User:Tgibbons:Project-Ideas

My weekly progress report just didn't seem appropriate for my brainstorming after a bit, so I've transferred everything here.

Potential Research Projects Inspired by Microbial Inhabitants of Humans

1. Searching for quorum sensing genes, both known and novel, and any pathways including them in human microbiome data
   • Search for and consider making quorum sensing gene DB
     • KEGG has pathways containing both acyl-homoserine lactone and it's synthase
   • After indexing known quorum sensing genes, search for homologues
     • WGS data - Obviously search for homologues directly
     • 16S data - Identify organisms and search for homologues in public DBs
2. Search for "core metabolome" in pioneer organisms from infant studies
   • On the off chance I get to publish on this subject, it might be interesting to draw an analogy between genetic evolution involving chance mutations that are occasionally beneficial and are therefore propagated, and microbial colonization which involves chance introduction of microorganisms that are occasionally beneficial and therefore become stable members of the microbiome.
3. Attempt to search for cases of symbiosis where possible
   • Search terms: commensalism, synergism (protocooperation), mutualism, competition, amensalism (antagonism), predation, parasitism, neutralism, syntrophism (nutritional synergism, cross-feeding, examples on pp.16-17)

Other Potential Research Projects

1. Metagenomic assembly
   • I've been kicking this idea around the floor for months, but none of the people I perceive as being better suited to tackle the problem have appeared all that interested. This could be due either to them already having large projects to which they're committed, or it could be that they sense trouble. I'll ask Mihai once I've spent a couple of days looking through literature.
   • Essentially I think the ideal metagenomic assembler would allow for, and gracefully represent, diversity within a single organism, without collapsing the genetic material of an entire community into a single messy contig.
   • The major theoretical challenge would be the development of an algorithm that could differentiate between variation and "speciation" in a biologically meaningful way. This is far from being a new problem.
   • In addition to the well-known theoretical challenges, coding this in such a way as to make it practical for current and future metagenomic problems would probably require more programming skills than I have the time to master. As such, I'm hoping that maybe I can work out the theory on a smaller scale using Python, and then maybe convince someone else to collaborate with me for the implementation, or just publish my findings and leave it to the scientific community to incorporate my methods into their-favorite-assembler.