Faculty
Madhavi Ganapathiraju, PhD
Research Interests
Dr. Ganapathiraju’s primary area of research is in Systems Biology, protein-protein interaction prediction at the system level. It will subsequently be applied to translational bioinformatics.
A second core area is in Structural Biology, with membrane protein structure prediction from primary sequences. The third core area is in Sequence Analysis, 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 and network analysis and other areas of computer science.
Appointments and Positions
Assistant Professor, Department of Biomedical Informatics, School of Medicine
(Artificial) 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
Host-Pathogen Systems Biology
Recent Publications
"Mycobacterium tuberculosis and Clostridium difficille interactomes: demonstration of rapid development of computational system for bacterial interactome prediction", Seshan Ananthasubramanian, Rahul Metri, Ankur Khetan, Aman Gupta, Adam Handen, Nagasuma Chandra and Madhavi K Ganapathiraju, Microbial Informatics and Experimentation, 2012 (in print).
"Applying N-Gram Language Modeling for Pattern Mining in Whole Genome Sequences", Madhavi Ganapathiraju, Mohamed Thahir, Asia D. Mitchell, LBM2011: Languages in Biology and Medicine, Singapore, 2011.
"N-gram analysis of 970 microbial organisms reveals presence of biological language models", Hatice U. Osmanbeyoglu and Madhavi Ganapathiraju, BMC Bioinformatics (in press).
"Rapid Deployment of Viral-Human Interactome Prediction for New Viruses", Hatice Osmanbeyoglu and Madhavi Ganapathiraju, AMIA Translational Bioinformatics Summit, San Francisco, USA, March 7-9, 2011.
"Active Learning for Human Protein-Protein Interaction Prediction", Thahir P. Mohamed, Jaime G. Carbonell and Madhavi Ganapathiraju, BMC Bioinformatics, vol 11, Suppl 1, 2010.