| Year |
Citation |
Score |
| 2023 |
Hertz LM, White EN, Kuznedelov K, Cheng L, Yu AM, Kakkaramadam R, Severinov K, Chen A, Lucks JB. The Effect of Pseudoknot Base Pairing on Cotranscriptional Structural Switching of the Fluoride Riboswitch. Biorxiv : the Preprint Server For Biology. PMID 38106011 DOI: 10.1101/2023.12.05.570056 |
0.473 |
|
| 2023 |
Li Y, Arce A, Lucci T, Rasmussen RA, Lucks JB. Dynamic RNA synthetic biology: new principles, practices and potential. Rna Biology. 20: 817-829. PMID 38044595 DOI: 10.1080/15476286.2023.2269508 |
0.462 |
|
| 2023 |
Berman KE, Steans R, Hertz LM, Lucks JB. A transient intermediate RNA structure underlies the regulatory function of the E. coli thiB TPP translational riboswitch. Rna (New York, N.Y.). PMID 37419663 DOI: 10.1261/rna.079427.122 |
0.33 |
|
| 2022 |
Harbaugh SV, Silverman AD, Chushak YG, Zimlich K, Wolfe M, Thavarajah W, Jewett MC, Lucks JB, Chávez JL. Engineering a Synthetic Dopamine-Responsive Riboswitch for Biosensing. Acs Synthetic Biology. PMID 35775197 DOI: 10.1021/acssynbio.1c00560 |
0.328 |
|
| 2022 |
Bushhouse DZ, Choi EK, Hertz LM, Lucks JB. How does RNA fold dynamically? Journal of Molecular Biology. 167665. PMID 35659535 DOI: 10.1016/j.jmb.2022.167665 |
0.483 |
|
| 2022 |
Cheng L, White EN, Brandt NL, Yu AM, Chen AA, Lucks JB. Cotranscriptional RNA strand exchange underlies the gene regulation mechanism in a purine-sensing transcriptional riboswitch. Nucleic Acids Research. PMID 35348734 DOI: 10.1093/nar/gkac102 |
0.388 |
|
| 2022 |
Jung JK, Archuleta CM, Alam KK, Lucks JB. Programming cell-free biosensors with DNA strand displacement circuits. Nature Chemical Biology. PMID 35177837 DOI: 10.1038/s41589-021-00962-9 |
0.759 |
|
| 2022 |
Jung JK, Alam KK, Lucks JB. ROSALIND: Rapid Detection of Chemical Contaminants with In Vitro Transcription Factor-Based Biosensors. Methods in Molecular Biology (Clifton, N.J.). 2433: 325-342. PMID 34985754 DOI: 10.1007/978-1-0716-1998-8_20 |
0.8 |
|
| 2021 |
Thavarajah W, Hertz LM, Bushhouse DZ, Archuleta CM, Lucks JB. RNA Engineering for Public Health: Innovations in RNA-Based Diagnostics and Therapeutics. Annual Review of Chemical and Biomolecular Engineering. 12: 263-286. PMID 33900805 DOI: 10.1146/annurev-chembioeng-101420-014055 |
0.486 |
|
| 2021 |
Verosloff MS, Corcoran WK, Dolberg TB, Bushhouse DZ, Leonard JN, Lucks JB. RNA sequence and structure determinants of Pol III transcriptional termination in human cells. Journal of Molecular Biology. 166978. PMID 33811918 DOI: 10.1016/j.jmb.2021.166978 |
0.456 |
|
| 2021 |
Yu AM, Gasper PM, Cheng L, Lai LB, Kaur S, Gopalan V, Chen AA, Lucks JB. Computationally reconstructing cotranscriptional RNA folding from experimental data reveals rearrangement of non-native folding intermediates. Molecular Cell. PMID 33453165 DOI: 10.1016/j.molcel.2020.12.017 |
0.458 |
|
| 2020 |
