Niles A. Pierce - Publications

Affiliations: 
Applied & Computational Mathematics California Institute of Technology, Pasadena, CA 
Area:
Engineering Molecular Devices
Website:
http://www.piercelab.caltech.edu/people/niles

57 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 Hochrein LM, Ge TJ, Schwarzkopf M, Pierce NA. Signal Transduction in Human Cell Lysate via Dynamic RNA Nanotechnology. Acs Synthetic Biology. PMID 30525469 DOI: 10.1021/acssynbio.8b00424  0.68
2018 Choi HMT, Schwarzkopf M, Fornace ME, Acharya A, Artavanis G, Stegmaier J, Cunha A, Pierce NA. Third-generation hybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust. Development (Cambridge, England). 145. PMID 29945988 DOI: 10.1242/dev.165753  0.68
2018 Trivedi V, Choi HMT, Fraser SE, Pierce NA. Multidimensional quantitative analysis of mRNA expression within intact vertebrate embryos. Development (Cambridge, England). 145. PMID 29311262 DOI: 10.1242/dev.156869  0.52
2017 Wolfe BR, Porubsky NJ, Zadeh JN, Dirks RM, Pierce NA. Constrained Multistate Sequence Design for Nucleic Acid Reaction Pathway Engineering. Journal of the American Chemical Society. PMID 28191938 DOI: 10.1021/jacs.6b12693  1
2016 Choi HM, Calvert CR, Husain N, Huss D, Barsi JC, Deverman BE, Hunter RC, Kato M, Lee SM, Abelin AC, Rosenthal AZ, Akbari OS, Li Y, Hay BA, Sternberg PW, ... ... Pierce NA, et al. Mapping a multiplexed zoo of mRNA expression. Development (Cambridge, England). 143: 3632-3637. PMID 27702788 DOI: 10.1242/dev.140137  0.52
2016 Shah S, Lubeck E, Schwarzkopf M, He TF, Greenbaum A, Sohn CH, Lignell A, Choi HM, Gradinaru V, Pierce NA, Cai L. Single-molecule RNA detection at depth via hybridization chain reaction and tissue hydrogel embedding and clearing. Development (Cambridge, England). PMID 27342713 DOI: 10.1242/dev.138560  1
2016 Schwarzkopf M, Pierce NA. Multiplexed miRNA northern blots via hybridization chain reaction. Nucleic Acids Research. PMID 27270083 DOI: 10.1093/nar/gkw503  0.68
2015 Huss D, Choi HM, Readhead C, Fraser SE, Pierce NA, Lansford R. Combinatorial analysis of mRNA expression patterns in mouse embryos using hybridization chain reaction. Cold Spring Harbor Protocols. 2015: 259-68. PMID 25734068 DOI: 10.1101/pdb.prot083832  1
2014 Wolfe BR, Pierce NA. Sequence Design for a Test Tube of Interacting Nucleic Acid Strands. Acs Synthetic Biology. PMID 25329866 DOI: 10.1021/sb5002196  1
2014 Choi HM, Beck VA, Pierce NA. Multiplexed in situ hybridization using hybridization chain reaction. Zebrafish. 11: 488-9. PMID 25188553 DOI: 10.1089/zeb.2014.1501  1
2014 Sternberg JB, Pierce NA. Exquisite sequence selectivity with small conditional RNAs. Nano Letters. 14: 4568-72. PMID 24979041 DOI: 10.1021/nl501593r  1
2014 Sadowski JP, Calvert CR, Zhang DY, Pierce NA, Yin P. Developmental self-assembly of a DNA tetrahedron. Acs Nano. 8: 3251-9. PMID 24720462 DOI: 10.1021/nn4038223  1
2014 Choi HM, Beck VA, Pierce NA. Next-generation in situ hybridization chain reaction: higher gain, lower cost, greater durability. Acs Nano. 8: 4284-94. PMID 24712299 DOI: 10.1021/nn405717p  1
2013 Hochrein LM, Schwarzkopf M, Shahgholi M, Yin P, Pierce NA. Conditional Dicer substrate formation via shape and sequence transduction with small conditional RNAs. Journal of the American Chemical Society. 135: 17322-30. PMID 24219616 DOI: 10.1021/ja404676x  1
2013 Rosenthal AZ, Zhang X, Lucey KS, Ottesen EA, Trivedi V, Choi HM, Pierce NA, Leadbetter JR. Localizing transcripts to single cells suggests an important role of uncultured deltaproteobacteria in the termite gut hydrogen economy. Proceedings of the National Academy of Sciences of the United States of America. 110: 16163-8. PMID 24043823 DOI: 10.1073/pnas.1307876110  1
