Madhavi Ganapathiraju, PhD

Research Interests: 

Most Significant Papers

Google Scholar Profile

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

Ganapathiraju MK, Subramanian S, Chaparala S, Karundkaran KB. A reference catalog of DNA palindromes in the human genome and their variations in 1000 Genomes. Human Genome Variation 2020 Nov 20;7(1):40. doi:10.1038/s41439-020-00127-5. PMID: 33298903 PMCID: PMC7680136

Karunakaran KB, Chaparala S, Ganapathiraju MK. Potentially repurposable drugs for schizophrenia identified from its interactome. Scientific Reports. 2019 Sep 3;9(1):1-4.

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.

Sundaravadivel P, Mohanty SP, Kougianos E, Yanambaka VP, Ganapathiraju MK. Smart-walk: An intelligent physiological monitoring system for smart families. 2018 IEEE International Conference on Consumer Electronics (ICCE). 2018 Jan 12-14, Las Vegas, NV. 1-4. doi: 10.1109/ICCE.2018.8326065.

Sundaravadivel P, Kesavan K, Kesavan L, Mohanty SP, Kougianos E, Ganapathiraju M. Smart-log: An automated, predictive nutrition monitoring system for infants through the IoT. 2018 IEEE International Conference on Consumer Electronics (ICCE). 2018 Jan 12-14, Las Vegas, NV. 1-4. doi: 10.1109/ICCE.2018.8326068.

Chattopadhyay A, Ganapathiraju MK. Demonstration Study: A Protocol to Combine Online Tools and Databases for Identifying Potentially Repurposable Drugs. Data. 2017 May 24;2(2).

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 Nov 21];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. 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.

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.

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.

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.

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

Zhu J, Zhang Y, Ghosh A, Cuevas RA, Forero A, Dhar J, Ibsen MS, Schmid-Burgk JL, Schmidt T, Ganapathiraju MK, Fujita T, Hartmann R, Barik S, Hornung V, Coyne CB, Sarkar SN. Antiviral Activity of Human OASL Protein Is Mediated by Enhancing Signaling of the RIG-I RNA Sensor. Immunity. 2014 Jun 19; 40(6): 936–48. doi: 10.1016/j.immuni.2014.05.007. Epub 2014 Jun 12. PubMed PMID: 24931123. PMCID: PMC4101812.

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. PubMed PMID: 24708602. PMCID: PMC4124845.

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. PubMed PMID: 24001106. PMCID: PMC3844564

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. Hum Mutat. 2013 Aug;34(8):1160-71. doi: 10.1002/humu.22348. Epub 2013 May 28. Erratum in: Hum Mutat. 2014 Jan;35(1):149. PubMed PMID: 23649844. PMCID: PMC3714349.

Thahir M, Sharma T, Ganapathiraju MK. An efficient heuristic method for active feature acquisition and its application to protein-protein interaction prediction. BMC Proc. 2012 Nov 13;6 Suppl 7:S2. doi: 10.1186/1753-6561-6-S7-S2. Epub 2012 Nov 13. PubMed PMID: 23173746. PMCID: PMC3504800.

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. Microb Inform Exp. 2012 Mar 21;2:4. doi: 10.1186/2042-5783-2-4. PubMed PMID: 22587966. PMCID: PMC3353838.

Orii N, Ganapathiraju MK. Wiki-Pi: A Web-Server of Annotated Human Protein-Protein Interactions to Aid in Discovery of Protein Function. PLoS ONE. 2012 Nov 28;7(11): e49029. doi: 10.1371/journal.pone.0049029. Epub 2012 Nov 28. PubMed PMID: 23209562. PMCID: PMC3509123.

Orii N, Ganapathiraju MK. 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. Epub 2012 Nov 28. PubMed PMID: 23209562. PMCID: PMC3509123.

Mohamed TP, Carbonell JG, Ganapathiraju MK. Active learning for human protein-protein interaction prediction. BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S57. doi: 10.1186/1471-2105-1-S1-S57. PubMed PMID: 20122232. PMCID: PMC3009530.

Osmanbeyoglu HU, Wehner JA, Carbonell JG, Ganapathiraju MK. Active machine learning for transmembrane helix prediction. BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S58. doi: 10.1186/1471-2105-11-S1-S58. PubMed PMID: 20122233. PMCID: PMC3009531.

Ganapathiraju M, Balakrishnan N, Reddy R, Klein-Seetharaman J. Transmembrane helix prediction using amino acid properties and latent semantic analysis. BMC Bioinformatics. 2008;9 Suppl 1:S4. doi: 10.1186/1471-2105-9-S1-S4. PubMed PMID: 18315857. PMCID: PMC2259405.