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Items: 31

1.

Signal Transduction in Human Cell Lysate via Dynamic RNA Nanotechnology.

Hochrein LM, Ge TJ, Schwarzkopf M, Pierce NA.

ACS Synth Biol. 2018 Dec 21;7(12):2796-2802. doi: 10.1021/acssynbio.8b00424. Epub 2018 Dec 7.

PMID:
30525469
2.

Third-generation in situ hybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust.

Choi HMT, Schwarzkopf M, Fornace ME, Acharya A, Artavanis G, Stegmaier J, Cunha A, Pierce NA.

Development. 2018 Jun 26;145(12). pii: dev165753. doi: 10.1242/dev.165753.

3.

Multidimensional quantitative analysis of mRNA expression within intact vertebrate embryos.

Trivedi V, Choi HMT, Fraser SE, Pierce NA.

Development. 2018 Jan 8;145(1). pii: dev156869. doi: 10.1242/dev.156869.

4.

Constrained Multistate Sequence Design for Nucleic Acid Reaction Pathway Engineering.

Wolfe BR, Porubsky NJ, Zadeh JN, Dirks RM, Pierce NA.

J Am Chem Soc. 2017 Mar 1;139(8):3134-3144. doi: 10.1021/jacs.6b12693. Epub 2017 Feb 13.

5.

Mapping a multiplexed zoo of mRNA expression.

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, Patterson PH, Davidson EH, Mazmanian SK, Prober DA, van de Rijn M, Leadbetter JR, Newman DK, Readhead C, Bronner ME, Wold B, Lansford R, Sauka-Spengler T, Fraser SE, Pierce NA.

Development. 2016 Oct 1;143(19):3632-3637.

6.

Single-molecule RNA detection at depth by hybridization chain reaction and tissue hydrogel embedding and clearing.

Shah S, Lubeck E, Schwarzkopf M, He TF, Greenbaum A, Sohn CH, Lignell A, Choi HM, Gradinaru V, Pierce NA, Cai L.

Development. 2016 Aug 1;143(15):2862-7. doi: 10.1242/dev.138560. Epub 2016 Jun 24.

7.

Multiplexed miRNA northern blots via hybridization chain reaction.

Schwarzkopf M, Pierce NA.

Nucleic Acids Res. 2016 Sep 6;44(15):e129. doi: 10.1093/nar/gkw503. Epub 2016 Jun 7.

8.

Combinatorial analysis of mRNA expression patterns in mouse embryos using hybridization chain reaction.

Huss D, Choi HM, Readhead C, Fraser SE, Pierce NA, Lansford R.

Cold Spring Harb Protoc. 2015 Mar 2;2015(3):259-68. doi: 10.1101/pdb.prot083832.

PMID:
25734068
9.

Sequence Design for a Test Tube of Interacting Nucleic Acid Strands.

Wolfe BR, Pierce NA.

ACS Synth Biol. 2015 Oct 16;4(10):1086-100. doi: 10.1021/sb5002196. Epub 2014 Oct 20.

PMID:
25329866
10.

Multiplexed in situ hybridization using hybridization chain reaction.

Choi HM, Beck VA, Pierce NA.

Zebrafish. 2014 Oct;11(5):488-9. doi: 10.1089/zeb.2014.1501. Epub 2014 Sep 4. No abstract available.

PMID:
25188553
11.

Exquisite sequence selectivity with small conditional RNAs.

Sternberg JB, Pierce NA.

Nano Lett. 2014 Aug 13;14(8):4568-72. doi: 10.1021/nl501593r. Epub 2014 Jun 30.

12.

Developmental self-assembly of a DNA tetrahedron.

Sadowski JP, Calvert CR, Zhang DY, Pierce NA, Yin P.

ACS Nano. 2014 Apr 22;8(4):3251-9. doi: 10.1021/nn4038223. Epub 2014 Apr 11.

13.

Next-generation in situ hybridization chain reaction: higher gain, lower cost, greater durability.

Choi HM, Beck VA, Pierce NA.

ACS Nano. 2014 May 27;8(5):4284-94. doi: 10.1021/nn405717p. Epub 2014 Apr 8.

14.

Conditional Dicer substrate formation via shape and sequence transduction with small conditional RNAs.

Hochrein LM, Schwarzkopf M, Shahgholi M, Yin P, Pierce NA.

J Am Chem Soc. 2013 Nov 20;135(46):17322-30. doi: 10.1021/ja404676x. Epub 2013 Nov 12.

15.

Localizing transcripts to single cells suggests an important role of uncultured deltaproteobacteria in the termite gut hydrogen economy.

