Catalytic site identification - a web server to identify catalytic site structural matches throughout PDB. - Daniel A. Kirshner; Jerome P. Nilmeier; Felice C. Lightstone (Nucleic Acids Res., 2013)

A rigorous sequential update strategy for parallel kinetic Monte Carlo simulation. - Jerome P. Nilmeier; Jaime Marian (Comput. Phys. Commun., 2014)

A Peptide-Based Method for 13C Metabolic Flux Analysis in Microbial Communities. - Amit Ghosh; Jerome P. Nilmeier; Daniel Weaver; Paul D. Adams; Jay D. Keasling; Aindrila Mukhopadhyay; Christopher J. Petzold; Héctor García Martín (PLoS Comput. Biol., 2014)

CLAIMED - the open source framework for building coarse-grained operators for accelerated discovery in science. - Romeo Kienzler; Rafflesia Khan; Jerome P. Nilmeier; Ivan Nesic; Ibrahim Haddad (CoRR, 2023)