Dr. Shubhada Hegde

Dr. Shubhada Hegde

Faculty Scientist (DST-Inspire)

Research Focus Key Words

Infectious diseases, Network Biology, Systems Biology, Tuberculosis, Host-pathogen interactions


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. Her thesis work largely focused on constructing and analysing genome-wide protein interaction networks. Thereafter, she worked in the Department of Microbiology and Cell Biology, Indian Institute of Science (IISc) Bangalore as a Dr. D S Kothari Postdoctoral fellow. Shubhada joined IBAB as a DST-Inspire faculty scientist, and her research areas include systems biology, network analysis and genome analysis.


  1. Ph.D: Centre for DNA Fingerprinting and Diagnostics (CDFD), Hyderabad, 2012
  1. Post-doctoral Research: Indian Institute of Science (IISc) Bangalore, 2013-2014
  1. Professional Experience: Research Associate at National Centre for Cell Science, Pune, 2012

Research Interest Profile

My group uses computational and systems biological approaches to understand disease mechanisms. We employ large scale genomics, transcriptomics and other high-throughput datasets and analyse them in the context of molecular interaction networks. Broadly, our research projects fall into these categories: a) Understanding long term persistence of Mycobacterium tuberculosis in the host b) Building protein and gene-regulatory networks of pathogenic organisms and c) Mining expression data in oral cancer to discover potential biomarkers for clinical diagnosis.

Group Members

1. Ms. Rami Balasubramanian (Research Assistant)

2. Ms. PM Deepshika (Research Assistant)

Publications and Patents

  1. Ami VKG, Balasubramanian R, Hegde SR
    Genome-wide identification of the context-dependent sRNA expression in Mycobacterium tuberculosis.
    BMC Genomics, 21(1):167. doi: 10.1186/s12864-020-6573-5 (2020)
  2. Hegde SR
    Computational Identification of the Proteins associated with Quorum sensing and Biofilm formation in Mycobacterium tuberculosis.
    Frontiers in Microbiology (in press)
  3. Ahmad E, Hegde SR and Nagaraja V
    Revisiting intrinsic transcription termination in mycobacteria: U-tract downstream of secondary structure is dispensable for termination.
    Biochem Biophys Res Commun. 2019 Nov 20. doi: 10.1016/j.bbrc.2019.11.062.
  4. 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 Virologica 62:68-77
  5. 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 Genetics 2;13(5):e1006754
  6. 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 Systems Biology 8:26
  7. 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. Journal of Biomolecular Structure and Dynamics 31(1):115-24
  8. 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 One 7(3):e33893
  9. 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 Research 21(12):2067-81
  10. Hegde SR, Klimova EY, Mande SC, Medvedeva YA, Makeev VY and Permina EA (2011)
    Using operonic gene pairs to set the threshold correlation coefficient for differentially expressed genes, Biophysics 56(6):1041-42
  11. P Manimaran, Hegde SR and Mande SC (2009)
    Prediction of Conditional Gene Essentiality through Graph theoretical Analysis of genome-wide Functional Linkages, Molecular Biosystems DOI: 10.1039/b905264j
  12. Hegde SR, P Manimaran and Mande SC (2008)
    Dynamic Changes in Protein Functional Linkage Networks Revealed by Integration with Gene Expression Data. PLoS Computational Biology 4: e1000237


Institute of Bioinformatics and Applied Biotechnology
Biotech Park, Electronic City Phase I,
Bengaluru 560100,


080 285 289 00/01/02, extension 119