Domagoj Dorešić

This paper introduces Octomod, a workflow using large language models to aid in mechanistic model construction and refinement in systems biology, demonstrating its effectiveness across multiple applications.

PEtab Select provides a standardized format and software for automated model selection in systems biology, supporting diverse modeling frameworks and enabling efficient evaluation of large model spaces.

The paper develops a computational model to show that MID1 binding increases mutant huntingtin RNA stability, validated experimentally.

The paper uses mathematical modeling to show P-TEFb phosphorylates CTD repeats with local cooperativity but no directional bias.

This paper introduces a spline-based method for parameter estimation in ODE models using semi-quantitative data, improving estimation efficiency and enabling discovery of unknown measurement transformations.