Margaret Silliker's lab is interested in using lower eukaryotes to understand molecular mechanisms. Most recently she has been studying the plasmodial slime mold Didymium iridis in the Myxomycetes, kingdom Mycetozoa. This group is most closely allied with the animal-fungal clade. Haploid cells of Didymium will only mate when cell densities are high, therefore they must be able to sense cell density and respond differently to low and high cell densities. This ability has the hallmark of a quorum sensing mechanism. Silliker's​ current research project involves using suppression subtractive hybridization to identify genes involved in this process.

Hendrickson, P.G. and Silliker, M.E. 2010 RNA editing is absent in a single mitochondrial gene of Didymium iridis. Mycologia 106:1288-1294 Hendrickson, P.G. and Silliker, M.E. 2010 RNA editing in six mitochondrial ribosomal protein genes of Didymium iridis. Current Genetics 56(3):203-213 Traphagen, Stephen J., DiMarco, Michael J. and Margaret E. Silliker. 2010 RNA editing of ten Didymium iridis mitochondrial genes and comparison to the homologous genes in Physarum polycephalum. RNA 16:828-838