2013 Vieregg JR, Nelson HM, Stoltz BM, Pierce NA. Selective nucleic acid capture with shielded covalent probes. Journal of the American Chemical Society. 135: 9691-9. PMID 23745667 DOI: 10.1021/ja4009216  1
2013 Dirks RM, Ueda CT, Pierce NA. Retraction for Venkataraman et al., Selective cell death mediated by small conditional RNAs. Proceedings of the National Academy of Sciences of the United States of America. 110: 384. PMID 23248321 DOI: 10.1073/pnas.1221212110  1
2011 Zadeh JN, Wolfe BR, Pierce NA. Nucleic acid sequence design via efficient ensemble defect optimization. Journal of Computational Chemistry. 32: 439-52. PMID 20717905 DOI: 10.1002/jcc.21633  1
2011 Zadeh JN, Steenberg CD, Bois JS, Wolfe BR, Pierce MB, Khan AR, Dirks RM, Pierce NA. NUPACK: Analysis and design of nucleic acid systems. Journal of Computational Chemistry. 32: 170-3. PMID 20645303 DOI: 10.1002/jcc.21596  1
2010 Choi HM, Chang JY, Trinh le A, Padilla JE, Fraser SE, Pierce NA. Programmable in situ amplification for multiplexed imaging of mRNA expression. Nature Biotechnology. 28: 1208-12. PMID 21037591 DOI: 10.1038/nbt.1692  1
2010 Venkataraman S, Dirks RM, Ueda CT, Pierce NA. Selective cell death mediated by small conditional RNAs. Proceedings of the National Academy of Sciences of the United States of America. 107: 16777-82. PMID 20823260 DOI: 10.1073/pnas.1006377107  1
2008 Yin P, Choi HM, Calvert CR, Pierce NA. Programming biomolecular self-assembly pathways. Nature. 451: 318-22. PMID 18202654 DOI: 10.1038/nature06451  1
2007 Venkataraman S, Dirks RM, Rothemund PW, Winfree E, Pierce NA. An autonomous polymerization motor powered by DNA hybridization. Nature Nanotechnology. 2: 490-4. PMID 18654346 DOI: 10.1038/nnano.2007.225  1
2007 Dirks RM, Bois JS, Schaeffer JM, Winfree E, Pierce NA. Thermodynamic analysis of interacting nucleic acid strands Siam Review. 49: 65-88. DOI: 10.1137/060651100  1
2006 Carbone A, Pierce NA. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics): Preface Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3892: v.  1
2006 Carbone A, Pierce NA. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics): Preface Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3892: v.  1
2005 Bois JS, Venkataraman S, Choi HM, Spakowitz AJ, Wang ZG, Pierce NA. Topological constraints in nucleic acid hybridization kinetics. Nucleic Acids Research. 33: 4090-5. PMID 16043632 DOI: 10.1093/nar/gki721  1
2005 Bois JS, Venkataraman S, Choi HM, Spakowitz AJ, Wang ZG, Pierce NA. Topological constraints in nucleic acid hybridization kinetics. Nucleic Acids Research. 33: 4090-5. PMID 16043632 DOI: 10.1093/nar/gki721  1
2004 Dirks RM, Pierce NA. Triggered amplification by hybridization chain reaction. Proceedings of the National Academy of Sciences of the United States of America. 101: 15275-8. PMID 15492210 DOI: 10.1073/pnas.0407024101  1
2004 Dirks RM, Pierce NA. Triggered amplification by hybridization chain reaction. Proceedings of the National Academy of Sciences of the United States of America. 101: 15275-8. PMID 15492210 DOI: 10.1073/pnas.0407024101  1
2004 Shin JS, Pierce NA. A synthetic DNA walker for molecular transport. Journal of the American Chemical Society. 126: 10834-5. PMID 15339155 DOI: 10.1021/ja047543j  1
2004 Shin JS, Pierce NA. A synthetic DNA walker for molecular transport. Journal of the American Chemical Society. 126: 10834-5. PMID 15339155 DOI: 10.1021/ja047543j  1
2004 Dirks RM, Pierce NA. An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots. Journal of Computational Chemistry. 25: 1295-304. PMID 15139042 DOI: 10.1002/jcc.20057  1
2004 Dirks RM, Pierce NA. An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots. Journal of Computational Chemistry. 25: 1295-304. PMID 15139042 DOI: 10.1002/jcc.20057  1
