Karthik Raman

Academic

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

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
• Karthik Raman, Preethi Rajagopalan and Nagasuma Chandra (2006) "Principles and Practices of Pathway Modelling" Current Bioinformatics 1(2):147—160
  Abstract
• Karthik Raman, Yeturu Kalidas and Nagasuma Chandra (2007, In Press) "Model Driven Drug Discovery: Principles and Practices", In: Biological Database Modeling, Artech House
• 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, In Press) "Metabolome based reaction graphs of M. tuberculosis and M. leprae: A comparative network analysis" PLoS ONE

Conferences

• Presentation on "targetTB: A drug target validation tool for tuberculosis" at the conference on Computational Insights into Biological Systems, Bangalore, India (2006)
• Presented a poster on "PathwayAnalyser: A Systems Biology Tool for Flux Analysis of Metabolic Pathways" at the 5th International Conference on Bioinformatics, New Delhi, India (2006)
• Presentation on "Flux Annotations in SBML" at the 11th Systems Biology Markup Language (SBML) Forum, Tokyo, Japan (2006)
• Presentation on "Pathway Analyser -- for FBA/MoMA analyses of metabolic pathways" at the 11th Systems Biology Markup Language (SBML) Forum, Tokyo, Japan (2006)
• Presented a poster on "Protein--protein influences in Saccharomyces cerevisiae" at the 7th International Conference on Systems Biology, Yokohama, Japan (2006)
• 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)

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!)

Personal

Bio

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.

Contact

KARTHIK RAMAN
Graduate Research Student
Bioinformatics Centre
Indian Institute of Science
Bangalore
Karnataka – 560 012
INDIA

Labs:

• SERC Students' Lab (SSL)
• Bioinformatics Centre

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/