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Madhavi Ganapathiraju

  • Associate Professor, Department of Biomedical Informatics

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.

Institution of Highest Degree

  • Carnegie Mellon University

Representative Publications

View in D-Scholarship

Chattopadhyay, A.; Ganapathiraju, M.K. Demonstration Study: A Protocol to Combine Online Tools and Databases for Identifying Potentially Repurposable Drugs. Data 2017, 2, 15.

X Liu, H Yagi, S Saeed, AS Bais, GC Gabriel, Z Chen, M Ganapathiraju… The complex genetics of hypoplastic left heart syndrome, Nature Genetics, 2017, http://dx.doi.org/10.1038/ng.3870

Ganapathiraju MK, Thahir M, Handen A, Sarkar SN, Sweet RA, Nimgaonkar VL, Loscher CE, Bauer EM, Chaparala S: Schizophrenia interactome with 504 novel protein–protein interactions. Npj Schizophrenia 2016, 2:16012. Link to Publication

Li Y, Klena NT, Gabriel GC, Liu X, Kim AJ, Lemke K, Chen Y, Chatterjee B, Devine W, Damerla RR, Chang C, Yagi H, San Agustin JT, Thahir M, Anderton S, Lawhead C, Vescovi A, Pratt H, Morgan J, Haynes L, Smith CL, Eppig JT, Reinholdt L, Francis R, Leatherbury L, Ganapathiraju MK, Tobita K, Pazour GJ, Lo CW. Global genetic analysis in mice unveils central role for cilia in congenital heart disease. Nature. 2015 Mar 25. doi: 10.1038/nature14269. [Epub ahead of print] PubMed PMID: 25807483.

Handen A, Ganapthiraju MK. LENS: web-based lens for enrichment and network studies of human proteins. BMC Medical Genomics. 2015;8(Suppl 4):S2. doi:10.1186/1755-8794-8-S4-S2.

Roth A, Subramanian S, Ganapathiraju MK. Towards extracting supporting information about predicted protein-protein interactions. IEEE/ACM Trans Comput Biol Bioinform. 2015 Dec 7. [Epub ahead of print] PubMed PMID: 26672046.

A. Gupta, H. Wang and M. Ganapathiraju, "Learning structure in gene expression data using deep architectures, with an application to gene clustering," Bioinformatics and Biomedicine (BIBM), 2015 IEEE International Conference on, Washington, DC, 2015, pp. 1328-1335. doi: 10.1109/BIBM.2015.7359871

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

Research Interests

Active Machine Learning
Systems Biology (Protein Interactions) and Structural Biology
Genomics of Diseases