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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
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44 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
2020 Fornace ME, Porubsky NJ, Pierce NA. A Unified Dynamic Programming Framework for the Analysis of Interacting Nucleic Acid Strands: Enhanced Models, Scalability, and Speed. Acs Synthetic Biology. PMID 32910644 DOI: 10.1021/Acssynbio.9B00523  0.387
2019 Hanewich-Hollatz MH, Chen Z, Hochrein LM, Huang J, Pierce NA. Conditional Guide RNAs: Programmable Conditional Regulation of CRISPR/Cas Function in Bacterial and Mammalian Cells via Dynamic RNA Nanotechnology. Acs Central Science. 5: 1241-1249. PMID 31403072 DOI: 10.1021/Acscentsci.9B00340  0.369
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  0.362
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  0.328
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  0.722
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  0.758
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  0.693
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  0.594
2016 Schwarzkopf M, Pierce NA. Multiplexed miRNA northern blots via hybridization chain reaction. Nucleic Acids Research. PMID 27270083 DOI: 10.1093/Nar/Gkw503  0.373
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  0.719
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  0.404
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  0.627
2014 Sternberg JB, Pierce NA. Exquisite sequence selectivity with small conditional RNAs. Nano Letters. 14: 4568-72. PMID 24979041 DOI: 10.1021/Nl501593R  0.346
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  0.772
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  0.629
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  0.506
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  0.723
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  0.416
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  0.724
2013 Vieregg JR, Pierce NA. Selective Oligonucleotide and MRNA Pull-Down with Shielded Covalent Probes Biophysical Journal. 104. DOI: 10.1016/J.Bpj.2012.11.2761  0.387
2012 Vieregg JR, Nelson H, Stoltz B, Pierce NA. Sensitive and Selective Nucleic Acid Capture with Shielded Covalent Probes Biophysical Journal. 102: 416a. DOI: 10.1016/J.Bpj.2011.11.2277  0.367
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  0.773
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  0.738
2011 Beck VA, Bois JS, Dirks RM, Pierce NA. Elucidation and Control of the Hybridization Chain Reaction Biophysical Journal. 100: 522a. DOI: 10.1016/J.Bpj.2010.12.3051  0.769
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  0.719
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  0.738
2008 Yin P, Choi HM, Calvert CR, Pierce NA. Programming biomolecular self-assembly pathways. Nature. 451: 318-22. PMID 18202654 DOI: 10.1038/Nature06451  0.686
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  0.766
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  0.777
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  0.796
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  0.796
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  0.762
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  0.762
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  0.765
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  0.765
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  0.815
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  0.815
2004 Shin JS, Pierce NA. Rewritable memory by controllable nanopatterning of DNA Nano Letters. 4: 905-909. DOI: 10.1021/Nl049658R  0.332
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  0.768
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  0.768
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  0.348
2002 Pierce NA, Winfree E. Protein design is NP-hard. Protein Engineering. 15: 779-82. PMID 12468711 DOI: 10.1093/Protein/15.10.779  0.699
2002 Pierce NA, Winfree E. Protein design is NP-hard. Protein Engineering. 15: 779-82. PMID 12468711 DOI: 10.1093/Protein/15.10.779  0.699
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. DOI: 10.1002/1096-987X(200008)21:11<999::Aid-Jcc9>3.0.Co;2-A  0.314
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