Hye-In Son

Gene circuit-driven amplified selection enables evolution of fast-growing Escherichia coli

This paper shows that a synthetic gene circuit can break a growth rate plateau in E. coli by selectively suppressing slow-growing cells, leading to faster growth.

A foundation model for microbial growth dynamics

This paper develops a foundation model for microbial growth dynamics using self-supervised learning on diverse datasets, enabling accurate reconstruction and prediction of growth patterns and antibiotic responses.

Dynamical memory underlies prolonged plasmid persistence after transient antibiotic treatment

The paper shows that prolonged plasmid persistence after antibiotic treatment is due to dynamical memory, not horizontal transfer or low plasmid cost.

Scaling laws of plasmids across the microbial tree of life

The paper develops a new computational method to analyze plasmid copy numbers across microbial genomes and identifies three scaling laws relating plasmid length, gene content, and metabolic function.

Transposon-plasmid nesting enables fast response to fluctuating environments

The paper shows transposon-plasmid nesting allows microbes to rapidly respond to environmental changes by combining genetic mobility with copy number amplification.

Antibiotic-mediated microbial community restructuring is dictated by variability in antibiotic susceptibility and population interactions

The paper shows antibiotic-mediated community restructuring is driven by subpopulation variability in antibiotic susceptibility and their interactions.

Programming dynamic division of labor using horizontal gene transfer

This paper shows that horizontal gene transfer can enable dynamic division of labor in microbes to stabilize complex metabolic pathways.

Discovery and Engineering of a Therapeutic Interfering Particle (TIP): a combination self-renewing antiviral

This paper discovers and engineers an HIV-1 Therapeutic Interfering Particle (TIP) that suppresses viral replication and protects CD4+ T cells in humanized mice.