Karthik Raman

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<!-- *''My page at http://karthikraman.dyndns.org/ is a more current and updated version of this page.'' -->
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__NOTOC__
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I am presently an Assistant Professor at the Department of Biotechnology, at the [http://www.iitm.ac.in/ Indian Institute of Technology Madras].
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==Academic==
==Academic==
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===PhD Thesis [ongoing]===
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===Research Interests===
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'''System Design and Modelling in Drug Discovery'''<br>
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My primary research interests are in computational systems biology, particularly the modelling and simulation of complex systems and networks. Presently, I am quite interested in understanding the design principles of biological systems through multi-scale computational modelling/theoretical studies, and how a knowledge of these principles can be exploited in applications such as synthetic biology. I am also interested in the application of complex network science to various disciplines, in and outside biology.
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My PhD involved the modelling and simulation of (myco)bacterial metabolism, metabolic networks and protein--protein interactions, to identify better drug targets for tuberculosis. I have also modelled of the human immune system and its interaction with mycobacteria. During my post-doc, I have studied the robustness and evolvability of biological systems (TOR signalling), as well as artificial systems (programmable hardware).
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===Post-doctoral Research===
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I completed my post-doctoral research at the [http://www.bioc.unizh.ch/index.php?id=3&L=1 Department of Biochemistry], [http://www.uzh.ch/index_en.html University of Zurich], in the lab of [http://www.bioc.unizh.ch/wagner/ Prof. Andreas Wagner]. My research mainly concerned the analysis of the evolvability and robustness of biological networks, particularly yeast signal transduction networks. I have also looked at the robustness and evolvability of an artificial system, namely programmable hardware.
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===PhD Thesis===
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'''Systems-level Modelling and Simulation of ''Mycobacterium tuberculosis'': Insights for Drug Discovery'''<br>
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(submitted, October 2008)<br>
Research Supervisor: [[Nagasuma Chandra|Dr. Nagasuma Chandra]]<br>
Research Supervisor: [[Nagasuma Chandra|Dr. Nagasuma Chandra]]<br>
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[http://serc.iisc.ernet.in/ Supercomputer Education and Research Centre]/[http://physics.iisc.ernet.in/~dichome/ Bioinformatics Centre]<br>
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[http://serc.iisc.ernet.in/ Supercomputer Education and Research Centre]/[http://physics.iisc.ernet.in/~dichome/ Bioinformatics Centre], [http://www.iisc.ernet.in/ Indian Institute of Science]<br>
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<font dize=3px>[http://www.iisc.ernet.in/ Indian Institute of Science]</font><br>
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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.
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===Research Interests===
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*Systems Biology:Pathway Modelling
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*Protein–Protein interactions
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*''in silico'' drug discovery
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*Structural Bioinformatics
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===Publications===
===Publications===
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*Karthik Raman and Nagasuma Chandra (2011) "Systems Biology of tuberculosis: Insights for drug discovery", In: W. Dubitzky, J Southgate and H. Fuss (editors), In:''Understanding the Dynamics of Biological Systems: Lessons Learned from Integrative Systems Biology'' (Chapter 5, pages 83-110),  Springer '''ISBN 9781441979636'''<br> [http://www.springerlink.com/content/w823q330u8j22302/fulltext.pdf PDF] [http://dx.doi.org/10.1007/978-1-4419-7964-3_5 DOI:10.1007/978-1-4419-7964-3_5]
