<h1>Pierce, Niles</h1> <h2>Article from <a href="https://authors.library.caltech.edu">CaltechAUTHORS</a></h2> <ul> <li>Schulte, Samuel J. and Shin, Boyoung, el al. (2024) <a href="https://authors.library.caltech.edu/records/5tqf9-jve59">Multiplex, Quantitative, High-Resolution Imaging of Protein:Protein Complexes via Hybridization Chain Reaction</a>; ACS Chemical Biology; Vol. 19; No. 2; 280-288; PMCID PMC10877569; <a href="https://doi.org/10.1021/acschembio.3c00431">10.1021/acschembio.3c00431</a></li> <li>Schulte, Samuel J. and Fornace, Mark E., el al. (2024) <a href="https://authors.library.caltech.edu/records/hncah-g5h50">HCR spectral imaging: 10-plex, quantitative, high-resolution RNA and protein imaging in highly autofluorescent samples</a>; Development; Vol. 151; No. 4; dev202307; PMCID PMC10941662; <a href="https://doi.org/10.1242/dev.202307">10.1242/dev.202307</a></li> <li>Schulte, Samuel J. and Huang, Jining, el al. (2023) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20230227-258668000.1">Hybridization Chain Reaction Lateral Flow Assays for Amplified Instrument-Free At-Home SARS-CoV-2 Testing</a>; ACS Infectious Diseases; Vol. 9; No. 3; 450-458; PMCID PMC9924079; <a href="https://doi.org/10.1021/acsinfecdis.2c00472">10.1021/acsinfecdis.2c00472</a></li> <li>Bokhari, Rihana S. and Beheshti, Afshin, el al. (2022) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20220808-223919000">Looking on the Horizon; Potential and Unique Approaches to Developing Radiation Countermeasures for Deep Space Travel</a>; Life Sciences in Space Research; Vol. 35; 105-112; <a href="https://doi.org/10.1016/j.lssr.2022.08.003">10.1016/j.lssr.2022.08.003</a></li> <li>Schwarzkopf, Maayan and Liu, Mike C., el al. (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20210604-111535359">Hybridization chain reaction enables a unified approach to multiplexed, quantitative, high-resolution immunohistochemistry and in situ hybridization</a>; Development; Vol. 148; No. 22; Art. No. dev199847; PMCID PMC8645210; <a href="https://doi.org/10.1242/dev.199847">10.1242/dev.199847</a></li> <li>Hochrein, Lisa M. and Li, Heyun, el al. (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20210503-115702708">High-Performance Allosteric Conditional Guide RNAs for Mammalian Cell-Selective Regulation of CRISPR/Cas</a>; ACS Synthetic Biology; Vol. 10; No. 5; 964-971; <a href="https://doi.org/10.1021/acssynbio.1c00037">10.1021/acssynbio.1c00037</a></li> <li>Fornace, Mark E. and Porubsky, Nicholas J., el al. (2020) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200911-133138429">A Unified Dynamic Programming Framework for the Analysis of Interacting Nucleic Acid Strands: Enhanced Models, Scalability, and Speed</a>; ACS Synthetic Biology; Vol. 9; No. 10; 2665-2678; <a href="https://doi.org/10.1021/acssynbio.9b00523">10.1021/acssynbio.9b00523</a></li> <li>Hanewich-Hollatz, Mikhail H. and Chen, Zhewei, el al. (2019) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20190123-124341981">Conditional Guide RNAs: Programmable Conditional Regulation of CRISPR/Cas Function in Bacterial and Mammalian Cells via Dynamic RNA Nanotechnology</a>; ACS Central Science; Vol. 5; No. 7; 1241-1249; PMCID PMC6661866; <a href="https://doi.org/10.1021/acscentsci.9b00340">10.1021/acscentsci.9b00340</a></li> <li>Hochrein, Lisa M. and Ge, Tianjia J., el al. (2018) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20181030-075958683">Signal Transduction in Human Cell Lysate via Dynamic RNA Nanotechnology</a>; ACS Synthetic Biology; Vol. 7; No. 12; 2796-2802; PMCID PMC6305621; <a href="https://doi.org/10.1021/acssynbio.8b00424">10.1021/acssynbio.8b00424</a></li> <li>Choi, Harry M. T. and Schwarzkopf, Maayan, el al. (2018) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20180702-084055324">Third-generation in situ hybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust</a>; Development; Vol. 145; No. 12; Art. No. dev165753; PMCID PMC6031405; <a