Ellis works primarily in observational cosmology, considering the origin and evolution of galaxies, the evolution of large scale structure in the universe, and the nature and distribution of dark matter. He worked on the Morphs collaboration studying the formation and morphologies of distant galaxies.[7] Particular interests include applications using gravitational lensing and high-redshift supernovae. He was a member of the Supernova Cosmology Project whose leader, Saul Perlmutter, shared the 2011 Nobel Prize for Physics for the team's surprising discovery of the accelerating expansion of the Universe. His most recent discoveries relate to searches for the earliest known galaxies, seen when the Universe was only a few percent of its present age.
At Caltech, Ellis was director of the Palomar Observatory from 2000 to 2005 and played a key role in developing the scientific and technical case, as well as building the partnership, for the Thirty Meter Telescope - a collaborative effort involving Caltech, the University of California, Canada, Japan, China and India destined for Mauna Kea, Hawaii. If constructed this will be the largest ground-based optical and near-infrared telescope in the northern hemisphere.
Ellis wrote When Galaxies Were Born: The Quest for Cosmic Dawn (Princeton University Press 2022) in which he describes the observational progress made by astronomers over his career of five decades in probing galaxies to ever greater distances, and hence to earlier periods of cosmic history. The story culminates with the prospects for witnessing cosmic dawn - the emergence of the first generation of galaxies from darkness - with NASA's James Webb Space Telescope.
Ellis also contributed the text to a collection of striking photographs by Julian Abrams of the many large telescopes he has used in Modern Observatories of the World.