Thavarajah W, Verosloff MS, Jung JK, Alam KK, Miller JD, Jewett MC, Young SL, Lucks JB. A Primer on Emerging Field-Deployable Synthetic Biology Tools for Global Water Quality Monitoring. Npj Clean Water. 3. PMID 34267944 DOI: 10.1038/s41545-020-0064-8 |
0.735 |
|
| 2020 |
Jung JK, Alam KK, Verosloff MS, Capdevila DA, Desmau M, Clauer PR, Lee JW, Nguyen PQ, Pastén PA, Matiasek SJ, Gaillard JF, Giedroc DP, Collins JJ, Lucks JB. Cell-free biosensors for rapid detection of water contaminants. Nature Biotechnology. PMID 32632301 DOI: 10.1038/S41587-020-0571-7 |
0.806 |
|
| 2020 |
Strobel EJ, Lis JT, Lucks JB. Chemical roadblocking of DNA transcription for nascent RNA display. The Journal of Biological Chemistry. PMID 32209658 DOI: 10.1074/Jbc.Ra120.012641 |
0.807 |
|
| 2020 |
Silverman AD, Akova U, Alam KK, Jewett MC, Lucks JB. Design and optimization of a cell-free atrazine biosensor. Acs Synthetic Biology. PMID 32078765 DOI: 10.1021/Acssynbio.9B00388 |
0.745 |
|
| 2020 |
Thavarajah W, Verosloff MS, Jung JK, Alam KK, Miller JD, Jewett MC, Young SL, Lucks JB. A primer on emerging field-deployable synthetic biology tools for global water quality monitoring Npj Clean Water. 3. DOI: 10.1038/s41545-020-0064-8 |
0.724 |
|
| 2019 |
Thavarajah W, Silverman AD, Verosloff M, Kelley-Loughnane N, Jewett MC, Lucks JB. Point-of-Use Detection of Environmental Fluoride via a Cell-Free Riboswitch-Based Biosensor. Acs Synthetic Biology. PMID 31829623 DOI: 10.1021/Acssynbio.9B00347 |
0.384 |
|
| 2019 |
Liu X, Silverman AD, Alam KK, Iverson E, Lucks JB, Jewett MC, Raman S. Design of a transcriptional biosensor for the portable, on-demand detection of cyanuric acid. Acs Synthetic Biology. PMID 31825601 DOI: 10.1021/Acssynbio.9B00348 |
0.762 |
|
| 2019 |
Meyer AJ, Saaem I, Silverman A, Varaljay V, Mickol R, Blum SM, Tobias AV, Schwalm ND, Mojadedi W, Onderko E, Bristol C, Liu S, Casini A, Eluere R, Moser F, ... ... Lucks JB, et al. Organism engineering for the bioproduction of the triaminotrinitrobenzene (TATB) precursor phloroglucinol (PG). Acs Synthetic Biology. PMID 31750651 DOI: 10.1021/Acssynbio.9B00393 |
0.473 |
|
| 2019 |
Kim J, Zhou Y, Carlson PD, Teichmann M, Chaudhary S, Simmel FC, Silver PA, Collins JJ, Lucks JB, Yin P, Green AA. De novo-designed translation-repressing riboregulators for multi-input cellular logic. Nature Chemical Biology. PMID 31686032 DOI: 10.1038/S41589-019-0388-1 |
0.421 |
|
| 2019 |
Strobel EJ, Cheng L, Berman KE, Carlson PD, Lucks JB. A ligand-gated strand displacement mechanism for ZTP riboswitch transcription control. Nature Chemical Biology. 15: 1067-1076. PMID 31636437 DOI: 10.1038/S41589-019-0382-7 |
0.807 |
|
| 2019 |
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. Computational design of three-dimensional RNA structure and function. Nature Nanotechnology. PMID 31427748 DOI: 10.1038/S41565-019-0517-8 |
0.556 |
|
| 2019 |
Xue AY, Yu AM, Lucks JB, Bagheri N. DUETT quantitatively identifies known and novel events in nascent RNA structural dynamics from chemical probing data. Bioinformatics (Oxford, England). PMID 31389563 DOI: 10.1093/Bioinformatics/Btz449 |