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*Karthik Raman and Andreas Wagner (2011) "Evolvability and robustness in a complex signalling circuit" ''Molecular BioSystems'' '''7''':1081-1092<br> '''PMID 21225054''' [http://pubs.rsc.org/en/Content/ArticlePDF/2011/MB/C0MB00165A PDF] [http://dx.doi.org/10.1039/C0MB00165A DOI:10.1039/C0MB00165A]
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*Karthik Raman and Andreas Wagner (2011) "The evolvability of programmable hardware" ''Journal of the Royal Society Interface'' '''8''':269-281<br> '''PMID 20534598''' [http://rsif.royalsocietypublishing.org/content/8/55/269.full.pdf PDF] [http://dx.doi.org/10.1098/rsif.2010.0212 DOI:10.1098/rsif.2010.0212]
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*Karthik Raman (2010) "Construction and analysis of protein-protein interaction networks" ''Automated Experimentation'' '''2''':2<br> '''PMID 20334628''' [http://www.aejournal.net/content/pdf/1759-4499-2-2.pdf PDF] [http://dx.doi.org/10.1186/1759-4499-2-2 DOI:10.1186/1759-4499-2-2]
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*Karthik Raman and Nagasuma Chandra (2010) "Systems Biology" ''Resonance'' 15:131--153<br> [http://www.ias.ac.in/resonance/February2010/p131-153.pdf PDF] [http://dx.doi.org/10.1007/s12045-010-0015-7 DOI:10.1007/s12045-010-0015-7]
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*Karthik Raman, Ashwini Gurudas Bhat and Nagasuma Chandra (2010) "A systems perspective of host–pathogen interactions: predicting disease outcome in tuberculosis" ''Molecular BioSystems'' '''6''':516-530 <br> '''PMID 20174680''' [http://www.rsc.org/ej/MB/2010/b912219c.pdf PDF]  [http://dx.doi.org/10.1039/b912129c DOI:10.1039/b912129c]
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*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 <br>'''PMID 19593474''' [http://www.rsc.org/ej/MB/2009/b905817f.pdf PDF] [http://dx.doi.org/10.1039/b905817f DOI:10.1039/b905817f]
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*Karthik Raman, Nagasuma Chandra (2009) "Flux balance analysis of biological systems: applications and challenges " ''Briefings in Bioinformatics'' '''10''':435—449<br>'''PMID 19287049''' [http://dx.doi.org/10.1093/bib/bbp011 DOI:10.1093/bib/bbp011]
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*Karthik Raman, Nagasuma Chandra (2008) "''Mycobacterium tuberculosis'' interactome analysis unravels potential pathways to drug resistance" ''BMC Microbiology'' '''8''':234<br> '''PMID 19105810''' [http://dx.doi.org/10.1186/1471-2180-8-234 DOI:10.1186/1471-2180-8-234]
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*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 <br> '''PMID 19099550''' [http://dx.doi.org/10.1186/1752-0509-2-109 DOI: 10.1186/1752-0509-2-109]
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*Karthik Raman, Yeturu Kalidas and Nagasuma Chandra (2007) "Model Driven Drug Discovery: Principles and Practices", In: Biological Database Modeling, Artech House ISBN 1596932589
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*Ketki Verkhedkar, Karthik Raman, Nagasuma Chandra and Saraswathi Vishveshwara (2007) "Metabolome based reaction graphs of ''M.&nbsp;tuberculosis'' and ''M.&nbsp;leprae'': A comparative network analysis" ''PLoS ONE'' '''2(9)''':e881<br> '''PMID 17849010''' [http://www.plosone.org/article/fetchObjectAttachment.action?representation=PDF&uri=info%3Adoi%2F10.1371%2Fjournal.pone.0000881 PDF] [http://dx.doi.org/10.1371/journal.pone.0000881 DOI: 10.1371/journal.pone.0000881]
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*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. <br> '''PMID 17600834''' [http://www3.interscience.wiley.com/cgi-bin/fulltext/114285245/PDFSTART PDF] [http://dx.doi.org/10.1002/prot.21591 DOI: 10.1002/prot.21591]
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*Karthik Raman, Preethi Rajagopalan and Nagasuma Chandra (2006) "Principles and Practices of Pathway Modelling" ''Current Bioinformatics'' '''1(2)''':147—160<br>[http://bentham.org/cbio/contabs/cbio1-2.htm#3 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<br> '''PMID 16261191''' [http://compbiol.plosjournals.org/perlserv/?request=get-pdf&file=10.1371_journal.pcbi.0010046-S.pdf PDF] [http://dx.doi.org/10.1371%2Fjournal.pcbi.0010046 DOI: 10.1371/journal.pcbi.0010046]
*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<br> '''PMID 16261191''' [http://compbiol.plosjournals.org/perlserv/?request=get-pdf&file=10.1371_journal.pcbi.0010046-S.pdf PDF] [http://dx.doi.org/10.1371%2Fjournal.pcbi.0010046 DOI: 10.1371/journal.pcbi.0010046]
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*Karthik Raman, Preethi Rajagopalan and Nagasuma Chandra (2006) "Principles and Practices of Pathway Modelling" ''Current Bioinformatics'' '''1(2)''':147—160<br>[http://bentham.org/cbio/CurrentIssue.htm#3 Abstract]
 
