Jing Zhang

Metabolic blueprints of monocultures enable prediction and design of synthetic microbial consortia

The paper uses consumer-resource models parametrized from monoculture exometabolite data to predict and design synthetic microbial consortia, revealing the importance of cross-feeding interactions and nonlinear dynamics.

Exploring chemotaxis in spatio-temporal stoichiometric models of metabolism: Pseudomonas simiae as a case study

The paper develops a chemotaxis module for COMETS, a microbial ecosystem simulation tool, and applies it to Pseudomonas simiae to study chemotaxis and metabolism coupling.

Biophysical metabolic modeling of complex bacterial colony morphology

The paper models bacterial colony morphology by integrating metabolic reactions and biomass propagation, showing realistic colony shapes and metabolic ring formation.

Riboformer: A Deep Learning Framework for Predicting Context-Dependent Translation Dynamics

Riboformer predicts context-dependent translation dynamics using deep learning, correcting artifacts and identifying sequence motifs affecting ribosome stalling.