Citation data: Google Scholar

NUPACK: analysis and design of nucleic acid structures, devices, and systems

M.E. Fornace, J. Huang, C.T. Newman, N.J. Porubsky, M.B. Pierce, and N.A. Pierce

ChemRxiv, 10.26434/chemrxiv-2022-xv98l, 2022.

HCR lateral flow assays for amplified instrument-free at-home SARS-CoV-2 testing

S.J. Schulte, J. Huang, and N.A. Pierce

bioRxiv, 2022.09.18.508442, 2022.

Hybridization chain reaction enables a unified approach to multiplexed, quantitative, high-resolution immunohistochemistry and in situ hybridization

M. Schwarzkopf, M.C. Liu, S.J. Schulte, R. Ives, N. Husain, Harry M.T. Choi, and N.A. Pierce

Development, 148(22):dev199847, 2021.

High-performance allosteric conditional guide RNAs for mammalian cell-selective regulation of CRISPR/Cas

L.M. Hochrein, H. Li, and N.A. Pierce

ACS Synth Biol, 10(5):964-971, 2021.

A unified dynamic programming framework for the analysis of interacting nucleic acid strands: enhanced models, scalability, and speed

M.E. Fornace, N.J. Porubsky, and N.A. Pierce

ACS Synth Biol, 9(10):2665-2678, 2020.

Conditional guide RNAs: programmable conditional regulation of CRISPR/Cas function in bacterial and mammalian cells via dynamic RNA nanotechnology

M.H. Hanewich-Hollatz, Z. Chen, L.M. Hochrein, J. Huang, N.A. Pierce

ACS Cent Sci, 5(7):1241-1249, 2019.

Signal transduction in human cell lysate via dynamic RNA nanotechnology

L.M. Hochrein, T.J. Ge, M. Schwarzkopf, N.A. Pierce

ACS Synth Biol, 7(12), 2796-2802, 2018.


Third-generation in situ hybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust

H.M.T. Choi, M. Schwarzkopf, M.E. Fornace, A. Acharya, G. Artavanis, J. Stegmaier, A. Cunha, N.A. Pierce

Development, 145:dev165753, 2018.

Multidimensional quantitative analysis of mRNA expression within intact vertebrate embryos

V. Trivedi, H.M.T. Choi, S.E. Fraser, and N.A. Pierce

Development, 145:dev156869, 2018.

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.

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.

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.

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.

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.

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.

Programming biomolecular self-assembly pathways 

P. Yin, H.M.T. Choi, C.R. Calvert, and N.A. Pierce 

Nature, 451:318-322, 2008.

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.

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.

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.

Triggered amplification by hybridization chain reaction

R.M. Dirks and N.A. Pierce

Proc Natl Acad Sci USA, 101(43):15275-15278, 2004.

A synthetic DNA walker for molecular transport

J.-S. Shin and N.A. Pierce

J Am Chem Soc, 126:10834-10835, 2004.

Rewritable memory by controllable nanopatterning of DNA

J.-S. Shin and N.A. Pierce

Nano Lett, 4(5):905-909, 2004.

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.

Adjoint and defect error bounding and correction for functional estimates

N.A. Pierce and M.B. Giles

J Comput Phys, 200:769-794, 2004.

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.

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.

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.

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.

Protein design is NP-hard

N.A. Pierce and E. Winfree

Protein Eng, 15(10):779-782, 2002.

Analytic adjoint solutions for the quasi-one-dimensional Euler equations

M.B. Giles and N.A. Pierce

J Fluid Mech, 426:327-345, 2001.

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.

Adjoint recovery of superconvergent functionals from PDE approximations

N.A. Pierce and M.B. Giles

SIAM Rev, 42(2):247-264, 2000.

An introduction to the adjoint approach to design

M.B. Giles and N.A. Pierce

Flow Turb Comb, 65:393-415, 2000.

Optimum aerodynamic design using the Navier-Stokes equations

A. Jameson, L. Martinelli, and N.A. Pierce

Theor Comput Fluid Dyn, 10:213-237, 1998.

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.

Preconditioned multigrid methods for compressible flow calculations on stretched meshes

N.A. Pierce and M.B. Giles

J Comput Phys, 136:425-445, 1997.