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NUPACK Web Application
  • M. E. Fornace, J. Huang, C. T. Newman, N. J. Porubsky, M. B. Pierce, N. A. Pierce. NUPACK: analysis and design of nucleic acid structures, devices, and systems. ChemRxiv, 2022.
  • J. N. Zadeh, C. D. Steenberg, J. S. Bois, B. R. Wolfe, M. B. Pierce, A. R. Khan, R. M. Dirks, N. A. Pierce. NUPACK: analysis and design of nucleic acid systems. J Comput Chem, 32:170–173, 2011. (pdf)
NUPACK Python Module
  • M. E. Fornace, J. Huang, C. T. Newman, N. J. Porubsky, M. B. Pierce, N. A. Pierce. NUPACK: analysis and design of nucleic acid structures, devices, and systems. ChemRxiv, 2022.
NUPACK Analysis Algorithms
  • M. E. Fornace, N. J. Porubsky, and N. A. Pierce. A unified dynamic programming framework for the analysis of interacting nucleic acid strands: enhanced models, scalability, and speed. ACS Synth Biol, 9:2665-2678, 2020. (pdf, supp info)
  • R. M. Dirks, J. S. Bois, J. M. Schaeffer, E. Winfree, and N. A. Pierce. Thermodynamic analysis of interacting nucleic acid strands. SIAM Rev, 49:65-88, 2007. (pdf)
  • R. M. Dirks and N. A. Pierce. An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots. J Comput Chem, 25:1295-1304, 2004. (pdf)
  • R. M. Dirks and N. A. Pierce. A partition function algorithm for nucleic acid secondary structure including pseudoknots. J Comput Chem, 24:1664-1677, 2003. (pdf, supp info)
NUPACK Design Algorithms
  • B. R. Wolfe, N. J. Porubsky, J. N. Zadeh, R. M. Dirks, and N. A. Pierce. Constrained multistate sequence design for nucleic acid reaction pathway engineering. J Am Chem Soc, 139:3134-3144, 2017. (pdf, supp info)
  • B. R. Wolfe and N. A. Pierce. Sequence design for a test tube of interacting nucleic acid strands. ACS Synth Biol, 4:1086-1100, 2015. (pdf, supp info, supp tests)
  • J. N. Zadeh, B. R. Wolfe, and N. A. Pierce. Nucleic acid sequence design via efficient ensemble defect optimization. J Comput Chem, 32:439–452, 2011. (pdf, supp info, supp tests)
  • R. M. Dirks, M. Lin, E. Winfree, and N. A. Pierce. Paradigms for computational nucleic acid design. Nucl Acids Res, 32:1392-1403, 2004. (pdf, supp info, supp seqs)