Eran Agmon

The paper updates and corrects SED-ML files for 1055 models in BioModels to improve reproducibility and verification across simulation engines.

The paper models and experimentally validates how HIF-1 dynamics in cycling hypoxia lead to specific gene expression patterns linked to cancer progression.

The paper shows oscillatory hypoxia induces a unique gene expression signature in breast cancer linked to poor survival.

The paper integrates multiplexed imaging and multiscale modeling to show that T cell phenotype influences tumor phenotype conversion, critical for therapeutic efficacy.

This paper introduces Vivarium, a software tool for building integrative multiscale models in computational biology, demonstrating its utility by combining multiple modeling frameworks.

The paper develops a whole-colony model of E. coli integrating single-cell mechanisms with population-level interactions, showing that AmpC expression, not AcrAB-TolC, drives antibiotic survival.