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Items: 47

1.

De novo-designed translation-repressing riboregulators for multi-input cellular logic.

Kim J, Zhou Y, Carlson PD, Teichmann M, Chaudhary S, Simmel FC, Silver PA, Collins JJ, Lucks JB, Yin P, Green AA.

Nat Chem Biol. 2019 Nov 4. doi: 10.1038/s41589-019-0388-1. [Epub ahead of print]

PMID:
31686032
2.

A ligand-gated strand displacement mechanism for ZTP riboswitch transcription control.

Strobel EJ, Cheng L, Berman KE, Carlson PD, Lucks JB.

Nat Chem Biol. 2019 Nov;15(11):1067-1076. doi: 10.1038/s41589-019-0382-7. Epub 2019 Oct 21.

PMID:
31636437
3.

Computational design of three-dimensional RNA structure and function.

Yesselman JD, Eiler D, Carlson ED, Gotrik MR, d'Aquino AE, Ooms AN, Kladwang W, Carlson PD, Shi X, Costantino DA, Herschlag D, Lucks JB, Jewett MC, Kieft JS, Das R.

Nat Nanotechnol. 2019 Sep;14(9):866-873. doi: 10.1038/s41565-019-0517-8. Epub 2019 Aug 19.

PMID:
31427748
4.

DUETT quantitatively identifies known and novel events in nascent RNA structural dynamics from chemical probing data.

Xue AY, Yu AM, Lucks JB, Bagheri N.

Bioinformatics. 2019 Aug 7. pii: btz449. doi: 10.1093/bioinformatics/btz449. [Epub ahead of print]

PMID:
31389563
5.

Tracking RNA structures as RNAs transit through the cell.

Yu AM, Lucks JB.

Nat Struct Mol Biol. 2019 Apr;26(4):256-257. doi: 10.1038/s41594-019-0213-2. No abstract available.

PMID:
30936529
6.

PLANT-Dx: A Molecular Diagnostic for Point-of-Use Detection of Plant Pathogens.

Verosloff M, Chappell J, Perry KL, Thompson JR, Lucks JB.

ACS Synth Biol. 2019 Apr 19;8(4):902-905. doi: 10.1021/acssynbio.8b00526. Epub 2019 Mar 11.

7.

Deconstructing Cell-Free Extract Preparation for in Vitro Activation of Transcriptional Genetic Circuitry.

Silverman AD, Kelley-Loughnane N, Lucks JB, Jewett MC.

ACS Synth Biol. 2019 Feb 15;8(2):403-414. doi: 10.1021/acssynbio.8b00430. Epub 2019 Jan 29.

8.

Elements of RNA Design.

Carlson PD, Lucks JB.

Biochemistry. 2019 Mar 19;58(11):1457-1459. doi: 10.1021/acs.biochem.8b01129. Epub 2018 Nov 15. No abstract available.

PMID:
30433768
9.

SnapShot: RNA Structure Probing Technologies.

Carlson PD, Evans ME, Yu AM, Strobel EJ, Lucks JB.

Cell. 2018 Oct 4;175(2):600-600.e1. doi: 10.1016/j.cell.2018.09.024.

10.

High-throughput determination of RNA structures.

Strobel EJ, Yu AM, Lucks JB.

Nat Rev Genet. 2018 Oct;19(10):615-634. doi: 10.1038/s41576-018-0034-x. Review.

PMID:
30054568
11.

Engineering a Functional Small RNA Negative Autoregulation Network with Model-Guided Design.

Hu CY, Takahashi MK, Zhang Y, Lucks JB.

ACS Synth Biol. 2018 Jun 15;7(6):1507-1518. doi: 10.1021/acssynbio.7b00440. Epub 2018 May 22.

PMID:
29733627
12.

A flow cytometric approach to engineering Escherichia coli for improved eukaryotic protein glycosylation.

Glasscock CJ, Yates LE, Jaroentomeechai T, Wilson JD, Merritt JH, Lucks JB, DeLisa MP.

Metab Eng. 2018 May;47:488-495. doi: 10.1016/j.ymben.2018.04.014. Epub 2018 Apr 25.

PMID:
29702274
13.

Probing of RNA structures in a positive sense RNA virus reveals selection pressures for structural elements.

Watters KE, Choudhary K, Aviran S, Lucks JB, Perry KL, Thompson JR.

Nucleic Acids Res. 2018 Mar 16;46(5):2573-2584. doi: 10.1093/nar/gkx1273.

14.

Characterizing the Structure-Function Relationship of a Naturally Occurring RNA Thermometer.

Meyer S, Carlson PD, Lucks JB.

Biochemistry. 2017 Dec 26;56(51):6629-6638. doi: 10.1021/acs.biochem.7b01170. Epub 2017 Dec 14.

15.

Computational design of small transcription activating RNAs for versatile and dynamic gene regulation.

Chappell J, Westbrook A, Verosloff M, Lucks JB.

Nat Commun. 2017 Oct 19;8(1):1051. doi: 10.1038/s41467-017-01082-6.

