Madhavi Ganapathiraju, PhD
Dr. Ganapathiraju’s primary area of research is in Systems Biology, specifically on protein-protein interaction prediction at the system level. The outcomes of this research will subsequently be applied to translational bioinformatics. A second core area is in Sequence Analysis, for pattern mining in whole-genome and whole-proteome sequences, with application of suffix array data structures for preprocessing the genome sequences.
For all of these biomedical domains, Dr. Ganapathiraju develops novel algorithms with research basis in machine learning, information integration and network analysis and other areas of computer science.
Appointments and Positions
Assistant Professor, Department of Biomedical Informatics, School of Medicine
Intelligent Systems Program, School of Arts and Sciences
Molecular and Cellular Cancer Biology Program, Cancer Institute
Joint Carnegie Mellon—University of Pittsburgh PhD Program in Computational Biology
Biomedical Informatics Training Program Core Faculty
Current Research Projects and Collaborations
Systematic Discovery of Protein-Protein Interactions
Discovery of Mental Health and Inflammation Interactome
Inference Analytics in Systems Biology
Thahir M, Sharma T, Ganapathiraju MK. Active feature acquisition for protein-protein interaction prediction. BMC Bioinformatics. 2012; 6:S2. (in press).
Orii N, Ganapathiraju MK (2012) Wiki-Pi: A Web-Server of Annotated Human Protein-Protein Interactions to Aid in Discovery of Protein Function. PLoS ONE 7(11): e49029. doi:10.1371/journal.pone.0049029.
Ganapathiraju MK, Mohamed T, Mitchell AD, Motwani K, Ananthasubramanian S. Suite of tools for statistical n-gram language modeling for pattern mining in whole genome sequences. Journal of Bioinformatics and Computational Biology. 2012; 10 (5). PMID: 22817111.
Ananthasubramanian S, Metri R, Khetan A, Gupta A, Handen A, Chandra N, Ganapathiraju M. Mycobacterium tuberculosis and Clostridium difficille interactomes: demonstration of rapid development of computational system for bacterial interactome prediction. Microbial informatics and experimentation. 2012; 2:4. PMCID: PMC3353838. PMID: 22587966.
Osmanbeyloglu HU, Ganapathiraju MK. Rapid Deployment of Viral-Human Interactome Prediction for New Viruses. AMIA TBI; 2011 Mar; San Francisco 2011.
Osmanbeyoglu HU, Ganapathiraju MK. N-gram analysis of 970 microbial organisms reveals presence of biological language models. BMC Bioinformatics. 2011; 12 (1):12. PMCID: PMC3027111. PMID: 21219653.
Mohamed TP, Carbonell JG, Ganapathiraju MK. Active learning for human protein-protein interaction prediction. BMC bioinformatics. 2010; 11:S57. PMCID: PMC3009530. PMID: 20122232.
Osmanbeyoglu HU, Wehner JA, Carbonell JG, Ganapathiraju MK. Active machine learning for transmembrane helix prediction. BMC Bioinformatics. 2010; 11:S58. PMCID: PMC3009531. PMID: 20122233.