- My page at Chandra Lab, IISc is a more current and updated version of this page.
I am presently pursuing my post-doctoral research at the Department of Biochemistry, University of Zurich, in the lab of Prof. Andreas Wagner. My research revolves around the analysis of the evolvability and robustness of biological networks, particularly yeast signal transduction networks.
Systems-level Modelling and Simulation of Mycobacterium tuberculosis: Insights for Drug Discovery
(submitted, October 2008)
Research Supervisor: Dr. Nagasuma Chandra
Supercomputer Education and Research Centre/Bioinformatics Centre, Indian Institute of Science
My basic research interests are in the modelling and simulation of complex systems. My PhD basically revolves around the modelling and simulation of bacterial metabolism and metabolic networks. Lately, I have been engaged in the modelling of the human immune system and its interaction with mycobacteria. In the long run, I would like to see how the improved understanding of biological systems through modelling and simulation can lead to newer (non-classical) computational paradigms.
- 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
- Karthik Raman, Nagasuma Chandra (2008) "Mycobacterium tuberculosis interactome analysis unravels potential pathways to drug resistance" BMC Microbiology 8:230 DOI:10.1186/1471-2180-8-234
- Karthik Raman, Yeturu Kalidas and Nagasuma Chandra (2008) "targetTB: A target identification pipeline for Mycobacterium tuberculosis through an interactome, reactome and genome-scale structural analysis" BMC Systems Biology 2:109 PMID 19099550 DOI: 10.1186/1752-0509-2-109
- 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!)
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 Chemical Technology and joined IISc in 2003, for a Masters in Computational Science. In 2005, I successfully applied for an upgrade to the PhD programme, to pursue a PhD thesis in Systems Biology, with Dr Nagasuma Chandra and Prof Saraswathi Vishveshwara as my advisors. I submitted my PhD thesis in October 2008, and moved to the lab of Prof. Andreas Wagner, Department of Biochemistry, University of Zurich, for a postdoc. My post-doctoral research involves the study of the evolvability and robustness of biological networks.
Department of Biochemistry, Computer Biology and Bioinformatics
University of Zurich (Irchel Campus)
- +41-44-635-61-50 (Y27 J49, Irchel campus)
E-Mail: id=k.raman AT server=bioc dot unizh dot ch