Greider accepted a faculty position at The Johns Hopkins University School of Medicine in 1997. Greider continued to study telomerase deficient mice and saw that her sixth generation of mice had become entirely sterile, but when mated with control mice the telomerase deficient mice were able to regenerate their telomeres. Greider continued to work on telomerase biochemistry, defining the secondary structure (2000) and template boundary (2003) of vertebrate telomerase RNA as well as analyzing the pseudoknot structure in human telomerase RNA (2005). In addition to working in "Tetrahymena" and mammalian systems, Greider also studied telomeres and telomerase in the yeast "Saccharomyces cerevisiae", further characterizing the recombination-based gene conversion mechanism that yeast cells null for telomerase use to maintain telomeres (1999) (2001). Greider also showed that short telomeres elicit a DNA damage response in yeast (2003).