• 1413 Citations
20022022
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Research Interests

RNA Engineering, RNA Folding and Function, Gene Expression Control, Cell-Free Synthetic Biology, Diagnostics

The Lucks Group aims to understand and harness the ability of RNA molecules to control cellular processes for an array of applications in biomanufacturing, diagnostics and disease. Our focus is on making RNA a powerful molecular substrate for engineering gene expression by leveraging its functional versatility, our ability to control its function by designing its structure, and our ability to characterize its biochemistry and biophysics in unprecedented throughput and scale with next generation sequencing tools that we have pioneered. Specifically, we: (1) Engineer new RNA regulatory mechanisms and build RNA genetic networks to precisely program gene expression in applications that range from metabolic engineering to smart diagnostics; and (2) Develop new technologies to uncover RNA sequence/structure/function relationships that feed back into our RNA engineering. We also use our tools to understand natural RNAs that regulate fundamental cellular processes and diseases.

Our research is highly interdisciplinary and links core concepts from chemical engineering, physics, and molecular and structural biology to develop theoretical and experimental techniques for understanding and controlling cellular function with RNAs. To do this we utilize both wet lab and computational techniques. In the wet lab, we use methods spanning molecular biology and biochemistry to next generation RNA sequencing technologies to measure RNA structures in a massively parallel fashion. On the computational side we develop models of RNA genetic networks, develop new techniques for computational RNA design and develop new RNA structure prediction algorithms.

Our current research activities are structured into two thrust areas: (1) Engineering enhanced RNA genetic regulators and networks for control of cellular systems, with a growing interest in using these regulators in cell-free smart diagnostics, and (2) Uncovering the biological design principles of cellular RNA folding and function by developing and applying our SHAPE-Seq technology for measuring RNA structures with next-generation sequencing. These two areas are synergistic, with engineering projects identifying gaps in our knowledge that are filled through fundamental biology investigations.

Education/Academic qualification

Chemical Physics, PhD, Harvard University

… → 2007

Theoretical Chemistry, MPhil, University of Cambridge

… → 2002

Chemical Physics, MS, Harvard University

Chemistry, BS, University of North Carolina

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Grants 2016 2022

Research Output 2002 2018

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

Glasscock, C. J., Yates, L. E., Jaroentomeechai, T., Wilson, J. D., Merritt, J. H., Lucks, J. B. & DeLisa, M. P., May 1 2018, In : Metabolic Engineering. 47, p. 488-495 8 p.

Research output: Contribution to journalArticle

Glycosylation
Glycosyltransferases
Biosynthesis
Gene expression
Escherichia coli
1 Citations

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

Hu, C. Y., Takahashi, M. K., Zhang, Y. & Lucks, J. B., Jun 15 2018, In : ACS Synthetic Biology. 7, 6, p. 1507-1518 12 p.

Research output: Contribution to journalArticle

Parameterization
Sensitivity analysis
RNA
Transcription
Gene expression
1 Citations

High-throughput determination of RNA structures

Strobel, E. J., Yu, A. M. & Lucks, J. B., Oct 1 2018, In : Nature Reviews Genetics. 19, 10, p. 615-634 20 p.

Research output: Contribution to journalReview article

RNA
RNA Probes
Technology

Mathematical Modeling of RNA-Based Architectures for Closed Loop Control of Gene Expression

Agrawal, D. K., Tang, X., Westbrook, A., Marshall, R., Maxwell, C. S., Lucks, J. B., Noireaux, V., Beisel, C. L., Dunlop, M. J. & Franco, E., May 18 2018, In : ACS Synthetic Biology. 7, 5, p. 1219-1228 10 p.

Research output: Contribution to journalArticle

RNA
Gene expression
Gene Expression
Feedback
Control systems
3 Citations

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

Watters, K. E., Choudhary, K., Aviran, S., Lucks, J. B., Perry, K. L. & Thompson, J. R., Jan 1 2018, In : Nucleic acids research. 46, 5, p. 2573-2584 12 p.

Research output: Contribution to journalArticle

Acylation
RNA Viruses
Plant Cells
Hydroxyl Radical
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