href="https://doi.org/10.1242/dev.165753">10.1242/dev.165753</a></li> <li>Trivedi, Vikas and Choi, Harry M. T., el al. (2018) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20180110-083122477">Multidimensional quantitative analysis of mRNA expression within intact vertebrate embryos</a>; Development; Vol. 145; No. 1; Art. No. 156869; PMCID PMC5825878; <a href="https://doi.org/10.1242/dev.156869">10.1242/dev.156869</a></li> <li>Wolfe, Brian R. and Porubsky, Nicholas J., el al. (2017) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170213-164458132">Constrained Multistate Sequence Design for Nucleic Acid Reaction Pathway Engineering</a>; Journal of the American Chemical Society; Vol. 139; No. 8; 3134-3144; <a href="https://doi.org/10.1021/jacs.6b12693">10.1021/jacs.6b12693</a></li> <li>Choi, Harry M. T. and Calvert, Colby R., el al. (2016) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20161011-070233463">Mapping a multiplexed zoo of mRNA expression</a>; Development; Vol. 143; No. 19; 3632-3637; PMCID PMC5087610; <a href="https://doi.org/10.1242/dev.140137">10.1242/dev.140137</a></li> <li>Schwarzkopf, Maayan and Pierce, Niles A. (2016) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20160610-141528257">Multiplexed miRNA northern blots via hybridization chain reaction</a>; Nucleic Acids Research; Vol. 44; No. 15; Art. No. e129; PMCID PMC5009741; <a href="https://doi.org/10.1093/nar/gkw503">10.1093/nar/gkw503</a></li> <li>Shah, Sheel and Lubeck, Eric, el al. (2016) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20160628-085406782">Single-molecule RNA detection at depth via hybridization chain reaction and tissue hydrogel embedding and clearing</a>; Development; Vol. 143; No. 15; 2862-2867; PMCID PMC5004914; <a href="https://doi.org/10.1242/dev.138560">10.1242/dev.138560</a></li> <li>Wolfe, Brian R. and Pierce, Niles A. (2015) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20141027-090434819">Sequence Design for a Test Tube of Interacting Nucleic Acid Strands</a>; ACS Synthetic Biology; Vol. 4; No. 10; 1086-1100; <a href="https://doi.org/10.1021/sb5002196">10.1021/sb5002196</a></li> <li>Huss, David and Choi, Harry M. T., el al. (2015) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20150311-133810360">Combinatorial Analysis of mRNA Expression Patterns in Mouse Embryos Using Hybridization Chain Reaction</a>; Cold Spring Harbor Protocols; Vol. 2015; No. 3; 259-268; <a href="https://doi.org/10.1101/pdb.prot083832">10.1101/pdb.prot083832</a></li> <li>Choi, Harry M. T. and Beck, Victor A., el al. (2014) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20141013-100900538">Multiplexed In Situ Hybridization Using Hybridization Chain Reaction</a>; Zebrafish; Vol. 11; No. 5; 488-489; <a href="https://doi.org/10.1089/zeb.2014.1501">10.1089/zeb.2014.1501</a></li> <li>Sternberg, Jonathan B. and Pierce, Niles A. (2014) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20140919-101701968">Exquisite Sequence Selectivity with Small Conditional RNAs</a>; Nano Letters; Vol. 14; No. 8; 4568-4572; PMCID PMC4134187; <a href="https://doi.org/10.1021/nl501593r">10.1021/nl501593r</a></li> <li>Choi, Harry M. T. and Beck, Victor A., el al. (2014) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20140414-095156294">Next-Generation in Situ Hybridization Chain Reaction: Higher Gain, Lower Cost, Greater Durability</a>; ACS Nano; Vol. 8; No. 5; 4284-4294; PMCID PMC4046802; <a href="https://doi.org/10.1021/nn405717p">10.1021/nn405717p</a></li> <li>Sadowski, John P. and Calvert, Colby R., el al. (2014) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20140603-072449619">Developmental Self-Assembly of a DNA Tetrahedron</a>; ACS Nano; Vol. 8; No. 4; 3251-3259; PMCID PMC4004324; <a href="https://doi.org/10.1021/nn4038223">10.1021/nn4038223</a></li> <li>Vieregg, Jeffrey and Pierce, Niles A. (2014) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20140710-084440757">Selective Nucleic Acid Capture with Shielded Covalent