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January's Bioinformatics Papers of Note

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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.
MetaNetX.org: 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]


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The Scan

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.

Team Presents Cattle Genotype-Tissue Expression Atlas

Using RNA sequences representing thousands of cattle samples, researchers looked at relationships between cattle genotype and tissue expression in Nature Genetics.

Researchers Map Recombination in Khoe-San Population

With whole-genome sequences for dozens of individuals from the Nama population, researchers saw in Genome Biology fine-scale recombination patterns that clustered outside of other populations.

Myotonic Dystrophy Repeat Detected in Family Genome Sequencing Analysis

While sequencing individuals from a multi-generation family, researchers identified a myotonic dystrophy type 2-related short tandem repeat in the European Journal of Human Genetics.