Events

Synthetic biology has enabled the construction of increasingly complex genetic systems, yet the ability to predict and control gene expression beyond controlled laboratory or fermenter settings remains limited. As a result, many biological applications, from environmental bioremediation to living therapeutics, fail when deployed in natural or physiological contexts, revealing fundamental gaps in genetic design principles and in how gene expression is measured and modeled.

This seminar will present a quantitative framework for studying gene expression by integrating two complementary approaches. First, I will describe the development of hyperspectral reporters, small molecules with unique spectral absorbance signatures that can be detected remotely using drone- and satellite-based imaging. These reporters enable non-invasive, spatially resolved measurement of gene expression in complex environments, allowing environmental biosensing at unprecedented scales. Second, I will introduce MIT-seq (Measurement of Initiation using Titration followed by Sequencing), a transcriptome-scale method that directly measures translation initiation kinetics. MIT-seq quantifies initiation kinetic parameters across cells and conditions for millions of mRNA designs in parallel. These data enable interpretable, biophysically informed models and allow direct mapping of initiation kinetics and modes across transcriptomes and large synthetic mRNA libraries.

Together, these findings redefine how gene expression can be measured and engineered in natural contexts, supporting predictive mRNA design, enabling the construction of complex genetic operons, and improving cell specificity to enhance the safety and efficacy of mRNA therapeutics.

Yonatan Chemla earned a B.Sc. in Biological Engineering from Ben-Gurion University (2014) and a B.A. in General History from the Open University of Israel (2015). He completed a Ph.D. in Biology, with an emphasis on Synthetic and Quantitative Biology, at Ben-Gurion University in October 2020 under the supervision of Prof. Lital Alfonta and Prof. Michael Meijler. His doctoral research investigated bacterial translation using genetic code expansion, cell-free systems, and biophysical modeling, revealing how mRNA structure governs ribosomal translation initiation.

As a Human Frontier Science Program Postdoctoral Fellow, he joined Prof. Christopher A. Voigt’s laboratory at MIT, where he develops tools such as hyperspectral reporters to monitor gene expression beyond controlled laboratory settings and to improve the safety and efficacy of engineered cells in natural contexts. He recently received an NIH Pathway to Independence Award (K99) to unite his doctoral and postdoctoral research, advancing mRNA design in complex biological systems across the tree of life. His work aims to define quantitative design principles that guide biological engineering to address challenges in environmental sustainability and human health.