Michael L. Blinov

Verification and reproducible curation of the BioModels repository

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

From spots to stripes: Evolution of pigmentation patterns in monkeyflowers via modulation of a reaction-diffusion system and its prepatterns

This study identifies genetic changes that modulate a reaction-diffusion system and its prepatterns to explain the evolutionary transition from spots to stripes in Mimulus flowers.

MolClustPy: A Python Package to Characterize Multivalent Biomolecular Clusters

The paper introduces a Python package for simulating and analyzing multivalent biomolecular clusters using stochastic simulations.

runBioSimulations: an extensible web application that simulates a wide range of computational modeling frameworks, algorithms, and formats

runBioSimulations provides a web platform to execute diverse computational models, enabling easier access to simulation tools and promoting reproducibility in modeling.

SBGN Bricks Ontology as a tool to describe recurring concepts in molecular networks

The paper introduces SBGN bricks and their ontology to provide structured semantics for recurring molecular network concepts, enabling better annotation and construction of molecular maps.

Molecular Process Diagram: a precise, scalable and compact visualization of rule-based models

The paper introduces Molecular Process Diagrams to visually represent rule-based models with precision and clarity, extending SBGN standards for better pathway understanding.