16.

Distributed biotin-streptavidin transcription roadblocks for mapping cotranscriptional RNA folding.

Strobel EJ, Watters KE, Nedialkov Y, Artsimovitch I, Lucks JB.

Nucleic Acids Res. 2017 Jul 7;45(12):e109. doi: 10.1093/nar/gkx233.

17.

Achieving large dynamic range control of gene expression with a compact RNA transcription-translation regulator.

Westbrook AM, Lucks JB.

Nucleic Acids Res. 2017 May 19;45(9):5614-5624. doi: 10.1093/nar/gkx215.

18.

Turning It Up to 11: Modular Proteins Amplify RNA Sensors for Sophisticated Circuitry.

Chappell J, Lucks JB.

Cell Syst. 2016 Dec 21;3(6):509-511. doi: 10.1016/j.cels.2016.12.004.

19.

Cotranscriptional folding of a riboswitch at nucleotide resolution.

Watters KE, Strobel EJ, Yu AM, Lis JT, Lucks JB.

Nat Struct Mol Biol. 2016 Dec;23(12):1124-1131. doi: 10.1038/nsmb.3316. Epub 2016 Oct 31.

20.

Mapping RNA Structure In Vitro with SHAPE Chemistry and Next-Generation Sequencing (SHAPE-Seq).

Watters KE, Lucks JB.

Methods Mol Biol. 2016;1490:135-62. doi: 10.1007/978-1-4939-6433-8_9.

PMID:
27665597
21.

RNA systems biology: uniting functional discoveries and structural tools to understand global roles of RNAs.

Strobel EJ, Watters KE, Loughrey D, Lucks JB.

Curr Opin Biotechnol. 2016 Jun;39:182-191. doi: 10.1016/j.copbio.2016.03.019. Epub 2016 Apr 30. Review.

22.

Using in-cell SHAPE-Seq and simulations to probe structure-function design principles of RNA transcriptional regulators.

Takahashi MK, Watters KE, Gasper PM, Abbott TR, Carlson PD, Chen AA, Lucks JB.

RNA. 2016 Jun;22(6):920-33. doi: 10.1261/rna.054916.115. Epub 2016 Apr 21.

23.

Characterizing RNA structures in vitro and in vivo with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq).

Watters KE, Yu AM, Strobel EJ, Settle AH, Lucks JB.

Methods. 2016 Jul 1;103:34-48. doi: 10.1016/j.ymeth.2016.04.002. Epub 2016 Apr 12.

24.

Engineered Protein Machines: Emergent Tools for Synthetic Biology.

Glasscock CJ, Lucks JB, DeLisa MP.

Cell Chem Biol. 2016 Jan 21;23(1):45-56. doi: 10.1016/j.chembiol.2015.12.004. Review.

25.

Simultaneous characterization of cellular RNA structure and function with in-cell SHAPE-Seq.

Watters KE, Abbott TR, Lucks JB.

Nucleic Acids Res. 2016 Jan 29;44(2):e12. doi: 10.1093/nar/gkv879. Epub 2015 Sep 8.

26.

Improving fold activation of small transcription activating RNAs (STARs) with rational RNA engineering strategies.

Meyer S, Chappell J, Sankar S, Chew R, Lucks JB.

Biotechnol Bioeng. 2016 Jan;113(1):216-25. doi: 10.1002/bit.25693. Epub 2015 Sep 9.

PMID:
26134708
27.

A renaissance in RNA synthetic biology: new mechanisms, applications and tools for the future.

Chappell J, Watters KE, Takahashi MK, Lucks JB.

Curr Opin Chem Biol. 2015 Oct;28:47-56. doi: 10.1016/j.cbpa.2015.05.018. Epub 2015 Jun 18. Review.

28.

Generating Effective Models and Parameters for RNA Genetic Circuits.

Hu CY, Varner JD, Lucks JB.

ACS Synth Biol. 2015 Aug 21;4(8):914-26. doi: 10.1021/acssynbio.5b00077. Epub 2015 Jul 2.

29.

Characterizing and prototyping genetic networks with cell-free transcription-translation reactions.

Takahashi MK, Hayes CA, Chappell J, Sun ZZ, Murray RM, Noireaux V, Lucks JB.

Methods. 2015 Sep 15;86:60-72. doi: 10.1016/j.ymeth.2015.05.020. Epub 2015 May 27.

PMID:
26022922
30.

Creating small transcription activating RNAs.

Chappell J, Takahashi MK, Lucks JB.

Nat Chem Biol. 2015 Mar;11(3):214-20. doi: 10.1038/nchembio.1737. Epub 2015 Feb 2.

PMID:
25643173
31.

SHAPE-Seq 2.0: systematic optimization and extension of high-throughput chemical probing of RNA secondary structure with next generation sequencing.

Loughrey D, Watters KE, Settle AH, Lucks JB.

Nucleic Acids Res. 2014 Dec 1;42(21). doi: 10.1093/nar/gku909. Epub 2014 Oct 10.

