The Pierce Lab

Journal Publications

Citation data: Web of Science, Google Scholar

  • Constrained multistate sequence design for nucleic acid reaction pathway engineering B.R. Wolfe, N.J. Porubsky, J.N. Zadeh, R.M. Dirks, and N.A. Pierce J Am Chem Soc, 39:3134−3144, 2017.
  • Mapping a multiplexed zoo of mRNA expression H.M.T. Choi, C.R. Calvert, N. Husain, D. Huss, J.C. Barsi, B.E. Deverman, R.C. Hunter, M. Kato, S.M. Lee, A.C.T. Abelin, A.Z. Rosenthal, O.S. Akbari, Y. Li, B.A. Hay, P.W. Sternberg, P.H. Patterson, E.H. Davidson, S.K. Mazmanian, D.A. Prober, M. van de Rijn, J.R. Leadbetter, D.K. Newman, C. Readhead, M.E. Bronner, B. Wold, R. Lansford, T. Sauka-Spengler, S.E. Fraser, and N.A. Pierce Development, 143:3632-3637, 2016.
  • Single-molecule RNA detection at depth via hybridization chain reaction and tissue hydrogel embedding and clearing S. Shah, E. Lubeck, M. Schwarzkopf, T.-f. He, A. Greenbaum, C.h. Sohn, A. Lignell, H.M.T. Choi, V. Gradinaru, N.A. Pierce, and L. Cai Development, 143:2862-2867, 2016.
  • Multiplexed miRNA northern blots via hybridization chain reaction M. Schwarzkopf and N.A. Pierce Nucleic Acids Res, 44(15):e129, 2016.
  • Sequence design for a test tube of interacting nucleic acid strands B.R. Wolfe and N.A. Pierce ACS Synth Biol, 4(10):1086–1100, 2015.
  • Combinatorial analysis of mRNA expression patterns in mouse embryos using hybridization chain reaction D. Huss, H.M.T. Choi, C. Readhead, S.E. Fraser, N.A. Pierce and R. Lansford Cold Spring Harb Protoc, 2015(3):259-268, 2015.
  • Exquisite sequence selectivity with small conditional RNAs J.B. Sternberg and N.A. Pierce Nano Lett, 14(8):4568-4572, 2014.
  • Next-generation in situ hybridization chain reaction: higher gain, lower cost, greater durability H.M.T. Choi, V.A. Beck, and N.A. Pierce ACS Nano, 8(5):4284-4294, 2014. (open access)
  • Developmental self-assembly of a DNA tetrahedron J.P. Sadowski, C.R. Calvert, D.Y. Zhang, N.A. Pierce, and P. Yin ACS Nano, 8(4):3251-3259, 2014.
  • Conditional Dicer substrate formation via shape and sequence transduction with small conditional RNAs L.M. Hochrein, M. Schwarzkopf, M. Shahgholi, P. Yin, and N.A. Pierce J Am Chem Soc, 135(46):17322-17330, 2013. (open access)
  • Localizing transcripts to single cells suggests an important role of uncultured deltaproteobacteria in the termite gut hydrogen economy A.Z. Rosenthal, X. Zhang, K.S. Lucey, E.A. Ottesen, V. Trivedi, H.M.T. Choi, N.A. Pierce, and J.R. Leadbetter Proc Natl Acad Sci USA, 110(40):16163-16168, 2013.
  • 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, 135(26):9691-9699, 2013. (open access)
  • 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)

