Pierce, Niles A.

Combined from CaltechAUTHORS

• Schulte, Samuel J. and Shin, Boyoung, et el. (2024) Multiplex, Quantitative, High-Resolution Imaging of Protein:Protein Complexes via Hybridization Chain Reaction; ACS Chemical Biology; Vol. 19; No. 2; 280-288; PMCID PMC10877569; 10.1021/acschembio.3c00431
• Schulte, Samuel J. and Fornace, Mark E., et el. (2024) HCR spectral imaging: 10-plex, quantitative, high-resolution RNA and protein imaging in highly autofluorescent samples; Development; Vol. 151; No. 4; dev202307; PMCID PMC10941662; 10.1242/dev.202307
• Fornace, Mark E. and Huang, Jining, et el. (2023) NUPACK: Analysis and Design of Nucleic Acid Structures, Devices, and Systems; 10.26434/chemrxiv-2022-xv98l
• Schulte, Samuel J. and Huang, Jining, et el. (2023) HCR Lateral Flow Assays for Amplified Instrument-Free At-Home SARS-CoV-2 Testing; 10.1101/2022.09.18.508442
• Schulte, Samuel J. and Huang, Jining, et el. (2023) Hybridization Chain Reaction Lateral Flow Assays for Amplified Instrument-Free At-Home SARS-CoV-2 Testing; ACS Infectious Diseases; Vol. 9; No. 3; 450-458; PMCID PMC9924079; 10.1021/acsinfecdis.2c00472
• Bokhari, Rihana S. and Beheshti, Afshin, et el. (2022) Looking on the Horizon; Potential and Unique Approaches to Developing Radiation Countermeasures for Deep Space Travel; Life Sciences in Space Research; Vol. 35; 105-112; 10.1016/j.lssr.2022.08.003
• Schwarzkopf, Maayan and Liu, Mike C., et el. (2021) Hybridization chain reaction enables a unified approach to multiplexed, quantitative, high-resolution immunohistochemistry and in situ hybridization; Development; Vol. 148; No. 22; Art. No. dev199847; PMCID PMC8645210; 10.1242/dev.199847
• Hochrein, Lisa M. and Li, Heyun, et el. (2021) High-Performance Allosteric Conditional Guide RNAs for Mammalian Cell-Selective Regulation of CRISPR/Cas; ACS Synthetic Biology; Vol. 10; No. 5; 964-971; 10.1021/acssynbio.1c00037
• Fornace, Mark E. and Porubsky, Nicholas J., et el. (2020) A Unified Dynamic Programming Framework for the Analysis of Interacting Nucleic Acid Strands: Enhanced Models, Scalability, and Speed; ACS Synthetic Biology; Vol. 9; No. 10; 2665-2678; 10.1021/acssynbio.9b00523
• Choi, Harry M. T. and Schwarzkopf, Maayan, et el. (2020) Multiplexed Quantitative In Situ Hybridization with Subcellular or Single-Molecule Resolution Within Whole-Mount Vertebrate Embryos: qHCR and dHCR Imaging (v3.0); ISBN 978-1-0716-0622-3; In Situ Hybridization Protocols; 159-178; 10.1007/978-1-0716-0623-0_10
• Schwarzkopf, Maayan and Choi, Harry M. T., et el. (2020) Multiplexed Quantitative In Situ Hybridization for Mammalian Cells on a Slide: qHCR and dHCR Imaging (v3.0); ISBN 978-1-0716-0622-3; In Situ Hybridization Protocols; 143-156; 10.1007/978-1-0716-0623-0_9
• Schwarzkopf, Maayan and Choi, Harry M. T., et el. (2020) Multiplexed Quantitative In Situ Hybridization for Mammalian or Bacterial Cells in Suspension: qHCR Flow Cytometry (v3.0); ISBN 978-1-0716-0622-3; In Situ Hybridization Protocols; 127-141; 10.1007/978-1-0716-0623-0_8
• Hanewich-Hollatz, Mikhail H. and Chen, Zhewei, et el. (2019) Conditional Guide RNAs: Programmable Conditional Regulation of CRISPR/Cas Function in Bacterial and Mammalian Cells via Dynamic RNA Nanotechnology; ACS Central Science; Vol. 5; No. 7; 1241-1249; PMCID PMC6661866; 10.1021/acscentsci.9b00340
• Hochrein, Lisa M. and Ge, Tianjia J., et el. (2018) Signal Transduction in Human Cell Lysate via Dynamic RNA Nanotechnology; ACS Synthetic Biology; Vol. 7; No. 12; 2796-2802; PMCID PMC6305621; 10.1021/acssynbio.8b00424
• Choi, Harry M. T. and Schwarzkopf, Maayan, et el. (2018) Third-generation in situ hybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust; Development; Vol. 145; No. 12; Art. No. dev165753; PMCID PMC6031405; 10.1242/dev.165753
