William Gilly was trained in molecular physiology and biophysics and has contributed to our basic understanding of electrical excitability in nerve and muscle cells, but his recent work primarily addresses biological and environmental topics. Current research concentrates on the physiological ecology of Dosidicus gigas, the jumbo or Humboldt squid, in the Gulf of California and focuses on short-term vertical movements and long-distance migrations, the physiology of hypoxia tolerance, and control of chromatophores, the color-changing organs in the skin.  Additional research by his group involves the biology of toxin diversity in venomous cone snails (genus Conus).