User:Karthik/Academic

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Academic Background

• Schooling: DAV Boys' Senior Secondary School, Gopalapuram, Chennai (Central Board of Secondary Education)
• Graduation: University of Mumbai Institute of Chemical Technology, Mumbai (Bachelor of Technology, Food Technology and Engineering)
• Currently a graduate research student at Indian Institute of Science, Bangalore

PhD Thesis [ongoing]

System Design and Modelling in Drug Discovery
Research Supervisor: 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

Publications

• 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

Conferences

• Presented a poster on "Drug Target Identification for Tuberculosis: A Systems Approach" at IBC Asia's International Conference on Drug Discovery to Clinical Trials, Mumbai, India (2005)
• Participated in the 3rd SBML Hackathon at Tokyo, Japan (2005)
• Presented a poster on "A Systems Study of the computational pharmacology of H2 Anti-histamines" at the Young Bioinformaticians' Forum 2004, Oxford, United Kingdom (2004)
• Presentation on "Merging and Visualisation of SBML Models" at the 9th Systems Biology Markup Language (SBML) Forum, Heidelberg, Germany
• Presented a review on "DNA Analytical Methods for Detection of Transgenic Organisms" at Anna University, Chennai on the event of Biotechcellence 2003, a national-level symposium on biotechnology (2003)

Talks etc

Check out Talks.. I've put most of my assignments, talks, reviews and seminars that could be of use to someone else. The topics are quite varied, as are the courses I've done so far, from UDCT to IISc!

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!)