Probes</a>; Biophysical Journal; Vol. 106; No. 2; 617A; <a href="https://doi.org/10.1016/j.bpj.2013.11.3412">10.1016/j.bpj.2013.11.3412</a></li> <li>Hochrein, Lisa M. and Schwarzkopf, Maayan, el al. (2013) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20131205-083955291">Conditional Dicer Substrate Formation via Shape and Sequence Transduction with Small Conditional RNAs</a>; Journal of the American Chemical Society; Vol. 135; No. 46; 17322-17330; PMCID PMC3842090; <a href="https://doi.org/10.1021/ja404676x">10.1021/ja404676x</a></li> <li>Rosenthal, Adam Z. and Zhang, Xinning, el al. (2013) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20130930-102728287">Localizing transcripts to single cells suggests an important role of uncultured deltaproteobacteria in the termite gut hydrogen economy</a>; Proceedings of the National Academy of Sciences of the United States of America; Vol. 110; No. 40; 16163-16168; PMCID PMC3791709; <a href="https://doi.org/10.1073/pnas.1307876110">10.1073/pnas.1307876110</a></li> <li>Vieregg, Jeffrey R. and Nelson, Hosea M., el al. (2013) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20130905-155148025">Selective Nucleic Acid Capture with Shielded Covalent Probes</a>; Journal of the American Chemical Society; Vol. 135; No. 26; 9691-9699; PMCID PMC3703666; <a href="https://doi.org/10.1021/ja4009216">10.1021/ja4009216</a></li> <li>Vieregg, Jeffrey R. and Pierce, Niles A. (2013) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20130501-084442039">Selective Oligonucleotide and MRNA Pull-Down with Shielded Covalent Probes</a>; Biophysical Journal; Vol. 104; No. 2; 500A; <a href="https://doi.org/10.1016/j.bpj.2012.11.2761">10.1016/j.bpj.2012.11.2761</a></li> <li>Zadeh, Joseph N. and Wolfe, Brian R., el al. (2011) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20110202-095344276">Nucleic Acid Sequence Design via Efficient Ensemble Defect Optimization</a>; Journal of Computational Chemistry; Vol. 32; No. 3; 439-452; <a href="https://doi.org/10.1002/jcc.21633">10.1002/jcc.21633</a></li> <li>Zadeh, Joseph N. and Steenberg, Conrad D., el al. (2011) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170224-152102280">NUPACK: Analysis and design of nucleic acid systems</a>; Journal of Computational Chemistry; Vol. 32; No. 1; 170-173; <a href="https://doi.org/10.1002/jcc.21596">10.1002/jcc.21596</a></li> <li>Choi, Harry M. T. and Chang, Joann Y., el al. (2010) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20160112-090928317">Programmable in situ amplification for multiplexed imaging of mRNA expression</a>; Nature Biotechnology; Vol. 28; No. 11; 1208-1212; PMCID PMC3058322; <a href="https://doi.org/10.1038/nbt.1692">10.1038/nbt.1692</a></li> <li>Yin, Peng and Choi, Harry M. T., el al. (2008) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170224-143742507">Programming biomolecular self-assembly pathways</a>; Nature; Vol. 451; No. 7176; 318-322; <a href="https://doi.org/10.1038/nature06451">10.1038/nature06451</a></li> <li>Venkataraman, Suvir and Dirks, Robert M., el al. (2007) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20110216-154211699">An autonomous polymerization motor powered by DNA hybridization</a>; Nature Nanotechnology; Vol. 2; No. 8; 490-494; <a href="https://doi.org/10.1038/nnano.2007.225">10.1038/nnano.2007.225</a></li> <li>Dirks, Robert M. and Bois, Justin S., el al. (2007) <a href="https://resolver.caltech.edu/CaltechAUTHORS:DIRsiamrev07">Thermodynamic Analysis of Interacting Nucleic Acid Strands</a>; SIAM Review; Vol. 49; No. 1; 65-88; <a href="https://doi.org/10.1137/060651100">10.1137/060651100</a></li> <li>Bois, Justin S. and Venkataraman, Suvir, el al. (2005) <a href="https://resolver.caltech.edu/CaltechAUTHORS:BOInar05">Topological constraints in nucleic acid hybridization kinetics</a>; Nucleic Acids Research; Vol. 33; No. 13; 4090-4095; PMCID PMC1180668; <a href="https://doi.org/10.1093/nar/gki721">10.1093/nar/gki721</a></li> <li>Dirks, Robert M. and