Lucian P. Smith

Antimony 3 updates the human-readable modeling language to support SBML Level 3 features, enabling unified model definitions with kinetic reactions, uncertainty, annotations, and visualizations.

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

SBMLNetwork provides a framework for standards-based visualization of biochemical models by automating the generation of SBML-compliant visualization data.

This paper develops a novel evolutionary algorithm for generating mass-action chemical reaction networks with oscillatory behavior, using speciation and demonstrating it through a Julia package.

The paper curates 50 BioModels by reproducing results with Tellurium and creating OMEX files for reproducibility.

The paper investigates how biochemical reaction networks perform signal integration and integral feedback control, finding that these capabilities overlap but are not always mutually exclusive.

The paper identifies three novel complex structural variation patterns in cancer genomes using genome graph analysis across 2,833 tumor WGS.

Tellurium Notebook enables reproducible and reusable dynamical models in systems biology by integrating community standards and literate coding practices.