Code behind the work "Single Cortical Neurons as Deep Artificial Neural Networks", published in Neuron 2021

Finite State Projection algorithms for chemical reaction networks

Development version of phaseR, an R package for phase plane analysis of one- and two-dimensional autonomous ODE systems

iCodon customizes gene expression based on the codon composition

Code behind the work "Multiple Synaptic Contacts Combined with Dendritic Filtering Enhance Spatio-Temporal Pattern Recognition of Single Neurons", bioRxiv 2022

Virtual population generation, fitting, and benchmarking.

In silico therapeutic target discovery using network attractors: avoiding pathological phenotypes

Python toolkit for Bayesian parameter inference, model calibration, and model selection using Nested Sampling

Implementation of a PINN solver for biological differential equations

An object-oriented model of the workings of the human body written in java and scala

A Game Theoretic Approach For Rendering Immersive Experiences In The Metaverse

Analysis pipeline for single-cell RNA sequencing (scRNA-seq) data focused on T cells in COVID-19. Includes scripts and workflows for data processing, visualization, and identifying immune cell signatures and responses. Designed to accelerate reproducible research in immunology and single-cell genomics.

Bayesian inference of stochastic cellular processes with and without memory in Python.

A repository for the final project in MathBio class, exploring the dynamics of natural pattern adaptation through the lens of a cellular automata model. Contains code, documentation, and resources related to the project.

4 dimensional model for neuronal modelling in Julia

Simulation of agents competing for resources with different strategies

Methods and Tools to Facilitate RE:IN Modeling and Analysis of GRNs

PAR2 Activation and calcium signaling Reaction Model in PySB

Streaming over networks

Enhancing Boolean networks with continuous logical operators and edge tuning: smoothing simulations