32.

Rapidly characterizing the fast dynamics of RNA genetic circuitry with cell-free transcription-translation (TX-TL) systems.

Takahashi MK, Chappell J, Hayes CA, Sun ZZ, Kim J, Singhal V, Spring KJ, Al-Khabouri S, Fall CP, Noireaux V, Murray RM, Lucks JB.

ACS Synth Biol. 2015 May 15;4(5):503-15. doi: 10.1021/sb400206c. Epub 2014 Mar 28.

33.

SHAPE-Seq: High-Throughput RNA Structure Analysis.

Mortimer SA, Trapnell C, Aviran S, Pachter L, Lucks JB.

Curr Protoc Chem Biol. 2012 Dec 1;4(4):275-97. doi: 10.1002/9780470559277.ch120019.

PMID:
23788555
34.

A modular strategy for engineering orthogonal chimeric RNA transcription regulators.

Takahashi MK, Lucks JB.

Nucleic Acids Res. 2013 Aug;41(15):7577-88. doi: 10.1093/nar/gkt452. Epub 2013 Jun 12.

35.

An adaptor from translational to transcriptional control enables predictable assembly of complex regulation.

Liu CC, Qi L, Lucks JB, Segall-Shapiro TH, Wang D, Mutalik VK, Arkin AP.

Nat Methods. 2012 Nov;9(11):1088-94. doi: 10.1038/nmeth.2184. Epub 2012 Sep 30.

PMID:
23023598
36.

An RNA Mapping DataBase for curating RNA structure mapping experiments.

Cordero P, Lucks JB, Das R.

Bioinformatics. 2012 Nov 15;28(22):3006-8. doi: 10.1093/bioinformatics/bts554. Epub 2012 Sep 12.

37.

Rationally designed families of orthogonal RNA regulators of translation.

Mutalik VK, Qi L, Guimaraes JC, Lucks JB, Arkin AP.

Nat Chem Biol. 2012 Mar 25;8(5):447-54. doi: 10.1038/nchembio.919.

PMID:
22446835
38.

Engineering naturally occurring trans-acting non-coding RNAs to sense molecular signals.

Qi L, Lucks JB, Liu CC, Mutalik VK, Arkin AP.

Nucleic Acids Res. 2012 Jul;40(12):5775-86. doi: 10.1093/nar/gks168. Epub 2012 Mar 1.

39.

Why on earth?: Evaluating hypotheses about the physiological functions of human geophagy.

Young SL, Sherman PW, Lucks JB, Pelto GH.

Q Rev Biol. 2011 Jun;86(2):97-120. Review.

PMID:
21800636
40.

Modeling and automation of sequencing-based characterization of RNA structure.

Aviran S, Trapnell C, Lucks JB, Mortimer SA, Luo S, Schroth GP, Doudna JA, Arkin AP, Pachter L.

Proc Natl Acad Sci U S A. 2011 Jul 5;108(27):11069-74. doi: 10.1073/pnas.1106541108. Epub 2011 Jun 3.

41.

Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq).

Lucks JB, Mortimer SA, Trapnell C, Luo S, Aviran S, Schroth GP, Pachter L, Doudna JA, Arkin AP.

Proc Natl Acad Sci U S A. 2011 Jul 5;108(27):11063-8. doi: 10.1073/pnas.1106501108. Epub 2011 Jun 3.

42.

Versatile RNA-sensing transcriptional regulators for engineering genetic networks.

Lucks JB, Qi L, Mutalik VK, Wang D, Arkin AP.

Proc Natl Acad Sci U S A. 2011 May 24;108(21):8617-22. doi: 10.1073/pnas.1015741108. Epub 2011 May 9.

43.

Evolution, ecology and the engineered organism: lessons for synthetic biology.

Skerker JM, Lucks JB, Arkin AP.

Genome Biol. 2009;10(11):114. doi: 10.1186/gb-2009-10-11-114. Epub 2009 Nov 30.

44.

Toward scalable parts families for predictable design of biological circuits.

Lucks JB, Qi L, Whitaker WR, Arkin AP.

Curr Opin Microbiol. 2008 Dec;11(6):567-73. doi: 10.1016/j.mib.2008.10.002. Epub 2008 Nov 12. Review.

PMID:
18983935
45.

Genome landscapes and bacteriophage codon usage.

Lucks JB, Nelson DR, Kudla GR, Plotkin JB.

PLoS Comput Biol. 2008 Feb 29;4(2):e1000001. doi: 10.1371/journal.pcbi.1000001.

46.

Crystallography on curved surfaces.

Vitelli V, Lucks JB, Nelson DR.

Proc Natl Acad Sci U S A. 2006 Aug 15;103(33):12323-8. Epub 2006 Aug 7.

47.

Pause point spectra in DNA constant-force unzipping.

Weeks JD, Lucks JB, Kafri Y, Danilowicz C, Nelson DR, Prentiss M.

Biophys J. 2005 Apr;88(4):2752-65. Epub 2005 Feb 4.

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