About

Julius B. Lucks is Professor of Chemical and Biological Engineering and Co-Director of the Center for Synthetic Biology at Northwestern University. He received his PhD in chemical physics from Harvard University as a Hertz Fellow, and transitioned to synthetic biology as a Miller Fellow at UC Berkeley. He is a leader in RNA research and synthetic biology, focusing on developing technologies that address global challenges, most recently in water insecurity. Professor Lucks has been recognized with numerous awards including a DARPA Young Faculty Award, an Alfred P. Sloan Foundation Research Fellowship, an ONR Young Investigator Award, an NIH New Innovator Award, an NSF CAREER award, and several others. He leads the first NSF graduate training program in synthetic biology, is a founding member of the Engineering Biology Research Consortium, and co-founded the Cold Spring Harbor Synthetic Biology Summer Course. Additionally, he is a co-founder of Stemloop, Inc., which aims to use cell-free biosensing technology to empower individuals with environmental and health information. His research focuses on understanding and harnessing RNA molecules to control cellular processes for applications in biomanufacturing, diagnostics, and disease. His group aims to engineer RNA regulatory mechanisms and build RNA genetic networks to precisely program gene expression, as well as develop technologies to uncover RNA sequence/structure/function relationships. The research is highly interdisciplinary, combining concepts from chemical engineering, physics, and molecular biology, utilizing both wet lab and computational techniques. His current activities include engineering RNA regulators for cellular control and diagnostics, and uncovering biological principles of RNA folding and function through advanced sequencing technologies. His work has significantly contributed to understanding RNA folding principles related to disease and engineering synthetic biology diagnostics for global health.

Research topics

• Biology
• Computer Science
• Chemistry
• Computational biology
• Engineering
• Biochemistry
• Organic chemistry
• Computer hardware
• Control engineering
• Algorithm
• Biophysics
• Electrical engineering
• Cell biology
• Genetics
• Molecular biology
• Materials science
• Chromatography
• Nanotechnology

Selected publications

• LucksLab/Choi_PRIME_Chemprobing_2026: v1.0.1

  Open MIND · 2026-01-28

  otherSenior author

  Housekeeping only (removed .DS_Store); no scientific content changed.

  DOI

• LucksLab/Rasmussen_Brown_in_vitro_detection_of_glyphosate_2025: Zenodo Release

  Open MIND · 2026-02-20

  other

  Zenodo DOI for submission release

  DOI

• LucksLab/Choi_PRIME_Chemprobing_2026: Paper release v1.0.0 — Ubiquitous low-energy RNA fluctuations measured by chemical probing

  Open MIND · 2026-01-28

  otherSenior author

  This release contains the exact code and analysis used in the manuscript: Ubiquitous low-energy RNA fluctuations and energetic coupling measured by chemical probing Authors: Edric K. Choi, Ritwika Bose, David H. Mathews, Anthony M. Mustoe, Julius B. Lucks The repository includes: Core analysis pipeline for processing time-course chemical probing data Kinetic model fitting and parameter extraction Scripts used to generate all main-text and supplementary figures This version is archived for reproducibility and corresponds to the results reported in the manuscript. Future development may extend functionality but will not alter the published results. Please cite this Zenodo record alongside the associated manuscript.

  DOI

• Ubiquitous low-energy RNA fluctuations and energetic coupling measured by chemical probing

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-01-30

  articleOpen accessSenior authorCorresponding

  RNA function is governed by RNA folding, but strategies for measuring RNA folding thermodynamics are limited, and fundamental questions such as the energy of base pair opening remain debated. Here we introduce Probing-Resolved Inference of Molecular Energetics (PRIME) to extract nucleotide-resolution RNA structural energetics from scalable chemical probing experiments. Applying PRIME to diverse RNAs, we find that RNA base pairs and tertiary interactions dynamically open with free energies of 0.5-3 kcal/mol, revealing that RNA nucleotides ubiquitously sample open conformations at biologically accessible energies. PRIME further resolves energetic coupling across RNAs, providing an energetic understanding of RNA structural dynamics and long-range coordination in RNA folding. PRIME represents a widely accessible strategy for interrogating RNA thermodynamics, enabling mechanistic understanding and engineering of RNA biology.

  PublisherOA PDFDOI

• LucksLab/Choi_PRIME_Chemprobing_2026: v1.0.2

  Zenodo (CERN European Organization for Nuclear Research) · 2026-02-13

  otherOpen accessSenior author

  This repository accompanies the Choi et al. manuscript and contains all code, configurations, and Jupyter notebooks used to perform and reproduce the analyses.

  PublisherDOI

• Cell-free biosensors: where have we been and where do we need to go?