Chapters & Proceedings

  • Combinatorial analysis of mRNA expression patterns in mouse embryos using hybridization chain reaction D. Huss, H.M.T. Choi, C. Readhead, S.E. Fraser, N.A. Pierce, and R. Lansford In Molecular Neuroscience: A Laboratory Manual, Ed. R. Lansford, Cold Spring Harbor Press, New York, 2014. doi:10.1101/pdb.prot083832
  • Nanoscale molecular transport by synthetic DNA machines J.-S. Shin and N.A. Pierce In Nanotechnology: Science and Computation (In honor of Ned Seeman), Eds J. Chen, N. Jonoska, and G. Rozenberg, Springer, 2006. (pdf)
  • Adjoint and defect error bounding and correction for functional estimates N.A. Pierce and M.B. Giles AIAA Paper 2003-3846, In 16th Computational Fluid Dynamics Conference Proceedings, Orlando, FL, 2003. (pdf)
  • Adjoint error correction for integral outputs M.B. Giles and N.A. Pierce In Lecture Notes in Computer Science & Engineering: Error Estimation and Adaptive Discretization Methods in Computational Fluid Dynamics, Vol. 25, Springer-Verlag, 2002. (ps.gz)
  • Superconvergent lift estimates through adjoint error analysis M.B. Giles and N.A. Pierce In Innovative methods for numerical solutions to partial differential equations (In honor of Phil Roe), Eds M. Hafez and J.J. Chattot, World Scientific, 2001. (ps.gz)
  • Improved lift and drag estimates using adjoint Euler equations M.B. Giles and N.A. Pierce AIAA Paper 99-3293, In 14th Computational Fluid Dynamics Conference Proceedings, Norfolk, VA, 1999. (ps.gz)
  • On the properties of solutions of the adjoint Euler equations M.B. Giles and N.A. Pierce In Numerical Methods for Fluid Dynamics VI, M. Baines, ed., ICFD, Oxford, UK, 1998. (ps.gz)
  • Adjoint equations in CFD: duality, boundary conditions and solution behavior M.B. Giles and N.A. Pierce AIAA Paper 97-1850, In 13th Computational Fluid Dynamics Conference Proceedings, Snowmass, CO, 1997. (ps.gz)
  • Accelerating three-dimensional Navier-Stokes calculations N.A. Pierce, M.B. Giles, A. Jameson and L. Martinelli AIAA Paper 97-1953, In 13th Computational Fluid Dynamics Conference Proceedings, Snowmass, CO, 1997. (ps.gz)
  • A preconditioned implicit multigrid algorithm for parallel computation of unsteady aeroelastic compressible flows N.A. Pierce and J.J. Alonso AIAA Paper 97-0444, 35th Aerospace Sciences Meeting and Exhibit, Reno, NV, 1997. (ps.gz)
  • Optimum aerodynamic design using the Navier-Stokes equations A. Jameson, N.A. Pierce and L. Martinelli AIAA Paper 97-0101, 35th Aerospace Sciences Meeting and Exhibit, Reno, NV, 1997. (ps.gz)
  • Preconditioning compressible flow calculations on stretched meshes N.A. Pierce and M.B. Giles AIAA Paper 96-0889, 34th Aerospace Sciences Meeting and Exhibit, Reno, NV, 1996. (ps.gz)

Reports

  • Algorithm developments for discrete adjoint methods M.B. Giles, M.C. Duta, J.D. Mueller and N.A. Pierce Oxford University Computing Laboratory Report NA 01/15, 2001. (ps.gz)
  • Analysis of adjoint error correction for superconvergent functional estimates M.B. Giles and N.A. Pierce Oxford University Computing Laboratory Report NA 01/14, 2001. (ps.gz)
  • An introduction to the adjoint approach to design M.B. Giles and N.A. Pierce Oxford University Computing Laboratory Report NA 00/04, 2000. (ps.gz)
  • Analytic adjoint solutions for the quasi-1D Euler equations M.B. Giles and N.A. Pierce Oxford University Computing Laboratory Report NA 00/03, 2000. (ps.gz)
  • Improved lift and drag estimates using adjoint Euler equations M.B. Giles and N.A. Pierce Oxford University Computing Laboratory Report NA 00/02, 2000. (ps.gz)
  • Adjoint recovery of superconvergent functionals from approximate solutions of partial differential equations N.A. Pierce and M.B. Giles Oxford University Computing Laboratory Report NA 98/18, 1998. (ps.gz)
  • Preconditioning on stretched meshes N.A. Pierce and M.B. Giles Oxford University Computing Laboratory Report NA 95/10, 1995. Presented at the 12th AIAA Computational Fluid Dynamics Conference, San Diego, CA, 1995. (ps.gz)

Theses

  • Preconditioned multigrid methods for compressible flow calculations on stretched meshes N.A. Pierce DPhil thesis, Oxford University, 1997. (ps.gz)
  • Characteristic-based dissipative schemes and characteristic time stepping for the Euler equations N.A. Pierce Qualifying dissertation for DPhil status, Oxford University, 1994. (ps.gz)