Shubhada Hegde joined Chanakya University’s School of Biosciences in 2024. She studies infectious diseases using computational biology and data analytics.

Hegde obtained post-graduate degree in Biochemistry from Central College, Bangalore University. Subsequently, she did her PhD at the Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, in Computational Systems Biology. During her PhD, she generated protein interaction network for Mycobacterium tuberculosis using machine learning and studied its dynamics in latency. Further, she joined Indian Institute of Science (IISc) Bengaluru as a D S Kothari post-doctoral fellow. Before her appointment at Chanakya University, she worked as a DST-Inspire faculty scientist, and later as a faculty fellow at IBAB, Bengaluru. Her group uses computational and systems biological approaches to understand disease mechanisms. Her research focus areas include systems biology, gene regulation, host-pathogen interactions, and Drug discovery.

She teaches bioinformatics and biological data analysis.

• Ph.D. in Computational Systems Biology, 2012, Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad
• Msc in Biochemistry, 2006, Central College, Bangalore University

1. B. Sharma, P. Kathirvel, and S. R. Hegde, “Identifying communities in the virushost proteinprotein interaction networks,” Methods Mol. Biol., vol. 2927, pp. 307–319, 2025.
2. S. Singh and S. R. Hegde, “Bipartite graph analysis of the virushost protein interaction network to identify key proteins mediating the infection,” Methods Mol. Biol., vol. 2927, pp. 99–113, 2025.
3. D. Acharya, A. N. Bavikatte, V. V. Ashok, S. R. Hegde, C. R. Macpherson, A. Scherf, and S. S. Vembar, “Ectopic overexpression of Plasmodium falciparum DNA-/RNA-binding Alba proteins misregulates virulence gene homeostasis during asexual blood development,” Microbiol. Spectr., vol. 13, no. 3, p. e0088524, Mar. 2025.
4. R. Sundararajan, S. R. Hegde, A. K. Panda, J. Christie, N. Gadewal, and P. Venkatraman, “Loss of correlated proteasomal subunit expression selectively promotes the 20SHigh state which underlies luminal breast tumorigenicity” Commun. Biol., vol. 8, no. 1, p. 55, Jan. 2025, doi: 10.1038/s42003-024-07432-7.
5. P. R. Sinha, S. R. Hegde, R. Mittal, C. C. Jagat, U. Gowda, R. Chandrashekhar, G. Muthaiah, S. Shamshad, M. M. Chanda, V. Ganji, K. Putty, and D. Hemadri, “In silico development of a multiepitope subunit vaccine against Bluetongue virus in Ovis aries using immunoinformatics,” Pathogens, vol. 13, no. 11, p. 944, Oct. 2024, doi: 10.3390/pathogens13110944.
6. U. Maity, R. Aggarwal, R. Balasubramanian, D. L. Venkatraman, and S. R. Hegde, “Devising Isolation Forestbased Method to Investigate the sRNAome of Mycobacterium tuberculosis Using sRNAseq Data,” Bioinform. Biol. Insights, vol. 18, p. 11779322241263674, 2024.
7. P. R. Sinha, R. Balasubramanian, and S. R. Hegde, “Integrated sequence and omic features reveal novel small proteome of Mycobacterium tuberculosis,” Front. Microbiol., vol. 15, p. 1335310, May 15, 2024.
8. E. Ahmad, A. Mitra, W. Ahmed, V. Mahapatra, S. R. Hegde, C. Sala, S. T. Cole, and V. Nagaraja, “Rhodependent transcription termination is the dominant mechanism in Mycobacterium tuberculosis,” Biochim. Biophys. Acta Gene Regul. Mech., vol. 1866, no. 2, p. 194923, Jun. 2023, doi: 10.1016/j.bbagrm.2023.194923.
9. D. L. Venkatraman, D. Pulimamidi, H. G. Shukla, and S. R. Hegde, “Tumor relevant protein functional interactions identified using bipartite graph analyses,” Sci. Rep., vol. 11, p. 21530, Nov. 2, 2021
