Here are a few recent papers I found interesting:
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 A. actinomycetemcomitans 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.
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.
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.