Pierce, Niles

Article from CaltechAUTHORS

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• Trivedi, Vikas and Choi, Harry M. T., el al. (2018) Multidimensional quantitative analysis of mRNA expression within intact vertebrate embryos; Development; Vol. 145; No. 1; Art. No. 156869; PMCID PMC5825878; 10.1242/dev.156869
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• Schwarzkopf, Maayan and Pierce, Niles A. (2016) Multiplexed miRNA northern blots via hybridization chain reaction; Nucleic Acids Research; Vol. 44; No. 15; Art. No. e129; PMCID PMC5009741; 10.1093/nar/gkw503
• Shah, Sheel and Lubeck, Eric, el al. (2016) Single-molecule RNA detection at depth via hybridization chain reaction and tissue hydrogel embedding and clearing; Development; Vol. 143; No. 15; 2862-2867; PMCID PMC5004914; 10.1242/dev.138560
• Wolfe, Brian R. and Pierce, Niles A. (2015) Sequence Design for a Test Tube of Interacting Nucleic Acid Strands; ACS Synthetic Biology; Vol. 4; No. 10; 1086-1100; 10.1021/sb5002196
• Huss, David and Choi, Harry M. T., el al. (2015) Combinatorial Analysis of mRNA Expression Patterns in Mouse Embryos Using Hybridization Chain Reaction; Cold Spring Harbor Protocols; Vol. 2015; No. 3; 259-268; 10.1101/pdb.prot083832
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• Sternberg, Jonathan B. and Pierce, Niles A. (2014) Exquisite Sequence Selectivity with Small Conditional RNAs; Nano Letters; Vol. 14; No. 8; 4568-4572; PMCID PMC4134187; 10.1021/nl501593r
• Choi, Harry M. T. and Beck, Victor A., el al. (2014) Next-Generation in Situ Hybridization Chain Reaction: Higher Gain, Lower Cost, Greater Durability; ACS Nano; Vol. 8; No. 5; 4284-4294; PMCID PMC4046802; 10.1021/nn405717p
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• Vieregg, Jeffrey and Pierce, Niles A. (2014) Selective Nucleic Acid Capture with Shielded Covalent Probes; Biophysical Journal; Vol. 106; No. 2; 617A; 10.1016/j.bpj.2013.11.3412
• Hochrein, Lisa M. and Schwarzkopf, Maayan, el al. (2013) Conditional Dicer Substrate Formation via Shape and Sequence Transduction with Small Conditional RNAs; Journal of the American Chemical Society; Vol. 135; No. 46; 17322-17330; PMCID PMC3842090; 10.1021/ja404676x
• Rosenthal, Adam Z. and Zhang, Xinning, el al. (2013) 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; Vol. 110; No. 40; 16163-16168; PMCID PMC3791709; 10.1073/pnas.1307876110
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• Vieregg, Jeffrey R. and Pierce, Niles A. (2013) Selective Oligonucleotide and MRNA Pull-Down with Shielded Covalent Probes; Biophysical Journal; Vol. 104; No. 2; 500A; 10.1016/j.bpj.2012.11.2761
• Zadeh, Joseph N. and Wolfe, Brian R., el al. (2011) Nucleic Acid Sequence Design via Efficient Ensemble Defect Optimization; Journal of Computational Chemistry; Vol. 32; No. 3; 439-452; 10.1002/jcc.21633
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• Yin, Peng and Choi, Harry M. T., el al. (2008) Programming biomolecular self-assembly pathways; Nature; Vol. 451; No. 7176; 318-322; 10.1038/nature06451
• Venkataraman, Suvir and Dirks, Robert M., el al. (2007) An autonomous polymerization motor powered by DNA hybridization; Nature Nanotechnology; Vol. 2; No. 8; 490-494; 10.1038/nnano.2007.225
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• Dirks, Robert M. and Pierce, Niles A. (2004) Triggered amplification by hybridization chain reaction; Proceedings of the National Academy of Sciences of the United States of America; Vol. 101; No. 43; 15275-15278; PMCID PMC524468; 10.1073/pnas.0407024101
• Shin, Jong-Shik and Pierce, Niles A. (2004) A Synthetic DNA Walker for Molecular Transport; Journal of the American Chemical Society; Vol. 126; No. 35; 10834-10835; 10.1021/ja047543j
• Dirks, Robert M. and Pierce, Niles A. (2004) An algorithm for computing nucleic acid base‐pairing probabilities including pseudoknots; Journal of Computational Chemistry; Vol. 25; No. 10; 1295-1304; 10.1002/jcc.20057
• Shin, Jong-Shik and Pierce, Niles A. (2004) Rewritable Memory by Controllable Nanopatterning of DNA; Nano Letters; Vol. 4; No. 5; 905-909; 10.1021/nl049658r
• Giles, Michael B. and Pierce, Niles, el al. (2004) Progress in adjoint error correction for integral functionals; Computing and Visualization in Science; Vol. 6; No. 2-3; 113-121; 10.1007/s00791-003-0115-y
• Dirks, Robert M. and Lin, Milo, el al. (2004) Paradigms for computational nucleic acid design; Nucleic Acids Research; Vol. 32; No. 4; 1392-1403; PMCID PMC390280; 10.1093/nar/gkh291
• Dirks, Robert M. and Pierce, Niles A. (2003) A Partition Function Algorithm for Nucleic Acid Secondary Structure Including Pseudoknots; Journal of Computational Chemistry; Vol. 24; No. 13; 1664-1677; 10.1002/jcc.10296
• Gordon, D. Benjamin and Hom, Geoffrey K., el al. (2003) Exact rotamer optimization for protein design; Journal of Computational Chemistry; Vol. 24; No. 2; 232-243; 10.1002/jcc.10121
• Pierce, Niles A. and Winfree, Erik (2002) Protein Design is NP-hard; Protein Engineering; Vol. 15; No. 10; 779-782; 10.1093/protein/15.10.779
• Giles, Michael B. and Pierce, Niles A. (2001) Analytic adjoint solutions for the quasi-one-dimensional Euler equations; Journal of Fluid Mechanics; Vol. 426; 327-345; 10.1017/S0022112000002366
• Pierce, Niles A. and Spriet, Jan A., el al. (2000) Conformational splitting: a more powerful criterion for dead-end elimination; Journal of Computational Chemistry; Vol. 21; No. 11; 999-1009; 10.1002/1096-987X(200008)21:11<999::AID-JCC9>3.0.CO;2-A
• Pierce, Niles A. and Giles, Michael B. (2000) Adjoint recovery of superconvergent functionals from PDE approximations; SIAM Review; Vol. 42; No. 2; 247-264; 10.1137/S0036144598349423