Prof. R Srivatsan

Research Focus Key Words

Systems biology, bio-informatics, Rheumatoid Arthritis

Background

Prof. Srivatsan is a trained experimental physicist working in the field of computational biology. After receiving his PhD in Physics from TIFR, Mumbai, Prof. Srivatsan worked for nearly ten years in the field of Plasma Physics and Astrophysics at premier research institutions. He switched his field of research to bioinformatics in 2006 and worked for five years in the life sciences industry before joining IBAB in 2011.

Education

1. M.Sc  (Physics),  1986,  Bharathiyar University, Coimbatore, India.
2. Ph.D  (Physics),  1995, Tata Institute of Fundamental Research, Mumbai, India.

Professional Experience

1. Faculty Scientist          
   Institute for Bioinformatics and Applied Biotechnology (IBAB)
   (2011 onwards)
2. Project Scientist            
   National Aerospace Laboratory, Bangalore, India  (2009-2010)
3. Senior Scientist             
   Strand Life Sciences,   Bangalore, India (2006-2009)
4. Scientist D                    
   Indian Institute of Astrophysics,  Bangalore, India (2005-2006)
5. Research Associate      
   Norfolk State University, Virginia, USA. (2002-2005)
6. Scientist D                    
   Institute for Plasma Research, Gandhinagar, India (1996-2002)
7. Post-doctoral Fellow   
   National Center for Radio Astrophysics, Pune, India   (1995-1996)
   

Research Interest Profile

We use a systems biology approach to develope models explaining various aspects of autoimmune diseases like Rheumatoid Arthritis. By analyzing microarray and RNAseq data in opensource repositories, we develop mathematical models, including that of the regulation of enzymes by the cytokine signalling network, for a better understanding of the phenomenan associated with the disease. We are also modelling specific aspects of regulation of metabolism under the conditions of rheumatoid arthritis. For model building we use mathematical methods like Ordinary Differential Equations (ODE), network analysis, enrichment analysis and protein interaction networks. Simulations are carried out using tools like Matlab, R statistcal package, Cell Designer and Cytoscape.

Group members

1. Shilpa Harshan (PhD student)
2. Anjali Ranga (IBAB MSc trainee)
3. Aditi Nagaraj (IBAB MSc trainee)
4. Arya Nair (IBAB MSc trainee)
5. Shrithi T.N. (Bangalore Univ MSc trainee)
6. Deekshit Kumar N. (Bangalore Univ MSc trainee)

Publications and Patents
Select research publications are as follows:

1. “Effects of rheumatoid arthritis associated transcriptional changes on osteoclast differentiation network in the synovium”
   Shilpa Harshan, Poulami Dey and Srivatsan Ragunathan
   PeerJ 6:e5743; DOI 10.7717/peerj.5743,  (2018)
2. “A cytokine protein-protein interaction network for identifying key molecules in Rheumatoid Arthritis”
   Venugopal Panga and Srivatsan Raghinathan
   PLOS ONE 13(6): e0199530  (2018)
3. “A Cytokine Signalling Network for theRegulation of Inducible Nitric Oxide Synthase Expression in Rheumatoid Arthritis”
   Poulami Dey, Venugopal Panga,  Srivatsan Raghunathan1
   PLOS ONE 11(9): e0161306  (2016)
4. “An analysis of sponsors/collaborators of 69,160 drug trials registered with ClinicalTrials.gov”
   Keezhupalat, S.M., Naik, A., Gupta, S., Raghunathan, S. and Saberwal, G. PLOS ONE 11(2): e0149416. doi:10.1371/journal.pone.0149416  (2016)
5. “Integrative Analysis of Normal Long Integenic Non-Coding RNAs in Prostate Cancer”.
   Pushpinder Bawa, Sajna Zackaria, Mohit Verma, Saurabh Gupta, R Srivatsan,
   Bibha Chaudhary, Subhashini Srinivasan.
   PLOS ONE | DOI:10.1371/journal.pone.0122143   (2015)
6. “Genome-wide Profiling of RNA splicing in prostate tumor from RNA-seq data using virtual microarrays”.
   Subhashini Srinivasan, Arun H Patil, Mohit Verma, Jonatahn L Bingham and Raghunathan Srivatsan
   Journal of Clinical Bioinformatics, 2012, 2:21
7. “From data repositories to potential biomarkers: application toprostate cancer.”
   Arun H. Patil, Manjari Deshmukh, Neeraj K. Singh, Roli Srivastava, K.Satya Swati, Mohit Verma, Saurabh Gupta, S. Veeresh, R. Srivatsan and Subhashini Srinivasan.
   Current Science, Vol. 102, No.8, 25 April 2012
8. “Maintaining patents protecting biologics or small molecular drugs”.
   Ganesan Marimuthu, Sangita Kumari, Muthukrishnakumar Kandasamy, Srivatsan Raghunathan& Gayatri Saberwal Nature Biotechnology, Volume 30, Number 1, January 2012
9. “A systems biology based integrative framework to enhance the predictivity of in vitro methods for drug- induced liver injury”
   Kalyanasundaram Subramanian, Sowmya Raghavan, Anupama Rajan Bhat, Sonali Das, Jyothi Bajpai Dikshit, Rajeev Kumar, Mandayam  Krishnakumar Narasimha, Rajeshwara Nalini, Rajesh Radhakrishnan  and  R. Srivatsan
   Expert opin. Drug Saf. (2008) 7(6):647-662  

Patent 

I am an inventor on one patent, as follows:

United States patent titled “A method for predicting organ toxicity and a system thereof”

Patent Number : US8645075

(Strand Life Sciences, Bangalore)

Personal Website

I have created a dedicated website www.countbio.com for performing computational biology in R.