for the identification and analysis of regulatory proteins in prokaryotic genomes.
BMC Genomics. 2013 Apr 20;14(1):269. [Epub ahead of print]

Giddings MC, Risk BA, Spitzer WJ.
Peppy: proteogenomic search software.
J Proteome Res. 2013 Apr 24. [Epub ahead of print]

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The Scan

Single-Cell Sequencing Points to Embryo Mosaicism

Mosaicism may affect preimplantation genetic tests for aneuploidy, a single-cell sequencing-based analysis of almost three dozen embryos in PLOS Genetics finds.

Rett Syndrome Mouse Model Study Points to RNA Editing Possibilities

Investigators targeted MECP2 in mutant mouse models of Rett syndrome, showing in PNAS that they could restore its expression and dial down symptoms.

Investigators Find Shared, Distinct Genetic Contributors to Childhood Hodgkin Lymphoma

An association study in JAMA Network Open uncovers risk variants within and beyond the human leukocyte antigen locus.

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.