Madhavi Ganapathiraju, PhD

Research Interests: 

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.

Associate Professor, Department of Biomedical Informatics
Associate Professor, Intelligent Systems, Intelligent Systems Program
Associate Professor, Computational Biology, Department of Computational Biology
University of Pittsburgh School of Medicine
Publications: 

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

Liu X, Yagi H, Saeed S, Bais AS, Gabriel GC, Chen Z, Peterson KA, Li Y, Schwartz MC, Reynolds WT, Saydmohammed M, Gibbs B, Wu Y, Devine W, Chatterjee B, Klena NT, Kostka D, de Mesy Bentley KL, Ganapathiraju MK, Dexheimer P, Leatherbury L, Khalifa O, Bhagat A, Zahid M, Pu W, Watkins S, Grossfeld P, Murray SA, Porter GA Jr, Tsang M, Martin LJ, Benson DW, Aronow BJ, Lo CW. The complex genetics of hypoplastic left heart syndrome. Nat Genet. 2017 Jul;49(7):1152-1159. doi: 10.1038/ng.3870. Epub 2017 May 22. PubMed PMID: 28530678.

Malavia TA, Chaparala S, Wood J, Chowdari K, Prasad KM, McClain L, Jegga AG, Ganapathiraju MK, Nimgaonkar VL. Generating Testable Hypotheses for Schizophrenia and Rheumatoid Arthritis Pathogenesis by Integrating Epidemiological, Genomic and Protein Interaction Data. NPJ Schizophr. 2017 Feb 24;3:11. doi: 10.1038/s41537-017-0010-z. eCollection 2017. PubMed PMID: 28560257. PMCID: PMC5441529.

Subramanian S, Ganapathiraju MK. Antibody Exchange: Information extraction of biological antibody donation and a web-portal to find donors and seekers. Data (Basel). 2017 Dec;2(4). pii: 38. doi: 10.3390/data2040038. Epub 2017 Nov 21. PubMed PMID: 30498741. PMCID: PMC6258257

Ganapathiraju MK, Karunakaran KB, Correa-Menendez J. Predicted protein interactions of IFITMs may shed light on mechanisms of Zika virus-induced microcephaly and host invasion. Version 2. F1000 Res. 2016 Aug 5 [revised 2017 Jan 1];5:1919. doi: 10.12688/f1000research9364.2. eCollection 2016. PubMed PMID: 2933329. PMCID: PMC5747333.

Ganapathiraju M, Chaparala S. Schizophrenia interactome: fully-labeled interactome network. NPJ Schizophr. 2016 Aug 24;2:16025. doi: 10.1038/npjschz.2016.25. eCollection 2016. No abstract available. PubMed PMID: 27602386. PMCID: PMC5007984.

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 Schizophr. 2016 Apr 27;2:16012. doi: 10.1038/npjschz.2016.12. eCollection 2016. PubMed PMID: 27336055. PMCID: PMC4898894.

Subramanian S, Chaparala S, Avali V, Ganapathiraju MK. A pilot study on the prevalence of DNA palindromes in breast cancer genomes. BMC Med Genomics. 2016 Dec;9(Suppl 3):73. doi: 10.1186/s12920-016-0232-3. PubMed PMID 28117658. PMCID: PMC5260791.

Embar V, Handen A, Ganapathiraju MK. Is the average shortest path length of gene set a reflection of their biological relatedness? J Bioinform Comput Biol. 2016 Dec;14(6):1660002. doi: 10.1142/S0129720016600027. PubMed PMID: 28073302. PMCID: PMC5726383.

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 May 28;521(7553):520-4. doi: 10.1038/nature14269. Epub 2015 Mar 25.  PubMed PMID: 25807483. PMCID: PMC4617540.

Handen A, Ganapthiraju MK. LENS: web-based lens for enrichment and network studies of human proteins. BMC Med Genomics. 2015;8(Suppl 4):S2. doi:10.1186/1755-8794-8-S4-S2. Epub 2015 Dec 9. PubMed PMID: 26680011. PMCID: PMC4682415.

Roth A, Subramanian S, Ganapathiraju MK. Towards extracting supporting information about predicted protein-protein interactions. IEEE/ACM Trans Comput Biol Bioinform. 2018 Jul-Aug;15(4):1239-1246. doi: 10.1109/TCBB.2015.2505278. Epub 2015 Dec 7. 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

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.

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.

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.

Osmanbeyoglu HU, Wehner JA, Carbonell JG, Ganapathiraju MK. Active machine learning for transmembrane helix prediction. BMC Bioinformatics. 2010; 11:S58. PMCID: PMC3009531. PMID: 20122233.

Ganapathiraju M, Balakrishnan N, Reddy R, Klein-Seetharaman J. TMpro: Transmembrane Helix Prediction Using Amino Acid Properties and Latent Semantic Analysis.  BMC Bioinformatics. 2008 Feb 13;9(Suppl 1):S4. doi: 10.1186/1471-2105-9-S1-S4

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