Dr. Shubhada Hegde

Dr. Shubhada Hegde obtained her 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. 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. Dr. Hegde’s 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. 

Research Interests

My group uses computational and systems biological approaches to understand disease mechanisms. We employ genomic, transcriptomic and other high-throughput biological data, and analyse them in the context of molecular interaction networks. Broadly, our research projects fall into these themes:

• Understanding long term persistence of Mycobacterium tuberculosis in the host
• Building protein and gene-regulatory networks of pathogens
• Small RNA mediated gene regulation
• Computational approaches to biomarkers and drug discovery

Publications

(* as corresponding author)

1. Maity U, Aggarwal R, Balasubramanian R, Vekantraman DL and Hegde SR* (2024) Devising Isolation Forest-Based Method to Investigate the sRNAome of Mycobacterium tuberculosis using sRNA-seq Data. Bioinformatics and Biology Insights. Volume 18. doi:10.1177/11779322241263674
2. Sinha PR, Balasubramanian R and Hegde SR* (2024) Integrated sequence and -omic features reveal novel small proteome of Mycobacterium tuberculosis. Front. Microbiol. 15:1335310.
3. Ahmad E, Mitra A, Ahmed W, Mahapatra V, Hegde SR, Sala C, Cole ST, Nagaraja V (2023)
   Rho-dependent transcription termination is the dominant mechanism in Mycobacterium tuberculosis. Biochim Biophys Acta Gene Regul Mech., 21:194923.
4. Vekantraman DL, Pulimamidi D, Shukla HG and Hegde SR* (2021) Tumor relevant protein functional interactions identified using bipartite graph analyses. Sci. Rep. 11:21530
5. Balasubramanian R and Hegde SR* (2020) Integrating multi-omics data to investigate pseudogene expression in Mycolicibacterium smegmatis. Gene 21:167.
6. Ami VKG, Balasubramanian R and Hegde SR* (2020) Genome-wide identification of the context-dependent sRNA expression in Mycobacterium tuberculosis. BMC Genomics 21:167.
7. Hegde SR* (2020) Computational Identification of the Proteins associated with Quorum sensing and Biofilm formation in Mycobacterium tuberculosis. Front Microbiol. 10:3011.
8. Ahmad E, Hegde SR and Nagaraja V (2020) Revisiting intrinsic transcription termination in mycobacteria: U-tract downstream of secondary structure is dispensable for termination. Biochem Biophys Res Commun. 522(1):226-232.
9. Uma M, Hegde SR, Rao PP, Nagalekshmi K, Gauthami S, Kumar D and Hegde NR (2018) A novel point mutation (L70P) inactivates poliovirus 3C protease. Acta Virol. 62:68-77.
10. Ahmed W, Sala C, Hegde SR, Jha RK, Cole ST and Nagaraja V (2017) Transcription facilitated genome-wide recruitment of topoisomerase I and DNA gyrase. PLoS Genet. 2;13(5):e1006754.
11. Hegde SR, Pal K and Mande SC (2014) Differential enrichment of regulatory Motifs in the composite network of Protein-protein and Gene regulatory Interactions. BMC Syst Biol. 8:26.
12. Permina EA, Medvedeva YA, Baeck PM, Hegde SR, Mande SC and Makeev VJ (2013) Identification of self-consistent Modulons from bacterial microarray expression data with the help of structured regulon gene sets. J Biomol Struct Dyn. 31(1):115-24.
13. Hegde SR, Rajasingh H, Das C, Mande SS and Mande SC (2012) Understanding communication signals during mycobacterial latency through predicted genome-wide protein interactions and Boolean modeling. PLoS One7(3):e33893.
14. Jailkhani N, Ravichandran S, Hegde SR, Siddiqui J, Mande SC and Rao KVS (2011) Delineation of key regulatory elements identifies points of vulnerability in the Mitogen- activated Signaling Network. Genome Res. 21(12):2067-81.
15. Hegde SR, Klimova EY, Mande SC, Medvedeva YA, Makeev VY and Permina EA (2011) Using Operonic pairs to set the threshold correlation coefficient for differentially expressed genes. Biophysics 56(6):1041-1042.
16. P Manimaran, Hegde SR and Mande SC (2009) Prediction of Conditional Gene Essentiality through Graph Theoretical Analysis of genome-wide Functional Linkages. Mol Biosyst DOI: 10.1039/b905264j.
17. Hegde SR, P Manimaran and Mande SC (2008) Dynamic Changes in Protein Functional Linkage Networks Revealed by Integration with Gene Expression Data. PLoS Comput Biol. 4: e1000237.
18. Hegde SR (2012) Understanding the Complexity of Biological Networks. Lindau Newsletter (Non-reviewed general article).