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January's Bioinformatics Papers of Note


Gomes J, Jayaram B, et al.
NeuroDNet - an open source platform for constructing and analyzing neurodegenerative disease networks.
BMC Neurosci. 2013 Jan 3 [Epub ahead of print]

Goloborodko AA, Gorshkov MV, et al.
Pyteomics-a Python Framework for Exploratory Data Analysis and RapidSoftware Prototyping in Proteomics.
J Am Soc Mass Spectrom. 2013 Jan 5 [Epub ahead of print]

Liu H, Ma C, et al.
TargetHunter: An In Silico Target Identification Tool for Predicting Therapeutic Potential of Small Organic Molecules Based on ChemogenomicDatabase.
AAPS J. 2013 Jan 5 [Epub ahead of print]

Bottomly D, Druker BJ, et al.
HitWalker: variant prioritization for personalized functional cancer genomics.
Bioinformatics 2013 Jan 22 [Epub ahead of print]

Clark SC, Egan R, et al.
ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies.
Bioinformatics 2013 Jan 21 [Epub ahead of print]

Busby MA, Grzeda K, et al.
Scotty: A Web Tool For Designing RNA-Seq Experiments to Measure Differential Gene Expression.
Bioinformatics 2013 Jan 12 [Epub ahead of print]

Babaei S, de Ridder J, et al.
Detecting recurrent gene mutation in interaction network context using multi-scale graph diffusion.
BMC Bioinformatics 2013 Jan 23;14(1):29

Blackburn J, Martens L, et al.
ProteoCloud: A full-featured open source proteomics cloud computing pipeline.
J Proteomics. 2013 Jan 8 [Epub ahead of print]

Liang H, Li G, et al.
A structural-based strategy for recognition of transcription factor binding sites.
PLoS One. Epub 2013 Jan 8.

Groth P, Thieme S.
Genome Fusion Detection: A novel method to detect fusion genes from SNP-array data.
Bioinformatics. 2013 Jan 22. [Epub ahead of print]

Becnel L, Chen ES, et al.
Research Resource: The Endometrium Database Resource (EDR).
Mol Endocrinol. 2013 Jan 22. [Epub ahead of print]

Carter H, Cooper DN, et al.
CRAVAT: Cancer-Related Analysis of VAriants Toolkit.
Bioinformatics. 2013 Jan 16. [Epub ahead of print]

Jin L, Yi H.
Co-phylog: an assembly-free phylogenomic approach for closely related organisms.
Nucleic Acids Res. 2013 Jan 18. [Epub ahead of print]

Beilin LJ, Briollais L, et al.
Co-phylog: an assembly-free phylogenomic approach for closely related organisms.
PLoS One. Epub 2013 Jan 17.

Bernard T, Ganter M, et al. a website and repository for accessing, analyzing, and manipulating metabolic networks.
Bioinformatics. 2013 Jan 28. [Epub ahead of print]

Ahlers V, Dand N, et al.
BioGranat-IG: A network analysis tool to suggest mechanisms of genetic heterogeneity from exome sequencing data.
Bioinformatics. 2013 Jan 29. [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.