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*Karthik Raman, Yeturu Kalidas and Nagasuma Chandra (2007, ''In Press'') "Model Driven Drug Discovery: Principles and Practices", In: Biological Database Modeling, Artech House
 
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*Karthik Raman, Preethi Rajagopalan and Nagasuma Chandra (2007) "Hallmarks of Mycolic Acid Biosynthesis: A Comparative Genomics Study" ''Proteins: Structure, Function and Bioinformatics'' '''PMID 17600834''' [http://www3.interscience.wiley.com/cgi-bin/fulltext/114285245/HTMLSTART Full text]
 
===Conferences===
===Conferences===
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*Presentation on “Merging and Visualisation of SBML Models” at the [http://www.sbml.org/workshops/ninth ''9th Systems Biology Markup Language (SBML) Forum''], Heidelberg, Germany  
*Presentation on “Merging and Visualisation of SBML Models” at the [http://www.sbml.org/workshops/ninth ''9th Systems Biology Markup Language (SBML) Forum''], Heidelberg, Germany  
*Presented a review on “DNA Analytical Methods for Detection of Transgenic Organisms” at [http://www.annauniv.edu/ Anna University], Chennai on the event of ''Biotechcellence 2003'', a national-level symposium on biotechnology (2003)
*Presented a review on “DNA Analytical Methods for Detection of Transgenic Organisms” at [http://www.annauniv.edu/ Anna University], Chennai on the event of ''Biotechcellence 2003'', a national-level symposium on biotechnology (2003)
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===Other Interests (mainly reading...)===
 
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<font size=2px>(or what I would have been doing, if not a thesis in systems biology)</font>
 
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* Number Theory – High precision calculations
 
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* Primality Testing and Factorisation algorithms
 
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* Numerical Software (better than [http://mathassist.tripod.com/ MathAssistant]!)
 
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* Bio-mimetic programming e.g. Genetic Algorithms
 
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* Semi-numerical Algorithms (yeah, Knuth vol 2!)
 
==Personal==
==Personal==
===Bio===
===Bio===
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I did my schooling in [http://dav99batch.tripod.com/ DAV Boys Senior Secondary School, Chennai]. I graduated from [http://www.udct.org/ UDCT (University of Mumbai, Department of Chemical Technology)] in 1999, with a bachelor's degree in ''Food Technology and Engineering'' and joined [http://www.iisc.ernet.in 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 [[Nagasuma Chandra|Dr Nagasuma Chandra]] and [http://mbu.iisc.ernet.in/%7Evishgp/ 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.
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I did my schooling in [http://dav99batch.tripod.com/ DAV Boys Senior Secondary School, Chennai]. I graduated from [http://www.udct.org/ UDCT (University of Mumbai, Department of Chemical Technology)] in 1999, with a bachelor's degree in ''Chemical Technology'' and joined [http://www.iisc.ernet.in 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 [[Nagasuma Chandra|Dr Nagasuma Chandra]] and [http://mbu.iisc.ernet.in/%7Evishgp/ 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 involved the study of the evolvability and robustness of biological networks. In April 2011, I joined the [http://biotech.iitm.ac.in/ Department of Biotechnology], [http://www.iitm.ac.in Indian Institute of Technology Madras], as an Assistant Professor.
==Contact==
==Contact==
'''KARTHIK RAMAN'''<br>
'''KARTHIK RAMAN'''<br>
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Graduate Research Student<br>
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BT 104 Bhupat and Jyoti Mehta School of Biosciences<br>
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Bioinformatics Centre<br>
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Indian Institute of Technology Madras<br>
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Indian Institute of Science<br>
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Chennai 600 036<br>
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Bangalore<br>
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Karnataka – 560 012<br>
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INDIA<br>
INDIA<br>
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'''Labs:'''
 