Rosenthal AZ, Zhang X, Lucey KS, Ottesen EA, Trivedi V, Choi HM, Pierce NA, Leadbetter JR.

Proc Natl Acad Sci U S A. 2013 Oct 1;110(40):16163-8. doi: 10.1073/pnas.1307876110. Epub 2013 Sep 16.

16.

Selective nucleic acid capture with shielded covalent probes.

Vieregg JR, Nelson HM, Stoltz BM, Pierce NA.

J Am Chem Soc. 2013 Jul 3;135(26):9691-9. doi: 10.1021/ja4009216. Epub 2013 Jun 18.

17.

Retraction for Venkataraman et al., Selective cell death mediated by small conditional RNAs.

Dirks RM, Ueda CT, Pierce NA.

Proc Natl Acad Sci U S A. 2013 Jan 2;110(1):384. doi: 10.1073/pnas.1221212110. Epub 2012 Dec 17. No abstract available.

18.

Programmable in situ amplification for multiplexed imaging of mRNA expression.

Choi HM, Chang JY, Trinh le A, Padilla JE, Fraser SE, Pierce NA.

Nat Biotechnol. 2010 Nov;28(11):1208-12. doi: 10.1038/nbt.1692. Epub 2010 Oct 31.

19.

Selective cell death mediated by small conditional RNAs.

Venkataraman S, Dirks RM, Ueda CT, Pierce NA.

Proc Natl Acad Sci U S A. 2010 Sep 28;107(39):16777-82. doi: 10.1073/pnas.1006377107. Epub 2010 Sep 7. Retraction in: Dirks RM, Ueda CT, Pierce NA. Proc Natl Acad Sci U S A. 2013 Jan 2;110(1):384.

20.

Nucleic acid sequence design via efficient ensemble defect optimization.

Zadeh JN, Wolfe BR, Pierce NA.

J Comput Chem. 2011 Feb;32(3):439-52. doi: 10.1002/jcc.21633. Epub 2010 Aug 17.

PMID:
20717905
21.

NUPACK: Analysis and design of nucleic acid systems.

Zadeh JN, Steenberg CD, Bois JS, Wolfe BR, Pierce MB, Khan AR, Dirks RM, Pierce NA.

J Comput Chem. 2011 Jan 15;32(1):170-3. doi: 10.1002/jcc.21596.

PMID:
20645303
22.

An autonomous polymerization motor powered by DNA hybridization.

Venkataraman S, Dirks RM, Rothemund PW, Winfree E, Pierce NA.

Nat Nanotechnol. 2007 Aug;2(8):490-4. doi: 10.1038/nnano.2007.225. Epub 2007 Jul 29.

PMID:
18654346
23.

Programming biomolecular self-assembly pathways.

Yin P, Choi HM, Calvert CR, Pierce NA.

Nature. 2008 Jan 17;451(7176):318-22. doi: 10.1038/nature06451.

PMID:
18202654
24.

Topological constraints in nucleic acid hybridization kinetics.

Bois JS, Venkataraman S, Choi HM, Spakowitz AJ, Wang ZG, Pierce NA.

Nucleic Acids Res. 2005 Jul 25;33(13):4090-5. Print 2005.

25.

Triggered amplification by hybridization chain reaction.

Dirks RM, Pierce NA.

Proc Natl Acad Sci U S A. 2004 Oct 26;101(43):15275-8. Epub 2004 Oct 18.

26.

A synthetic DNA walker for molecular transport.

Shin JS, Pierce NA.

J Am Chem Soc. 2004 Sep 8;126(35):10834-5.

PMID:
15339155
27.

An algorithm for computing nucleic acid base-pairing probabilities including pseudoknots.

Dirks RM, Pierce NA.

J Comput Chem. 2004 Jul 30;25(10):1295-304.

PMID:
15139042
28.

Paradigms for computational nucleic acid design.

Dirks RM, Lin M, Winfree E, Pierce NA.

Nucleic Acids Res. 2004 Feb 27;32(4):1392-403. Print 2004.

29.

A partition function algorithm for nucleic acid secondary structure including pseudoknots.

Dirks RM, Pierce NA.

J Comput Chem. 2003 Oct;24(13):1664-77.

PMID:
12926009
30.

Exact rotamer optimization for protein design.

Gordon DB, Hom GK, Mayo SL, Pierce NA.

J Comput Chem. 2003 Jan 30;24(2):232-43.

PMID:
12497602
31.

Protein design is NP-hard.

Pierce NA, Winfree E.

Protein Eng. 2002 Oct;15(10):779-82.

PMID:
12468711

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