David Phillip Nickerson

This paper develops a multiscale model to explain how plant genomic regulation enhances the mechanical stability of extracellular vesicles through composite reinforcement mechanisms.

The paper develops a bond graph model of enterocyte homeostasis, showing how physical laws constrain ion and glucose transport mechanisms to maintain cellular homeostasis.

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

The paper proposes adapting FAIR indicators to assess and improve the quality and transparency of computational models in biology.

The paper develops energy-based bond graph models of SLC transporters to conserve mass, charge, and energy, and demonstrates their application to glucose transport.

CASBERT improves entity retrieval in biosimulation models using BERT embeddings, outperforming bag-of-words methods in precision and recall.

NLIMED converts natural language queries into SPARQL to discover model entities from biosimulation model repositories.

SBMate evaluates annotation quality in systems biology models using coverage, consistency, and specificity metrics on 1,000 BioModels repository models.

The paper describes the development of a resource for the autonomic nervous system community, including databases, connectivity maps, and simulation tools.

The paper annotates biological models with semantic annotations and develops a web tool to help users discover relevant models in the Physiome Model Repository.

The paper introduces a web-based platform for constructing and assembling epithelial transport models using existing models from the Physiome Model Repository.