Pierce, Niles A. (2004) <a href="https://resolver.caltech.edu/CaltechAUTHORS:DIRpnas04">Triggered amplification by hybridization chain reaction</a>; Proceedings of the National Academy of Sciences of the United States of America; Vol. 101; No. 43; 15275-15278; PMCID PMC524468; <a href="https://doi.org/10.1073/pnas.0407024101">10.1073/pnas.0407024101</a></li> <li>Shin, Jong-Shik and Pierce, Niles A. (2004) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170224-152823096">A Synthetic DNA Walker for Molecular Transport</a>; Journal of the American Chemical Society; Vol. 126; No. 35; 10834-10835; <a href="https://doi.org/10.1021/ja047543j">10.1021/ja047543j</a></li> <li>Dirks, Robert M. and Pierce, Niles A. (2004) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20190503-151608000">An algorithm for computing nucleic acid baseāpairing probabilities including pseudoknots</a>; Journal of Computational Chemistry; Vol. 25; No. 10; 1295-1304; <a href="https://doi.org/10.1002/jcc.20057">10.1002/jcc.20057</a></li> <li>Shin, Jong-Shik and Pierce, Niles A. (2004) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170802-102130134">Rewritable Memory by Controllable Nanopatterning of DNA</a>; Nano Letters; Vol. 4; No. 5; 905-909; <a href="https://doi.org/10.1021/nl049658r">10.1021/nl049658r</a></li> <li>Giles, Michael B. and Pierce, Niles, el al. (2004) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200221-132333124">Progress in adjoint error correction for integral functionals</a>; Computing and Visualization in Science; Vol. 6; No. 2-3; 113-121; <a href="https://doi.org/10.1007/s00791-003-0115-y">10.1007/s00791-003-0115-y</a></li> <li>Dirks, Robert M. and Lin, Milo, el al. (2004) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20110309-104203820">Paradigms for computational nucleic acid design</a>; Nucleic Acids Research; Vol. 32; No. 4; 1392-1403; PMCID PMC390280; <a href="https://doi.org/10.1093/nar/gkh291">10.1093/nar/gkh291</a></li> <li>Dirks, Robert M. and Pierce, Niles A. (2003) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20170227-084204047">A Partition Function Algorithm for Nucleic Acid Secondary Structure Including Pseudoknots</a>; Journal of Computational Chemistry; Vol. 24; No. 13; 1664-1677; <a href="https://doi.org/10.1002/jcc.10296">10.1002/jcc.10296</a></li> <li>Gordon, D. Benjamin and Hom, Geoffrey K., el al. (2003) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20110913-173425474">Exact rotamer optimization for protein design</a>; Journal of Computational Chemistry; Vol. 24; No. 2; 232-243; <a href="https://doi.org/10.1002/jcc.10121">10.1002/jcc.10121</a></li> <li>Pierce, Niles A. and Winfree, Erik (2002) <a href="https://resolver.caltech.edu/CaltechAUTHORS:PIEpeds02.939">Protein Design is NP-hard</a>; Protein Engineering; Vol. 15; No. 10; 779-782; <a href="https://doi.org/10.1093/protein/15.10.779">10.1093/protein/15.10.779</a></li> <li>Giles, Michael B. and Pierce, Niles A. (2001) <a href="https://resolver.caltech.edu/CaltechAUTHORS:GILjfm01">Analytic adjoint solutions for the quasi-one-dimensional Euler equations</a>; Journal of Fluid Mechanics; Vol. 426; 327-345; <a href="https://doi.org/10.1017/S0022112000002366">10.1017/S0022112000002366</a></li> <li>Pierce, Niles A. and Spriet, Jan A., el al. (2000) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20110620-160432187">Conformational splitting: a more powerful criterion for dead-end elimination</a>; Journal of Computational Chemistry; Vol. 21; No. 11; 999-1009; <a href="https://doi.org/10.1002/1096-987X(200008)21:11%3C999::AID-JCC9%3E3.0.CO;2-A">10.1002/1096-987X(200008)21:11<999::AID-JCC9>3.0.CO;2-A</a></li> <li>Pierce, Niles A. and Giles, Michael B. (2000) <a href="https://resolver.caltech.edu/CaltechAUTHORS:PIEsiamrev00">Adjoint recovery of superconvergent functionals from PDE approximations</a>; SIAM Review; Vol. 42; No. 2; 247-264; <a href="https://doi.org/10.1137/S0036144598349423">10.1137/S0036144598349423</a></li> </ul>