Dr. Holmes has published over 200 scientific papers, one of which was designated a Scientific Citation Classic (1994). In 2015, he was elected to the American Academy of Microbiology and received its Award for Outstanding Achievement. He has been further recognized with Lifetime Achievement Awards for his contributions to biomining acidophile genomics and for his pioneering role in establishing bioinformatics in Latin America.

His current research focuses on the genomics of extremophiles inhabiting environments of ultra-low pH, elevated temperature, and high salinity. Central questions include: (i) the thermodynamic limits of life on Earth; (ii) how the unique metabolisms of extremophiles inform models of life’s origins; and (iii) how terrestrial extreme environments can serve as analogs for identifying potential habitable niches on exoplanets and moons.