  Current Opinion in Biotechnology · 2026-02-10 · 1 citations

  articleOpen accessSenior authorCorresponding

  Cell-free biosensors have the potential to become a low-cost, widely distributed technology. If deployed at scale, they can generate new large-scale data streams about human health and our environment, providing actionable information at the point of need. Here, we review the key technological advances of cell-free biosensors over the last five years and suggest a future path of technology development, including interfacing with circuits, devices, and materials that are becoming part of the next generation of biosensors. We then ask what is needed for these technologies to succeed at scale, focusing on lessons from field-deployment studies, policy, regulatory, safety, and other considerations to ensure alignment of technological developments with real-world necessities, market opportunities, and reliable use by non-experts. • Cell-free biosensors detect many chemical targets using varied mechanisms. • Molecular circuits, materials, and devices increase sensor performance. • Field studies indicate the importance of packaging, shelf-stability, and logistics. • User-centered design improves operation by non-expert users. • Progress in regulation and manufacturing is necessary for global adoption.

  PublisherDOI

• Efficient and scalable modelling of cotranscriptional RNA folding with deterministic and iterative RNA structure sampling

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-04-24

  articleOpen accessSenior authorCorresponding

  A bstract RNA structure sampling is central to modelling RNA ensembles, yet stochastic sampling methods are non-exhaustive, scale poorly, and are biased towards low-free-energy structures, while current suboptimal folding approaches generate an unpredictable exponential number of structures. These limitations are particularly problematic for modelling cotranscriptional folding, where vectorial synthesis continuously reshapes the energy landscape during transcription, stabilising transient out-of-equilibrium structures. Here we introduce iterative sampling , a deterministic framework that enumerates unique RNA secondary structures in strict order of increasing free energy, enabling progressive and exhaustive exploration of the structure space up to an arbitrary stopping criterion. To implement this approach, we developed two scalable algorithms, iterative deepening and a persistent data structure approach, that incrementally traverse the expansion tree by evolving partial structures in place, avoiding redundant recomputation and fixed energy windows. Implemented in memerna , this approach achieves orders-of-magnitude speedups over existing tools (10x over ViennaRNA ; 100x over RNAstructure ). Integration within the sample-and-select framework ( R2D2 ) improves structural diversity and identifies conformations with greater agreement with experimental data. Comprehensive sampling further enables direct comparison of equilibrium and cotranscriptionally restrained ensembles. Analysis of the resulting structural probability distributions uncovers kinetic traps and putative transcriptional pause sites, supporting an intuitive cotranscriptional folding mechanism in which local 3′-hairpin formation transiently stabilises upstream structure to delay large-scale rearrangement. Together, these results establish iterative sampling as a scalable and general framework for resolving out-of-equilibrium RNA cotranscriptional folding. Graphical abstract

  PublisherDOI

• LucksLab/Rasmussen_Brown_in_vitro_detection_of_glyphosate_2025: Zenodo Release

  Zenodo (CERN European Organization for Nuclear Research) · 2026-02-20

  otherOpen access

  Zenodo DOI for submission release

  PublisherDOI

• Author Correction: A cell-free biosensor signal amplification circuit with polymerase strand recycling

  Nature Chemical Biology · 2025-03-17

  erratumOpen accessSenior authorCorresponding
  PublisherOA PDFDOI

• A cell-free biosensor signal amplification circuit with polymerase strand recycling

  Nature Chemical Biology · 2025-01-13 · 21 citations

  articleOpen accessSenior author
  PublisherOA PDFDOI

Recent grants

• Dynamic Control of Glycan Biosynthesis with Synthetic RNA Circuitry

  NSF · $300k · 2014–2017

• Transitions: Evolving our Understanding of Dynamic RNA Folding and Function

  NSF · $750k · 2023–2026

• CAREER: Uncovering Quantitative Design Principles of RNA Regulators For Synthetic Biology

  NSF · $574k · 2016–2021

• Functional Roles of Nascent RNA Structure in Regulating and Coordinating Gene Expression

  NIH · $1.2M · 2020–2024

• NRT-URoL: Synthesizing Biology Across Scales – A Convergent Synthetic Biology Training Program

  NSF · $3.0M · 2020–2026

Frequent coauthors

• Angela M Yu

  University of Washington

  37 shared

• Michael C. Jewett

  Stanford University

  29 shared

• Adam P. Arkin

  University of California, Berkeley

  28 shared

• M Mundhenk

  Karlsruhe University of Education

  25 shared

• James R. Matz

  University of Wrocław

  25 shared

• Adam Ginsburg

  University of Florida

  25 shared

• Leszek Pacholski

  Poznań University of Technology

  25 shared

• P Rozoy

  Cornell University

  25 shared

Labs

• Lucks LabPI

Education

• PhD Chemical Physics, Chemistry/Physics

  Harvard University

  2007

• M. Phil., Chemistry

  Cambridge University

  2002

• B.S., Chemistry

  University of North Carolina

  2001

Awards & honors

• 2025 Fellow, American Association for the Advancement of Sci…
• 2023 Guggenheim Fellow, Biology
• 2022 Phi Lambda Upsilon Award Lecture, University of Nebrask…
• 2022 American Institute for Medical and Biological Engineeri…
• 2020 Blavatnik National Awards for Young Scientists, Finalis…