0.561 |
|
| 2019 |
Yu AM, Lucks JB. Tracking RNA structures as RNAs transit through the cell. Nature Structural & Molecular Biology. PMID 30936529 DOI: 10.1038/S41594-019-0213-2 |
0.562 |
|
| 2019 |
Verosloff M, Chappell J, Perry KL, Thompson JR, Lucks JB. PLANT-Dx: A Molecular Diagnostic for Point of Use Detection of Plant Pathogens. Acs Synthetic Biology. PMID 30790518 DOI: 10.1021/Acssynbio.8B00526 |
0.338 |
|
| 2019 |
Westbrook A, Tang X, Marshall R, Maxwell CS, Chappell J, Agrawal DK, Dunlop MJ, Noireaux V, Beisel CL, Lucks J, Franco E. Distinct timescales of RNA regulators enable the construction of a genetic pulse generator. Biotechnology and Bioengineering. PMID 30636320 DOI: 10.1002/Bit.26918 |
0.479 |
|
| 2018 |
Silverman A, Kelley-Loughnane N, Lucks JB, Jewett MC. Deconstructing cell-free extract preparation for in vitro activation of transcriptional genetic circuitry. Acs Synthetic Biology. PMID 30596483 DOI: 10.1021/Acssynbio.8B00430 |
0.389 |
|
| 2018 |
Carlson PD, Lucks JB. Elements of RNA Design. Biochemistry. PMID 30433768 DOI: 10.1021/Acs.Biochem.8B01129 |
0.486 |
|
| 2018 |
Carlson PD, Evans ME, Yu AM, Strobel EJ, Lucks JB. SnapShot: RNA Structure Probing Technologies. Cell. 175: 600-600.e1. PMID 30290145 DOI: 10.1016/J.Cell.2018.09.024 |
0.802 |
|
| 2018 |
Strobel EJ, Yu AM, Lucks JB. High-throughput determination of RNA structures. Nature Reviews. Genetics. PMID 30054568 DOI: 10.1038/S41576-018-0034-X |
0.806 |
|
| 2018 |
Strobel EJ, Yu AM, Lucks JB. High-throughput determination of RNA structures. Nature Reviews. Genetics. PMID 30054568 DOI: 10.1038/s41576-018-0034-x |
0.489 |
|
| 2018 |
Hu CY, Takahashi MK, Zhang Y, Lucks JB. Engineering a Functional small RNA Negative Autoregulation Network with Model-guided Design. Acs Synthetic Biology. PMID 29733627 DOI: 10.1021/Acssynbio.7B00440 |
0.423 |
|
| 2018 |
Agrawal DK, Tang X, Westbrook A, Marshall R, Maxwell C, Lucks JB, Noireaux V, Beisel CL, Dunlop M, Franco E. Mathematical modeling of RNA-based architectures for closed loop control of gene expression. Acs Synthetic Biology. PMID 29709170 DOI: 10.1021/Acssynbio.8B00040 |
0.385 |
|
| 2018 |
Glasscock CJ, Yates LE, Jaroentomeechai T, Wilson JD, Merritt JH, Lucks JB, DeLisa MP. A flow cytometric approach to engineering Escherichia coli for improved eukaryotic protein glycosylation. Metabolic Engineering. PMID 29702274 DOI: 10.1016/J.Ymben.2018.04.014 |
0.317 |
|
| 2017 |
Watters KE, Choudhary K, Aviran S, Lucks JB, Perry KL, Thompson JR. Probing of RNA structures in a positive sense RNA virus reveals selection pressures for structural elements. Nucleic Acids Research. PMID 29294088 DOI: 10.1093/Nar/Gkx1273 |
0.481 |
|
| 2017 |
Meyer S, Carlson PD, Lucks JB. Characterizing the Structure-Function Relationship of a Naturally Occurring RNA Thermometer. Biochemistry. PMID 29172455 DOI: 10.1021/Acs.Biochem.7B01170 |
0.546 |
|