2004 Dirks RM, Lin M, Winfree E, Pierce NA. Paradigms for computational nucleic acid design. Nucleic Acids Research. 32: 1392-403. PMID 14990744 DOI: 10.1093/nar/gkh291  1
2004 Dirks RM, Lin M, Winfree E, Pierce NA. Paradigms for computational nucleic acid design. Nucleic Acids Research. 32: 1392-403. PMID 14990744 DOI: 10.1093/nar/gkh291  1
2004 Shin JS, Pierce NA. Rewritable memory by controllable nanopatterning of DNA Nano Letters. 4: 905-909. DOI: 10.1021/nl049658r  1
2004 Pierce NA, Giles MB. Adjoint and defect error bounding and correction for functional estimates Journal of Computational Physics. 200: 769-794. DOI: 10.1016/j.jcp.2004.05.001  1
2004 Pierce NA, Giles MB. Adjoint and defect error bounding and correction for functional estimates Journal of Computational Physics. 200: 769-794. DOI: 10.1016/j.jcp.2004.05.001  1
2004 Giles MB, Pierce N, Süli E. Progress in adjoint error correction for integral functionals Computing and Visualization in Science. 6: 113-121. DOI: 10.1007/s00791-003-0115-y  1
2003 Dirks RM, Pierce NA. A partition function algorithm for nucleic acid secondary structure including pseudoknots. Journal of Computational Chemistry. 24: 1664-77. PMID 12926009 DOI: 10.1002/jcc.10296  1
2003 Dirks RM, Pierce NA. A partition function algorithm for nucleic acid secondary structure including pseudoknots. Journal of Computational Chemistry. 24: 1664-77. PMID 12926009 DOI: 10.1002/jcc.10296  1
2003 Gordon DB, Hom GK, Mayo SL, Pierce NA. Exact rotamer optimization for protein design. Journal of Computational Chemistry. 24: 232-43. PMID 12497602 DOI: 10.1002/jcc.10121  1
2003 Giles MB, Duta MC, Müller JD, Pierce NA. Algorithm developments for discrete adjoint methods Aiaa Journal. 41: 198-205.  1
2003 Giles MB, Duta MC, Müller JD, Pierce NA. Algorithm developments for discrete adjoint methods Aiaa Journal. 41: 198-205.  1
2002 Pierce NA, Winfree E. Protein design is NP-hard. Protein Engineering. 15: 779-82. PMID 12468711  1
2002 Pierce NA, Winfree E. Protein design is NP-hard. Protein Engineering. 15: 779-82. PMID 12468711  1
2001 Giles MB, Pierce NA. Analytic adjoint solutions for the quasi-one-dimensional Euler equations Journal of Fluid Mechanics. 426: 327-345. DOI: 10.1017/S0022112000002366  1
2001 Giles MB, Pierce NA. Analytic adjoint solutions for the quasi-one-dimensional Euler equations Journal of Fluid Mechanics. 426: 327-345. DOI: 10.1017/S0022112000002366  1
2000 Giles MB, Pierce NA. An introduction to the adjoint approach to design Flow, Turbulence and Combustion. 65: 393-415. DOI: 10.1023/A:1011430410075  1
2000 Giles MB, Pierce NA. An introduction to the adjoint approach to design Flow, Turbulence and Combustion. 65: 393-415. DOI: 10.1023/A:1011430410075  1
2000 Pierce NA, Spriet JA, Desmet J, Mayo SL. Conformational Splitting: A More Powerful Criterion for Dead-End Elimination Journal of Computational Chemistry. 21: 999-1009.  1
2000 Pierce NA, Giles MB. Adjoint recovery of superconvergent functionals from PDE approximations Siam Review. 42: 247-264.  1
2000 Pierce NA, Giles MB. Adjoint recovery of superconvergent functionals from PDE approximations Siam Review. 42: 247-264.  1
1998 Jameson A, Martinelli L, Pierce NA. Optimum aerodynamic design using the Navier-Stokes equations Theoretical and Computational Fluid Dynamics. 10: 213-237.  1
1998 Pierce NA, Alonso JJ. Efficient computation of unsteady viscous flows by an implicit preconditioned multigrid method Aiaa Journal. 36: 401-408.  1
1997 Pierce NA, Giles MB. Preconditioned multigrid methods for compressible flow calculations on stretched meshes Journal of Computational Physics. 136: 425-445. DOI: 10.1006/jcph.1997.5772  1
Show low-probability matches.