Cytoprophet is a project developed by the Laboratory for Computational Life Sciences at the Computer Science Department of the University of Notre Dame. It is a tool to help researchers to infer new potential protein (PPI) and domain (DDI) interactions. It is implemented as a Cytoscape plugin, where users input a set of proteins and retrieve a network of plausible protein and domain interactions with a score. Three algorithms are used for the estimation of PPI/DDI: Maximum Specificity Set Cover (MSSC) Approach, Maximum Likelihood Estimation (MLE) and the Sum-Product Algorithm (SPA) for protein networks.
JRIM is a package for Jointly Reconstructing cis-regulatory Interaction Maps of multiple cell populations using single-cell chromatin accessibility data and identifying shared and common interaction patterns. It uses an aggregation process to deal with the sparsity of single-cell data, exploits similarity between cell types via a group lasso penalty, and generates comparable networks. JRIM could be used to characterize difference between cell types or identify dynamic changes during cell development.
VirHostNet (Virus-Host Network) is a knowledgebase system dedicated to the curation, the integration, the management and the analysis of virus-host molecular (mainly protein-protein) interaction networks as well as their functional annotation (molecular functions, cellular pathways, protein domains).