The Pierce Lab

Journal Publications

Citation data: Web of Science, Google Scholar

  • Selective nucleic acid capture with shielded covalent probes J.R. Vieregg, H.M. Nelson, B.M. Stoltz, and N.A. Pierce J Am Chem Soc, DOI: 10.1021/ja4009216, 2013. (pdf) (supp info)
  • Nucleic acid sequence design via efficient ensemble defect optimization J.N. Zadeh, B.R. Wolfe, and N.A. Pierce J Comput Chem, 32:439-452, 2011. (pdf) (supp info) (supp structures)
  • NUPACK: Analysis and design of nucleic acid systems J.N. Zadeh, C.D. Steenberg, J.S. Bois, B.R. Wolfe, M.B. Pierce, A.R. Khan, R.M. Dirks, and N.A. Pierce J Comput Chem, 32:170-173, 2011. (pdf)
  • Programmable in situ amplification for multiplexed imaging of mRNA expression H.M.T. Choi, J.Y. Chang, L.A. Trinh, J.E. Padilla, S.E. Fraser, and N.A. Pierce Nature Biotechnol, 28:1208-1212, 2010. (pdf) (supp movie 1) (supp movie 2) (supp info)
  • Selective cell death mediated by small conditional RNAs S. Venkataraman, R.M. Dirks, C.T. Ueda, and N.A. Pierce Proc Natl Acad Sci USA, 107(39):16777-16782, 2010. (pdf) (supp info)
    Note: this paper has been retracted.     Retraction for Venkataraman et al., Selective cell death mediated by small conditional RNAs R.M. Dirks, C.T. Ueda, and N.A. Pierce Proc Natl Acad Sci USA, 110(1):384, 2013. (pdf)
  • Programming biomolecular self-assembly pathways P. Yin, H.M.T. Choi, C.R. Calvert, and N.A. Pierce Nature, 451:318-322, 2008. (pdf) (supp info)
  • An autonomous polymerization motor powered by DNA hybridization S. Venkataraman, R.M. Dirks, P.W.K. Rothemund, E. Winfree, and N.A. Pierce Nature Nanotech, 2(8):490-494, 2007. (pdf) (supp info)
  • Thermodynamic analysis of interacting nucleic acid strands R.M. Dirks, J.S. Bois, J.M. Schaeffer, E. Winfree, and N.A. Pierce SIAM Rev, 49(1):65-88, 2007. (pdf)
  • Topological constraints in nucleic acid hybridization kinetics J.S. Bois, S.Venkataraman, H.M.T. Choi, A.J. Spakowitz, Z.-G. Wang, and N.A. Pierce Nucleic Acids Res, 33(13):4090-4095, 2005. (pdf)
  • Triggered amplification by hybridization chain reaction R.M. Dirks and N.A. Pierce Proc Natl Acad Sci USA, 101(43):15275-15278, 2004. (pdf)
  • A synthetic DNA walker for molecular transport J.-S. Shin and N.A. Pierce J Am Chem Soc, 126:10834-10835, 2004. (pdf) (supp info)
  • Rewritable memory by controllable nanopatterning of DNA J.-S. Shin and N.A. Pierce Nano Lett, 4(5):905-909, 2004. (pdf) (supp info)
  • An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots R.M. Dirks and N.A. Pierce J Comput Chem, 25:1295-1304, 2004. (pdf)
  • Adjoint and defect error bounding and correction for functional estimates N.A. Pierce and M.B. Giles J Comput Phys, 200:769-794, 2004. (pdf)
  • Paradigms for computational nucleic acid design R.M. Dirks, M. Lin, E. Winfree, and N.A. Pierce Nucleic Acids Res, 32(4):1392-1403, 2004. (pdf) (supp info text) (supp info sequences)
  • A partition function algorithm for nucleic acid secondary structure including pseudoknots R.M. Dirks and N.A. Pierce J Comput Chem, 24(13):1664-1677, 2003. (pdf) (supp info)
  • Exact rotamer optimization for protein design D.B. Gordon, G.K. Hom, S.L. Mayo, and N.A. Pierce J Comput Chem, 24(2):232-243, 2003. (pdf)
  • Algorithm developments for discrete adjoint methods M.B. Giles, M.C. Duta, J.-D. Mueller, and N.A. Pierce AIAA J, 41(2):198-205, 2003. (pdf)
  • Protein design is NP-hard N.A. Pierce and E. Winfree Protein Engineering, 15(10):779-782, 2002. (pdf)
  • Analytic adjoint solutions for the quasi-one-dimensional Euler equations M.B. Giles and N.A. Pierce J Fluid Mech, 426:327-345, 2001. (pdf)
  • Conformational splitting: a more powerful criterion for dead-end elimination N.A. Pierce, J.A. Spriet, J. Desmet, and S.L. Mayo J Comput Chem, 21(11):999-1009, 2000. (pdf)
  • Adjoint recovery of superconvergent functionals from PDE approximations N.A. Pierce and M.B. Giles SIAM Rev, 42(2):247-264, 2000. (pdf)
  • An introduction to the adjoint approach to design M.B. Giles and N.A. Pierce Flow Turb Comb, 65:393-415, 2000. (pdf)
  • Optimum aerodynamic design using the Navier-Stokes equations A. Jameson, L. Martinelli, and N.A. Pierce Theor Comput Fluid Dyn, 10:213-237, 1998. (pdf)
  • Efficient computation of unsteady viscous flows by an implicit preconditioned multigrid method N.A. Pierce and J.J. Alonso AIAA J, 36(3):401-408, 1998. (pdf)
  • Preconditioned multigrid methods for compressible flow calculations on stretched meshes N.A. Pierce and M.B. Giles J Comput Phys, 136:425-445, 1997. (pdf)