10. R. Balasubramanian and S. R. Hegde, “Integrating multiomics data to investigate pseudogene expression in Mycolicibacterium smegmatis,” Gene, vol. 755, p. 144908, Sep. 2020, doi: 10.1016/j.gene.2020.144908.
11. V. K. G. Ami, R. Balasubramanian, and S. R. Hegde, “Genomewide identification of the contextdependent sRNA expression in Mycobacterium tuberculosis,” BMC Genomics, vol. 21, no. 1, p. 167, Feb 18, 2020.
12. S. R. Hegde, “Computational identification of the proteins associated with quorum sensing and biofilm formation in Mycobacterium tuberculosis,” Front. Microbiol., vol. 10, p. 3011, Jan 22, 2020.
13. E. Ahmad, S. R. Hegde, and V. Nagaraja, “Revisiting intrinsic transcription termination in mycobacteria: Utract downstream of secondary structure is dispensable for termination,” Biochem. Biophys. Res. Commun., vol. 522, no. 1, pp. 226–232, Jan 29, 2020.
14. M. Uma, S. R. Hegde, P. P. Rao, K. Nagalekshmi, S. Gauthami, D. Kumar, and N. R. Hegde, “A novel point mutation (L70P) inactivates poliovirus 3C protease,” Acta Virol., vol. 62, no. 1, pp. 68–77, 2018, doi: 10.4149/av_2018_108.
15. W. Ahmed, C. Sala, S. R. Hegde, R. K. Jha, S. T. Cole, and V. Nagaraja, “Transcription facilitated genomewide recruitment of topoisomerase I and DNA gyrase,” PLoS Genet., vol. 13, no. 5, art. e1006754, May 2017, doi: 10.1371/journal.pgen.1006754.
16. N. Jailkhani, S. Ravichandran, S. R. Hegde, Z. Siddiqui, S. C. Mande, and K. V. S. Rao, “Delineation of key regulatory elements identifies points of vulnerability in the mitogenactivated signaling network,” Genome Res., vol. 21, no. 12, pp. 2067–2081, Dec. 2011, doi: 10.1101/gr.116145.110.
17. E. A. Permina, Y. A. Medvedeva, P. M. Baeck, S. R. Hegde, S. C. Mande, and V. J. Makeev, “Identification of selfconsistent modulons from bacterial microarray expression data with the help of structured regulon gene sets,” J. Biomol. Struct. Dyn., vol. 31, no. 1, pp. 115–124, 2013, doi: 10.1080/07391102.2012.691368.
18. S. R. Hegde, H. Rajasingh, C. Das, S. S. Mande, and S. C. Mande, “Understanding communication signals during mycobacterial latency through predicted genomewide protein interactions and Boolean modeling,” PLoS One, vol. 7, no. 3, art. e33893, Mar. 2012, doi: 10.1371/journal.pone.0033893.
19. N. Jailkhani, S. Ravichandran, S. R. Hegde, Z. Siddiqui, S. C. Mande, and K. V. S. Rao, “Delineation of key regulatory elements identifies points of vulnerability in the mitogenactivated signaling network,” Genome Res., vol. 21, no. 12, pp. 2067–2081, Dec. 2011, doi: 10.1101/gr.116145.110
20. P. Manimaran, S. R. Hegde, and S. C. Mande, “Prediction of conditional gene essentiality through graph theoretical analysis of genomewide functional linkages,” Mol. Biosyst., vol. 5, no. 12, pp. 1936–1942, Dec. 2009, doi: 10.1039/B905264j.
21. S. R. Hegde, P. Manimaran, and S. C. Mande, “Dynamic changes in protein functional linkage networks revealed by integration with gene expression data,” PLoS Comput. Biol., vol. 4, no. 11, art. e1000237, Nov. 2008, doi: 10.1371/journal.pcbi.1000237

Popular Writings

1. S. R. Hegde (2012) Understanding the Complexity of Biological Networks. Lindau Newsletter

• 2014 Inspire Faculty Fellowship by the Dept. of Science and Technology
• 2013 Dr. D S Kothari Post Doctoral Fellowship by University Grants Commission
• 2011 Award for Participating 61st Meeting of Lindau Nobel Laureates by Dept. of Science and Technology
• Member, RNA India
• Member, Biogroup India

• https://scholar.google.com/citations?user=uS9wAcAAAAAJ&hl=en
• https://x.com/shubhadahegde