Simulation and inference of gene regulatory networks based on transcriptional bursting

PySB add-on providing domain-specific macros and models for empirical and mechanistic PK/PD modeling.

Mechanistic Pan-Cancer Signaling Model

The Dig4Bio worskhop series

PySB add-on providing utilities to add units to models and perform dimensional analysis.

This repository contains the codes for the article: Data-driven mechanistic modeling of oxygen distribution and hypoxia profile in tumor microenvironment

Nitrogen balance model components and test procedures

Reproducibility-first mechanistic biology research stack: CFM (SCNT feasibility), BSE (virtual PK/PD physiology), and NSCS (closed-loop equation discovery).

Reproducible Phase 1 pipeline for mechanistic modeling and OOD trust scoring in a CiPA-28 context.

Organism-agnostic MATLAB platform for mechanistic metabolic route discovery, multi-omics ranking and phenotype simulation from genome-scale models.

This project studies causal relationship between events in the Adverse Outcome Pathway.

Teaching-oriented ODE epidemic mini-lab with SI, SIR, and SEIR models, parameter sweeps, and interpretable metrics.