Lingchong You

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.

This paper introduces a method using microbial consortia and computational models to decode complex signals and predict input concentrations from microbial community responses.

This paper introduces a simulation-conditioned generative framework that combines mechanistic models with image generation to create biologically realistic patterns, enabling inference from experimental data.

The paper develops a machine learning model to predict plasmid copy numbers using protein domains and applies it to metagenomic and clinical plasmid data to identify ecological patterns.

The paper shows that microscale spatial fragmentation enhances bacterial survival under antibiotics through physical mechanisms, not genetic resistance.

The paper shows keystone engineering enables microbial range expansion by antibiotic-degrading bacteria, revealing spatial effects in microbial communities.

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.

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

This study shows how transposon-plasmid coevolution enables Escherichia coli to dynamically respond to antibiotics through population-level feedback control.

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.

The paper shows that microbial community dynamics can be represented by low-dimensional latent variables, with the critical dimension scaling linearly with observables.

This paper engineers a prodrug that selectively suppresses β-lactam-resistant bacteria in mixed cultures by exploiting ESBL activity.

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

The paper identifies a highly abundant circular RNA, Obelisk-S.s, in Streptococcus sanguinis SK36, despite its absence from the genome, and reports mutations in some samples.

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

The paper integrates mechanistic modeling with machine learning to accelerate the discovery of design rules for pattern formation in living cells.

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

The paper identifies GvpU as the protein governing gas vesicle clustering and shows how its phase transition behavior modulates cellular fitness and clustering states.

The paper demonstrates a method using self-organized patterns and machine learning to encode and decode information, showing scalability by mapping the English keyboard.

This study shows that SARS-CoV-2 N-protein uses two distinct RNA motifs, both requiring dsRNA, to drive phase separation at specific temperatures, enabling multiple viral functions.

The paper develops a framework to simulate growth and gene expression dynamics in radially symmetric colonies using repulsive-expansion kinetics.

The paper introduces a framework using neural networks to accelerate computational simulations of biological models by emulating their behavior across larger parametric spaces.

The paper develops a general rule for predicting mutualistic system outcomes and introduces a calibration method to apply it without full mechanistic understanding.

This paper defines and distinguishes resistance and resilience in bacterial responses to antibiotics, showing their distinct cellular and population-level mechanisms and implications for treatment optimization.