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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]

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.