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severalog

Three papers about sharing, even if it's just sharing data

Harry Caufield

If you search Wikimedia Commons for 'sharing' the most interesting results will involve milkshakes. This one is here.

If you search Wikimedia Commons for 'sharing' the most interesting results will involve milkshakes. This one is here.

 

Here are a few recent papers I found interesting:

1. A Commensal Bacterium Promotes Virulence of an Opportunistic Pathogen via Cross-Respiration.

Streptococcus gordonii is a commensal bacterial species in the human mouth. Aggregatibacter actinomycetemcomitans is an opportunistic pathogen, but not on its own: S. gordonii does something in the oral environment to allow Aactinomycetemcomitans to shift from anaerobic to aerobic growth, rendering it a more potent pathogen. 

Citation: Stacy A, Fleming D, Lamont RJ, Rumbaugh KP, Whiteley M. A Commensal Bacterium Promotes Virulence of an Opportunistic Pathogen via Cross-Respiration. MBio. American Society for Microbiology; 2016;7: e00782–16. doi:10.1128/mBio.00782-16.

2. A crowdsourcing approach for reusing and meta-analyzing gene expression data.

OMiCC is an interface for the NCBI Gene Expression Omnibus (GEO) designed for easier comparative analyses. It looks like it's limited to a set of curated human and mouse studies for now but could be useful for combing through voluminuous gene expression data sets. The OMiCC site is here.

Citation: Shah N, Guo Y, Wendelsdorf K V, Lu Y, Sparks R, Tsang JS. A crowdsourcing approach for reusing and meta-analyzing gene expression data. Nat Biotechnol. Nature Publishing Group; 2016; doi:10.1038/nbt.3603.

3. Goldilocks: a tool for identifying genomic regions that are ‘just right’

A small genome analysis toolkit. It's on Github. It doesn't try to do more than is necessary and I really like that. I may also be the target market for bioinformatics tools without alphabet soup names like CHWRtn.

See also: the first author's blog. He seems like a cool guy.

Citation: Nicholls SM, Clare A, Randall JC. Goldilocks: a tool for identifying genomic regions that are “just right.” Bioinformatics. Oxford University Press; 2016;32: 2047–2049. doi:10.1093/bioinformatics/btw116.