| 2017 |
Chappell J, Westbrook A, Verosloff M, Lucks JB. Computational design of small transcription activating RNAs for versatile and dynamic gene regulation. Nature Communications. 8: 1051. PMID 29051490 DOI: 10.1038/S41467-017-01082-6 |
0.499 |
|
| 2017 |
Strobel EJ, Watters KE, Nedialkov Y, Artsimovitch I, Lucks JB. Distributed biotin-streptavidin transcription roadblocks for mapping cotranscriptional RNA folding. Nucleic Acids Research. PMID 28398514 DOI: 10.1093/Nar/Gkx233 |
0.81 |
|
| 2017 |
Westbrook AM, Lucks JB. Achieving large dynamic range control of gene expression with a compact RNA transcription-translation regulator. Nucleic Acids Research. PMID 28387839 DOI: 10.1093/Nar/Gkx215 |
0.548 |
|
| 2016 |
Chappell J, Lucks JB. Turning It Up to 11: Modular Proteins Amplify RNA Sensors for Sophisticated Circuitry. Cell Systems. 3: 509-511. PMID 28009261 DOI: 10.1016/J.Cels.2016.12.004 |
0.492 |
|
| 2016 |
Watters KE, Strobel EJ, Yu AM, Lis JT, Lucks JB. Cotranscriptional folding of a riboswitch at nucleotide resolution. Nature Structural & Molecular Biology. PMID 27798597 DOI: 10.1038/Nsmb.3316 |
0.82 |
|
| 2016 |
Watters KE, Lucks JB. Mapping RNA Structure In Vitro with SHAPE Chemistry and Next-Generation Sequencing (SHAPE-Seq). Methods in Molecular Biology (Clifton, N.J.). 1490: 135-62. PMID 27665597 DOI: 10.1007/978-1-4939-6433-8_9 |
0.56 |
|
| 2016 |
Strobel EJ, Watters KE, Loughrey D, Lucks JB. RNA systems biology: uniting functional discoveries and structural tools to understand global roles of RNAs. Current Opinion in Biotechnology. 39: 182-191. PMID 27132125 DOI: 10.1016/J.Copbio.2016.03.019 |
0.807 |
|
| 2016 |
Takahashi MK, Watters KE, Gasper PM, Abbott TR, Carlson PD, Chen AA, Lucks JB. Using in-cell SHAPE-Seq and simulations to probe structure-function design principles of RNA transcriptional regulators. Rna (New York, N.Y.). PMID 27103533 DOI: 10.1261/Rna.054916.115 |
0.596 |
|
| 2016 |
Watters KE, Yu AM, Strobel EJ, Settle AH, Lucks JB. Characterizing RNA structures in vitro and in vivo with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq). Methods (San Diego, Calif.). PMID 27064082 DOI: 10.1016/J.Ymeth.2016.04.002 |
0.808 |
|
| 2016 |
Glasscock CJ, Lucks JB, DeLisa MP. Engineered Protein Machines: Emergent Tools for Synthetic Biology. Cell Chemical Biology. 23: 45-56. PMID 26933735 DOI: 10.1016/J.Chembiol.2015.12.004 |
0.413 |
|
| 2015 |
Watters KE, Abbott TR, Lucks JB. Simultaneous characterization of cellular RNA structure and function with in-cell SHAPE-Seq. Nucleic Acids Research. PMID 26350218 DOI: 10.1093/Nar/Gkv879 |
0.579 |
|
| 2015 |
Meyer S, Chappell J, Sankar S, Chew R, Lucks JB. Improving fold activation of small transcription activating RNAs (STARs) with rational RNA engineering strategies. Biotechnology and Bioengineering. PMID 26134708 DOI: 10.1002/Bit.25693 |
0.534 |
|
| 2015 |
