• ACRE -  absolute concentration robustness exploration in module-based networks

• Dragon TF-TcoF Classifier - predicts and assigns a functional class of a protein that binds a transcription factor (TF)

• Drug-Target Interaction tool (DDR) -  predicts drug target interactions using multiple similarities

• ElVira - an ontology modularization tool

• Gracob - a graph-based biclustering method that is designed to find maximal constant-column biclusters in any given two-dimensional data matrix, particularly growth phenotype data in which each row represents a gene deletion strain and each column represents a stress condition

• NMR slice picking and resonance assignment - This toos has two components, one for NMR slice picking and the other one for resonance assignment based on picked sliced

• PEDAL - discriminative identification of transcriptional responses of promoters and enhancers after stimulus (NAR)

• PEDI - parameter Estimation by Decomposition and Integration

• Walking RDF and OWL - feature learning on knowledge graphs and ontologies

Retired Application 

• DRAF -  a transcription factor (TF) binding site (TFBS) prediction tool

• DragonWFS - a parallel GA wrapper feature selection tool for optimizing the performance of different classification methods

• FSFE - identifying enhancer signatures based on state-of-the-art computational techniques

• OmniGA - a framework for the optimization of omnivariate decision trees (ODTs) based on a parallel genetic algorithm (GA)

• DEEP - a general computational framework for predicting enhancers (NAR)