Conformational splitting: A more powerful criterion for dead-end elimination. - Niles A. Pierce; Jan A. Spriet; J. Desmet; Stephen L. Mayo (J. Comput. Chem., 2000)

Adjoint Recovery of Superconvergent Functionals from PDE Approximations. - Niles A. Pierce; Michael B. Giles (SIAM Rev., 2000)

A partition function algorithm for nucleic acid secondary structure including pseudoknots. - Robert M. Dirks; Niles A. Pierce (J. Comput. Chem., 2003)

Exact rotamer optimization for protein design. - D. Benjamin Gordon; Geoffrey K. Hom; Stephen L. Mayo; Niles A. Pierce (J. Comput. Chem., 2003)

An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots. - Robert M. Dirks; Niles A. Pierce (J. Comput. Chem., 2004)

Nanoscale Molecular Transport by Synthetic DNA Machines. - Jong-Shik Shin; Niles A. Pierce (Nanotechnology: Science and Computation, 2006)

Thermodynamic Analysis of Interacting Nucleic Acid Strands. - Robert M. Dirks; Justin S. Bois; Joseph M. Schaeffer; Erik Winfree; Niles A. Pierce (SIAM Rev., 2007)

NUPACK: Analysis and design of nucleic acid systems. - Joseph N. Zadeh; Conrad Steenberg; Justin S. Bois; Brian R. Wolfe; Marshall B. Pierce; Asif R. Khan; Robert M. Dirks; Niles A. Pierce (J. Comput. Chem., 2011)

Nucleic acid sequence design via efficient ensemble defect optimization. - Joseph N. Zadeh; Brian R. Wolfe; Niles A. Pierce (J. Comput. Chem., 2011)

Accelerating universe with wet dark fluid in modified theory of gravity. - P. R. Agrawal; Niles A. Pierce (Astron. Comput., 2024)