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*[http://ssl.serc.iisc.ernet.in/ SERC Students' Lab (SSL)]
 
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*[[Chandra Lab|Bioinformatics Centre]]
 
'''Contact Numbers:'''
'''Contact Numbers:'''
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*+91-80-22932737 [Ext #303] – SSL
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*+91-44-2257-4139 (BT 104, IIT Madras)
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*+91-80-22932469 [Ext  #24] – Bioinformatics
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'''E-Mail:''' id=karthik AT server=rishi.serc.iisc.ernet.in
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'''Personal Website:''' http://www.bluwiki.org/go/Karthik
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'''Blog:''' http://karthikr.wordpress.com/
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'''E-Mail:''' id=kraman AT server=iitm dot ac dot in<br>
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'''Blog:''' http://karthikr.wordpress.com/<br>
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'''LinkedIn: [http://in.linkedin.com/in/ramankarthik Public Profile]'''<br>
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'''Other websites: [http://stotrasamhita.net/ StotraSamhita]'''

Current revision


I am presently an Assistant Professor at the Department of Biotechnology, at the Indian Institute of Technology Madras.

Academic

Research Interests

My primary research interests are in computational systems biology, particularly the modelling and simulation of complex systems and networks. Presently, I am quite interested in understanding the design principles of biological systems through multi-scale computational modelling/theoretical studies, and how a knowledge of these principles can be exploited in applications such as synthetic biology. I am also interested in the application of complex network science to various disciplines, in and outside biology.

My PhD involved the modelling and simulation of (myco)bacterial metabolism, metabolic networks and protein--protein interactions, to identify better drug targets for tuberculosis. I have also modelled of the human immune system and its interaction with mycobacteria. During my post-doc, I have studied the robustness and evolvability of biological systems (TOR signalling), as well as artificial systems (programmable hardware).

Post-doctoral Research

I completed my post-doctoral research at the Department of Biochemistry, University of Zurich, in the lab of Prof. Andreas Wagner. My research mainly concerned the analysis of the evolvability and robustness of biological networks, particularly yeast signal transduction networks. I have also looked at the robustness and evolvability of an artificial system, namely programmable hardware.

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

Publications

  • Karthik Raman and Nagasuma Chandra (2011) "Systems Biology of tuberculosis: Insights for drug discovery", In: W. Dubitzky, J Southgate and H. Fuss (editors), In:Understanding the Dynamics of Biological Systems: Lessons Learned from Integrative Systems Biology (Chapter 5, pages 83-110), Springer ISBN 9781441979636
    PDF DOI:10.1007/978-1-4419-7964-3_5
  • Karthik Raman and Andreas Wagner (2011) "Evolvability and robustness in a complex signalling circuit" Molecular BioSystems 7:1081-1092
    PMID 21225054 PDF DOI:10.1039/C0MB00165A
  • Karthik Raman and Andreas Wagner (2011) "The evolvability of programmable hardware" Journal of the Royal Society Interface 8:269-281
    PMID 20534598 PDF 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, Ashwini Gurudas Bhat and Nagasuma Chandra (2010) "A systems perspective of host–pathogen interactions: predicting disease outcome in tuberculosis" Molecular BioSystems 6:516-530
    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 Vishveshwara (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

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 involved the study of the evolvability and robustness of biological networks. In April 2011, I joined the Department of Biotechnology, Indian Institute of Technology Madras, as an Assistant Professor.

Contact

KARTHIK RAMAN
BT 104 Bhupat and Jyoti Mehta School of Biosciences
Indian Institute of Technology Madras
Chennai 600 036
INDIA

Contact Numbers:

  • +91-44-2257-4139 (BT 104, IIT Madras)

E-Mail: id=kraman AT server=iitm dot ac dot in
Blog: http://karthikr.wordpress.com/
LinkedIn: Public Profile
Other websites: StotraSamhita

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