• Trivedi, Vikas and Choi, Harry M. T., et el. (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
• Wolfe, Brian R. and Porubsky, Nicholas J., et el. (2017) Constrained Multistate Sequence Design for Nucleic Acid Reaction Pathway Engineering; Journal of the American Chemical Society; Vol. 139; No. 8; 3134-3144; 10.1021/jacs.6b12693
• Choi, Harry M. T. and Calvert, Colby R., et el. (2016) Mapping a multiplexed zoo of mRNA expression; Development; Vol. 143; No. 19; 3632-3637; PMCID PMC5087610; 10.1242/dev.140137
• 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, et el. (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., et el. (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
• Choi, Harry M. T. and Beck, Victor A., et el. (2014) Multiplexed In Situ Hybridization Using Hybridization Chain Reaction; Zebrafish; Vol. 11; No. 5; 488-489; 10.1089/zeb.2014.1501
• 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., et el. (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
• Sadowski, John P. and Calvert, Colby R., et el. (2014) Developmental Self-Assembly of a DNA Tetrahedron; ACS Nano; Vol. 8; No. 4; 3251-3259; PMCID PMC4004324; 10.1021/nn4038223
• 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, et el. (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, et el. (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
• Vieregg, Jeffrey R. and Nelson, Hosea M., et el. (2013) Selective Nucleic Acid Capture with Shielded Covalent Probes; Journal of the American Chemical Society; Vol. 135; No. 26; 9691-9699; PMCID PMC3703666; 10.1021/ja4009216
• Vieregg, Jeffrey R. and Pierce, Niles A. (2013) Selective oligonucleotide and mRNA pull-down with shielded covalent probes
• 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
• Vieregg, Jeffrey R. and Nelson, Hosea M., et el. (2012) Sensitive and selective nucleic acid capture with shielded covalent probes
• Zadeh, Joseph N. and Wolfe, Brian R., et el. (2011) Nucleic Acid Sequence Design via Efficient Ensemble Defect Optimization; Journal of Computational Chemistry; Vol. 32; No. 3; 439-452; 10.1002/jcc.21633
• Zadeh, Joseph N. and Steenberg, Conrad D., et el. (2011) NUPACK: Analysis and design of nucleic acid systems; Journal of Computational Chemistry; Vol. 32; No. 1; 170-173; 10.1002/jcc.21596
• Choi, Harry M. T. and Chang, Joann Y., et el. (2010) Programmable in situ amplification for multiplexed imaging of mRNA expression; Nature Biotechnology; Vol. 28; No. 11; 1208-1212; PMCID PMC3058322; 10.1038/nbt.1692
• Yin, Peng and Choi, Harry M. T., et el. (2008) Programming biomolecular self-assembly pathways; Nature; Vol. 451; No. 7176; 318-322; 10.1038/nature06451
• Venkataraman, Suvir and Dirks, Robert M., et el. (2007) An autonomous polymerization motor powered by DNA hybridization; Nature Nanotechnology; Vol. 2; No. 8; 490-494; 10.1038/nnano.2007.225
• Dirks, Robert M. and Bois, Justin S., et el. (2007) Thermodynamic Analysis of Interacting Nucleic Acid Strands; SIAM Review; Vol. 49; No. 1; 65-88; 10.1137/060651100
• Shin, Jong-Shik and Pierce, Niles A. (2006) Nanoscale Molecular Transport by Synthetic DNA Machines; ISBN 978-3-540-30295-7; Nanotechnology: Science and Computation; 175-188; 10.1007/3-540-30296-4_11
• Bois, Justin S. and Venkataraman, Suvir, et el. (2005) Topological constraints in nucleic acid hybridization kinetics; Nucleic Acids Research; Vol. 33; No. 13; 4090-4095; PMCID PMC1180668; 10.1093/nar/gki721
• 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, et el. (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, et el. (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., et el. (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., et el. (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