Possible Rotation Projects:
- Genetic variant to function studies for complex diseases using interactome network analysis
- Prioritizing of coding variants of complex diseases using protein structure, function and interaction studies
Training Technologies Used:
- Machine Learning
- Bioinformatics
- Ph.D. in Language and Information Technologies from the School of Computer Science, Carnegie Mellon University, 2007
- M.Eng. in Electrical Communications Engineering from Indian Institute of Science 1993
- B.Sc. in Electronics, Physics, Mathematics, from Delhi University, 1990
Ganapathiraju MK, Mohamed TP, Handen A, et al. Schizophrenia interactome with 504 novel protein-protein interactions (2016) npj Schizophrenia. 2: p. 16012, February 2016. PMCID: PMC4898894.
Karunakaran, KB, Chaparala S, and Ganapathiraju MK. Potentially repurposable drugs for schizophrenia identified from its interactome (2019) Scientific Reports, 9 (1), 1-14, Sept 2019.
Malavia TA, …, *Ganapathiraju MK, Nimgaonkar VL. Generating testable hypotheses for schizophrenia and rheumatoid arthritis pathogenesis by integrating epidemiological, genomic and protein interaction data (2017)npj Schizophrenia, Feb 24;3:11. doi: 10.1038/s41537-017-0010-z. 2017. PMCID: PMC5441529.
Karunakaran, K.B., Chaparala, S., Lo, C.W. et al. Cilia interactome with predicted protein–protein interactions reveals connections to Alzheimer’s disease, aging and other neuropsychiatric processes (2020) Scientific Reports 10, 15629 (2020).
Handen A and Ganapathiraju MK. LENS: Web-based Lens for Enrichment and Network Studies of Human Proteins (2015) BMC Medical Genomics, Volume 8, Suppl 4, S2. PMCID: PMC4682415.
Liu X, Yagi H, …, Ganapathiraju MK, …, Lo CW The complex genetics of hypoplastic left heart syndrome (2017) Nature Genetics. 2017 Jul;49(7):1152-1159. doi: 10.1038/ng.3870 PMID: 28530678.
Li Y, Klena N, Gabriel G, Liu X, Lemke K, Chen Y, Kim A, Chatterjee B, Damerla R, Chang C, Yagi H, Shan Y, Agustin JS, Mohamed TP, Anderton S, Lawhead C, Vescovi A, Weeks D, Pratt H, Morgan J, Haynes L, Smith C, Eppig J, Reinholdt L, Leatherbury L, Tobita K, Francis R, Ganapathiraju MK, Pazour G, Lo CW. Global genetic analysis in mice unveils central role for cilia in congenital heart disease (2015) Nature. 521(7553):520-4. PMCID: PMC4617540.
Primary focus of our group is on prediction, analysis and dissemination of novel protein-protein interactions of human genes. Our work on predicting mental health and inflammation (MHAIN) interactome (namely protein-protein interactions where at least one of the two proteins is involved in mental health or inflammation, is funded by the NIMH BRAINS award. On the algorithm development side, we employ machine learning, including active learning and transfer learning approaches to predict interactions. We also develop methods to analyze interaction network to draw biologically relevant inferences and disseminate them effectively to biologists. We are currently studying the role of cilia and inflammation in different diseases such as schizophrenia and congenital heart disease, through collaborations with faculty from Developmental Biology and Psychiatry.