Chappell J, Watters KE, Takahashi MK, Lucks JB. A renaissance in RNA synthetic biology: new mechanisms, applications and tools for the future. Current Opinion in Chemical Biology. 28: 47-56. PMID 26093826 DOI: 10.1016/J.Cbpa.2015.05.018 |
0.567 |
|
| 2015 |
Hu CY, Varner J, Lucks JB. Generating effective models and parameters for RNA genetic circuits. Acs Synthetic Biology. PMID 26046393 DOI: 10.1021/Acssynbio.5B00077 |
0.528 |
|
| 2015 |
Takahashi MK, Hayes CA, Chappell J, Sun ZZ, Murray RM, Noireaux V, Lucks JB. Characterizing and prototyping genetic networks with cell-free transcription-translation reactions. Methods (San Diego, Calif.). PMID 26022922 DOI: 10.1016/J.Ymeth.2015.05.020 |
0.365 |
|
| 2015 |
Chappell J, Takahashi MK, Lucks JB. Creating small transcription activating RNAs. Nature Chemical Biology. 11: 214-20. PMID 25643173 DOI: 10.1038/Nchembio.1737 |
0.531 |
|
| 2015 |
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. Rapidly characterizing the fast dynamics of RNA genetic circuitry with cell-free transcription-translation (TX-TL) systems. Acs Synthetic Biology. 4: 503-15. PMID 24621257 DOI: 10.1021/Sb400206C |
0.539 |
|
| 2014 |
Loughrey D, Watters KE, Settle AH, Lucks JB. SHAPE-Seq 2.0: systematic optimization and extension of high-throughput chemical probing of RNA secondary structure with next generation sequencing. Nucleic Acids Research. 42. PMID 25303992 DOI: 10.1093/Nar/Gku909 |
0.549 |
|
| 2014 |
Abbott TR, Watters KE, Lucks JB. In vivo SHAPE-seq: A method to determine the in-cell structure of RNA Food, Pharmaceutical and Bioengineering Division 2014 - Core Programming Area At the 2014 Aiche Annual Meeting. 2: 936. |
0.419 |
|
| 2014 |
Watters KE, Abbott TR, Lucks JB. In-cell RNA structure probing with SHAPE-Seq Food, Pharmaceutical and Bioengineering Division 2014 - Core Programming Area At the 2014 Aiche Annual Meeting. 1: 128. |
0.439 |
|
| 2013 |
Chappell J, Takahashi MK, Meyer S, Loughrey D, Watters KE, Lucks J. The centrality of RNA for engineering gene expression Biotechnology Journal. 8: 1379-1395. PMID 24124015 DOI: 10.1002/Biot.201300018 |
0.581 |
|
| 2013 |
Takahashi MK, Lucks JB. A modular strategy for engineering orthogonal chimeric RNA transcription regulators. Nucleic Acids Research. 41: 7577-88. PMID 23761434 DOI: 10.1093/Nar/Gkt452 |
0.581 |
|
| 2012 |
Mortimer SA, Trapnell C, Aviran S, Pachter L, Lucks JB. SHAPE-Seq: High-Throughput RNA Structure Analysis. Current Protocols in Chemical Biology. 4: 275-97. PMID 23788555 DOI: 10.1002/9780470559277.Ch120019 |
0.577 |
|
| 2012 |
Liu CC, Qi L, Lucks JB, Segall-Shapiro TH, Wang D, Mutalik VK, Arkin AP. An adaptor from translational to transcriptional control enables predictable assembly of complex regulation. Nature Methods. 9: 1088-94. PMID 23023598 DOI: 10.1038/Nmeth.2184 |
0.707 |
|
| 2012 |
Cordero P, Lucks JB, Das R. An RNA Mapping DataBase for curating RNA structure mapping experiments. Bioinformatics (Oxford, England). 28: 3006-8. PMID 22976082 DOI: 10.1093/Bioinformatics/Bts554 |
0.437 |
|
| 2012 |
