Shady is interested in studying symbiotic relationships between eukaryotes and their microbiome in aquatic ecosystems and their importance to ecosystem function, the evolution of eukaryotes, and the effect climate change has on these critical interactions. During his doctoral studies with the late Prof. Carl Carrano, he showed that some marine bacteria can provide bioavailable iron to their dinoflagellate and diatom hosts, which may enable these algal lineages to grow in large swaths of the oceans that are iron limited. During his postdoctoral work with Prof. Ginger Armbrust at UW, he uncovered a widespread signaling mechanism between diatoms and bacteria based on hormones. In 2015, he joined NYU Abu Dhabi, where his lab studies the influence of phytoplankton-microbiome interactions on global biogeochemistry, the role the coral microbiome plays in coral adaptation to climate change among other topics.