- Schulte, Samuel J.; 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.; Shin, Boyoung; et el. (2024) Multiplex,
Quantitative, High-Resolution Imaging of Protein:Protein Complexes via
Hybridization Chain Reaction; ACS Chemical Biology; 10.1021/acschembio.3c00431
- Schulte, Samuel J.; 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.; 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; 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.; 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.; 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
- Hanewich-Hollatz, Mikhail H.; 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.; 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.; 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; 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.; 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.; 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; 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; 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.; 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.; 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.; 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.; 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.; 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.; 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;
Biophysical Journal; Vol. 104; No. 2; 500A; 10.1016/j.bpj.2012.11.2761
- Zadeh, Joseph N.; 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.; 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.; 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; Choi, Harry M. T.; et el. (2008) Programming
biomolecular self-assembly pathways; Nature; Vol. 451; No. 7176;
318-322; 10.1038/nature06451
- Venkataraman, Suvir; 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.; Bois, Justin S.; et el. (2007) Thermodynamic
Analysis of Interacting Nucleic Acid Strands; SIAM Review; Vol. 49;
No. 1; 65-88; 10.1137/060651100
- Bois, Justin S.; 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.; 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.; 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; 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.; 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