Mutalik VK, Qi L, Guimaraes JC, Lucks JB, Arkin AP. Rationally designed families of orthogonal RNA regulators of translation. Nature Chemical Biology. 8: 447-54. PMID 22446835 DOI: 10.1038/Nchembio.919 |
0.741 |
|
| 2012 |
Qi L, Lucks JB, Liu CC, Mutalik VK, Arkin AP. Engineering naturally occurring trans-acting non-coding RNAs to sense molecular signals. Nucleic Acids Research. 40: 5775-86. PMID 22383579 DOI: 10.1093/Nar/Gks168 |
0.74 |
|
| 2011 |
Aviran S, Trapnell C, Lucks JB, Mortimer SA, Luo S, Schroth GP, Doudna JA, Arkin AP, Pachter L. Modeling and automation of sequencing-based characterization of RNA structure. Proceedings of the National Academy of Sciences of the United States of America. 108: 11069-74. PMID 21642536 DOI: 10.1073/Pnas.1106541108 |
0.63 |
|
| 2011 |
Lucks JB, Mortimer SA, Trapnell C, Luo S, Aviran S, Schroth GP, Pachter L, Doudna JA, Arkin AP. Multiplexed RNA structure characterization with selective 2'-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq). Proceedings of the National Academy of Sciences of the United States of America. 108: 11063-8. PMID 21642531 DOI: 10.1073/Pnas.1106501108 |
0.688 |
|
| 2011 |
Lucks JB, Qi L, Mutalik VK, Wang D, Arkin AP. Versatile RNA-sensing transcriptional regulators for engineering genetic networks. Proceedings of the National Academy of Sciences of the United States of America. 108: 8617-22. PMID 21555549 DOI: 10.1073/Pnas.1015741108 |
0.746 |
|
| 2011 |
Lucks J, Arkin A. The hunt for the biological transistor Ieee Spectrum. 48: 38-43. DOI: 10.1109/Mspec.2011.5719724 |
0.489 |
|
| 2011 |
Aviran S, Lucks JB, Pachter L. RNA structure characterization from chemical mapping experiments 2011 49th Annual Allerton Conference On Communication, Control, and Computing, Allerton 2011. 1743-1750. DOI: 10.1109/Allerton.2011.6120379 |
0.362 |
|
| 2009 |
Skerker JM, Lucks JB, Arkin AP. Evolution, ecology and the engineered organism: lessons for synthetic biology. Genome Biology. 10: 114. PMID 19941672 DOI: 10.1186/Gb-2009-10-11-114 |
0.493 |
|
| 2008 |
Lucks JB, Qi L, Whitaker WR, Arkin AP. Toward scalable parts families for predictable design of biological circuits. Current Opinion in Microbiology. 11: 567-73. PMID 18983935 DOI: 10.1016/J.Mib.2008.10.002 |
0.749 |
|
| 2008 |
Lucks JB, Nelson DR, Kudla GR, Plotkin JB. Genome landscapes and bacteriophage codon usage. Plos Computational Biology. 4: e1000001. PMID 18463708 DOI: 10.1371/Journal.Pcbi.1000001 |
0.413 |
|
| 2006 |
Vitelli V, Lucks JB, Nelson DR. Crystallography on curved surfaces. Proceedings of the National Academy of Sciences of the United States of America. 103: 12323-8. PMID 16894160 DOI: 10.1073/Pnas.0602755103 |
0.588 |
|
| 2005 |
Weeks JD, Lucks JB, Kafri Y, Danilowicz C, Nelson DR, Prentiss M. Pause point spectra in DNA constant-force unzipping. Biophysical Journal. 88: 2752-65. PMID 15695634 DOI: 10.1529/Biophysj.104.047340 |
0.406 |
|
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