Karthik Raman: Difference between revisions
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[http://serc.iisc.ernet.in/ Supercomputer Education and Research Centre]/[http://physics.iisc.ernet.in/~dichome/ Bioinformatics Centre]<br> | [http://serc.iisc.ernet.in/ Supercomputer Education and Research Centre]/[http://physics.iisc.ernet.in/~dichome/ Bioinformatics Centre]<br> | ||
<font dize=3px>[http://www.iisc.ernet.in/ Indian Institute of Science]</font><br> | <font dize=3px>[http://www.iisc.ernet.in/ Indian Institute of Science]</font><br> | ||
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, [[Chandra:Software and Databases:PathwayAnalyser|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 | 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, [[Chandra:Software and Databases:PathwayAnalyser|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=== | ===Research Interests=== | ||
Revision as of 04:25, 11 January 2006
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
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)
===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.
Blogs
Contact
KARTHIK RAMAN
Graduate Research Student
Bioinformatics Centre
Indian Institute of Science
Bangalore
Karnataka – 560 012
INDIA
Labs:
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
