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Software, Codes, and Websites

6. HMM Method for Uncovering Genes in the Same pathways

A Hidden Markov Model (HMM) based algorithm for detecting groups of genes functionally similar to a set of input genes from microarray expression data. (Paper Software and Data)

5. DDINet: Network of Interacting Protein Domains

DDINet provides a network of interacting protein domains, which is modeled by an undirected graph where vertices correspond to Pfam domains, and edges represent interactions inferred using our proposed model. (Paper Software and Data)

4. Binding: software for protein binding site prediction

Identification of protein interaction sites has significant impact on understanding protein function, elucidating signal transduction networks, and drug design studies. With the exponentially growing protein sequence data, predictive methods using sequence information only for protein interaction site prediction have drawn increasing interest. In this paper, we propose a predictive model for identifying protein interaction sites. (Paper Software and Data)

3. CSIDOP: software for protein function assignment

CSIDOP is a new method for protein function assignment based on the shared interacting domain patterns extracted from cross-species protein-protein interaction (PPI) data. (Paper Software and Data)

2. RFPPI: random forest based PPI prediction

RFPPI is a random forest-based approach for protein-protein interaction prediction using domain information. (Paper Software and Data)

1. DataKernel: Matlab codes for data-dependent kernel

We developed a data-dependent kernel for microarray data analysis

(Paper Codes)

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