SpecVar is a convenient tool for estimating interpretable genetic correlation of human complex traits and annotating the SNPs with context specific regulatory networks

Distributed simulations and analysis of synchronous Boolean networks

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

Finding paths of interest in networks

Correlation Guided Network Integration

Streaming over networks

Mechanistic Inference of Node-Edge Relationships (MINER)

biopatternsg is a system that builds gene regulatory networks from a basic collection of biological objects, gathering and processing PubMed abstracts, using Internet available informational resources like Mesh, GeneOntology, UniProt, PDB and others, and that uses java and logical engines like prolog to integrate and analyse them.

Connecting nodes

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

sRACIPE for bioconductor

Code for 2023 "Measuring Robustness of the Gap Gene Network" paper