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.
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
Jianzhong Zhu, Yugen Zhang, Arundhati Ghosh, Rolando A. Cuevas, Adriana Forero, Jayeeta Dhar, Mikkel Søes Ibsen, Jonathan Leo Schmid-Burgk, Tobias Schmidt, Madhavi K. Ganapathiraju, Takashi Fujita, Rune Hartmann, Sailen Barik, Veit Hornung, Carolyn B. Coyne, Saumendra N. Sarkar. Antiviral Activity of Human OASL Protein Is Mediated by Enhancing Signaling of the RIG-I RNA Sensor. Immunity. 2014 June 19; 40(6): 936–948.
Kuppuswamy U, Ananthasubramanian S, Wang Y, Balakrishnan N, Ganapathiraju MK. Predicting gene ontology annotations of orphan GWAS genes using protein-protein interactions. Algorithms Mol Biol. 2014 Apr 3;9(1):10. doi: 10.1186/1748-7188-9-10. PMID: 24708602
Ganapathiraju MK, Orii N. Research prioritization through prediction of future impact on biomedical science: a position paper on inference-analytics. Gigascience. 2013 Aug 30;2(1):11. doi: 10.1186/2047-217X-2-11. PMID: 24001106
Giorgio E, Rolyan H, Kropp L, Chakka AB, Yatsenko S, Gregorio ED, Lacerenza D, Vaula G, Talarico F, Mandich P, Toro C, Pierre EE, Labauge P, Capellari S, Cortelli P, Vairo FP, Miguel D, Stubbolo D, Marques LC, Gahl W, Boespflug-Tanguy O, Melberg A, Hassin-Baer S, Cohen OS, Pjontek R, Grau A, Klopstock T, Fogel B, Meijer I, Rouleau G, Bouchard JP, Ganapathiraju M, Vanderver A, Dahl N, Hobson G, Brusco A, Brussino A, Padiath QS. Analysis of LMNB1 Duplications in Autosomal Dominant Leukodystrophy Provides Insights into Duplication Mechanisms and Allele-Specific Expression. Human mutation. 2013 May 3. PMID:23649844.
Ananthasubramanian S, Carbonell JG, Ganapathiraju MK. Active learning with one-class and reluctant oracles in human protein-protein interaction prediction. WCSB 2013; Finland. 2013.
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.
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.
Thahir M, Sharma T, Ganapathiraju MK. An efficient heuristic method for active feature acquisition and its application to protein-protein interaction prediction. BMC Proceedings 2012, 6(Suppl 7):S2.
Osmanbeyloglu HU, Ganapathiraju MK. Rapid Deployment of Viral-Human Interactome Prediction for New Viruses. AMIA TBI; 2011 Mar; San Francisco 2011.
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.