Karthik Raman

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PhD Thesis [ongoing]

System Design and Modelling in Drug Discovery
Research Supervisor: Dr. Nagasuma Chandra
Supercomputer Education and Research Centre/Bioinformatics Centre
Indian Institute of Science
Involves the modelling and simulation of biological systems, for the design of better drugs and to achieve a better understanding of the biology of disease. Constructed an in silico model of the mycolic acid pathway in Mycobacterium tuberculosis and performed Flux Balance Analysis (FBA) and Minimisation of Metabolic Adjustment (MoMA) analysis on the model. Possible new targets for anti-tubercular drugs were also identified. A tool, PathwayAnalyser, for the analysis of metabolic pathways by FBA/MoMA was developed, based on open-source optimisation libraries. Further, a comprehensive phylogenetic profiling of the mycolic acid pathway proteins against over 250 completed genomes was carried out, yielding further insights into functional linkages between proteins. Analysis of protein-protein interactions through metabolic pathways is also underway.

Research Interests

  • Systems Biology:Pathway Modelling
  • Protein–Protein interactions
  • in silico drug discovery
  • Structural Bioinformatics


  • Karthik Raman, Preethi Rajagopalan and Nagasuma Chandra (2005) "Flux Balance Analysis of Mycobacterium tuberculosis: targets for anti-tubercular drugs" PLoS Computational Biology 1(5):e46
    PMID 16261191 PDF DOI: 10.1371/journal.pcbi.0010046
  • Karthik Raman, Preethi Rajagopalan and Nagasuma Chandra (2006) "Principles and Practices of Pathway Modelling" Current Bioinformatics 1(2):147—160
  • Karthik Raman, Preethi Rajagopalan and Nagasuma Chandra (2007) "Hallmarks of Mycolic Acid Biosynthesis: A Comparative Genomics Study" Proteins: Structure, Function and Bioinformatics 69(2):358–368.
    PMID 17600834 PDF DOI: 10.1002/prot.21591
  • Ketki Verkhedkar, Karthik Raman, Nagasuma Chandra and Saraswathi Visheveshwara (2007) "Metabolome based reaction graphs of M. tuberculosis and M. leprae: A comparative network analysis" PLoS ONE 2(9):e881
    PMID 17849010 PDF DOI: 10.1371/journal.pone.0000881
  • Karthik Raman, Yeturu Kalidas and Nagasuma Chandra (2007) "Model Driven Drug Discovery: Principles and Practices", In: Biological Database Modeling, Artech House ISBN 1596932589


Other Interests (mainly reading...)

(or what I would have been doing, if not a thesis in systems biology)

  • Number Theory – High precision calculations
  • Primality Testing and Factorisation algorithms
  • Numerical Software (better than MathAssistant!)
  • Bio-mimetic programming e.g. Genetic Algorithms
  • Semi-numerical Algorithms (yeah, Knuth vol 2!)



I did my schooling in DAV Boys Senior Secondary School, Chennai. I graduated from UDCT (University of Mumbai, Department of Chemical Technology) in 1999, with a bachelor's degree in Food Technology and Engineering and joined IISc in 2003, for a Masters in Computational Science. In 2005, I successfully applied for an upgrade to the PhD programme, and I am now pursuing my PhD in Systems Biology, with Dr Nagasuma Chandra and Prof Saraswathi Vishveshwara as my advisors. We work on the modelling of microbial systems, particularly in relation to disease and are interested in identifying possible new targets for drug design, based on metabolic analysis.


Graduate Research Student
Bioinformatics Centre
Indian Institute of Science
Karnataka – 560 012


Contact Numbers:

  • +91-80-22932737 [Ext #303] – SSL
  • +91-80-22932469 [Ext #24] – Bioinformatics

E-Mail: id=karthik AT server=rishi.serc.iisc.ernet.in

Personal Website: http://www.bluwiki.org/go/Karthik

Blog: http://karthikr.wordpress.com/