A partition function algorithm for nucleic acid secondary structure including pseudoknots. - Robert M. Dirks; 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)

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)

Anton 3: twenty microseconds of molecular dynamics simulation before lunch. - David E. Shaw; Peter J. Adams; Asaph Azaria; Joseph A. Bank; Brannon Batson; Alistair Bell; Michael Bergdorf; Jhanvi Bhatt; J. Adam Butts; Timothy Correia; Robert M. Dirks; Ron O. Dror; et al. (SC, 2021)