Karthik Raman

• My page at http://karthikraman.dyndns.org/ is a more current and updated version of this page.

Academic

Post-doctoral Research

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.

PhD Thesis

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

Research Interests

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.

Publications

• Karthik Raman and Andreas Wagner (2010) "The evolvability of programmable hardware" Journal of the Royal Society Interface 7:In press
  PMID 20534598 DOI:10.1098/rsif.2010.0212
• Karthik Raman (2010) "Construction and analysis of protein-protein interaction networks" Automated Experimentation 2:2
  PMID 20334628 PDF DOI:10.1186/1759-4499-2-2
• Karthik Raman and Nagasuma Chandra (2010) "Systems Biology" Resonance 15:131--153
  PDF DOI:10.1007/s12045-010-0015-7
• Karthik Raman and Nagasuma Chandra (2010) "Systems Biology of tuberculosis: Insights for drug discovery", In: W. Dubitzky, J Southgate and H. Fuss (editors), Understanding the Dynamics of Biological Systems: Lessons Learned from Integrative Systems Biology, Springer (to appear)
• Karthik Raman, Ashwini Gurudas Bhat and Nagasuma Chandra (2010) "A systems perspective of host–pathogen interactions: predicting disease outcome in tuberculosis" Molecular BioSystems 6:1740-1751
  PMID 20174680 PDF DOI:10.1039/b912129c
• Karthik Raman, Rohit Vashisht and Nagasuma Chandra (2009) "Strategies for efficient disruption of metabolism in Mycobacterium tuberculosis from network analysis" Molecular BioSystems 5:1740-1751
  PMID 19593474 PDF DOI:10.1039/b905817f
• Karthik Raman, Nagasuma Chandra (2009) "Flux balance analysis of biological systems: applications and challenges " Briefings in Bioinformatics 10:435—449
  PMID 19287049 DOI:10.1093/bib/bbp011
• Karthik Raman, Nagasuma Chandra (2008) "Mycobacterium tuberculosis interactome analysis unravels potential pathways to drug resistance" BMC Microbiology 8:234
  PMID 19105810 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
• Karthik Raman, Yeturu Kalidas and Nagasuma Chandra (2007) "Model Driven Drug Discovery: Principles and Practices", In: Biological Database Modeling, Artech House ISBN 1596932589
• 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, 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
• Karthik Raman, Preethi Rajagopalan and Nagasuma Chandra (2006) "Principles and Practices of Pathway Modelling" Current Bioinformatics 1(2):147—160
  Abstract
• 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

• 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)

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 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.

Contact

KARTHIK RAMAN
Y27 J49
Department of Biochemistry, Computer Biology and Bioinformatics
190 Winterthurerstrasse
University of Zurich (Irchel Campus)
CH-8057
Switzerland

Contact Numbers:

• +41-44-635-61-50 (Y27 J49, Irchel campus)

E-Mail: id=k.raman AT server=bioc dot unizh dot ch
Blog: http://karthikr.wordpress.com/