R. Srivatsan and his group use a systems biology approach to develope mathematical models explaining various aspects of autoimmune diseases like Rheumatoid Arthritis. He regularly teaches courses on basic mathematics, biostatistics, systems biology and computer programming to masters’ degree students at IBAB. He also conducts hands-on training programs on the usage of R statistical package for computational biology and data analytics.
Dr. Srivatsan is developing free tutorials on computer languages, statistical methods and algorithms that are useful for creating innovative analysis tools for computational biology. Click here to access the first tutorials to be hosted, concerning ‘R’.
1. Systems biology of Rheumatoid arthritis (RA)
Rheumatoid arthritis is a complex, polygenic autoimmune disease with unknown etiology. The disease is characterized by chronic inflammation and angiogenesis along with bone and cartilage damage. Multiple pathways triggered by pro- and anti-inflammatory cytokines like TNF-alpha, IL1-beta, TGF-beta are responsible for the disease phenotype.
Currently we are developing 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 develop models using mathematical methods like Ordinary Differential Equations (ODE) and network analysis. Simulations are carried out using tools like Matlab, R statistcal package, Cell Designer and Cytoscape.
Two PhD students, Ms. Poulami Dey and Mr. P. Venugopal are involved in this work.
2. Developing algorithms and tools for computational biology
Another area of interest is the development of user-friendly tools for the statistical analysis of data from biological experiments. This work is mostly carried out by MSc students for their student projects. For specific applications, we develop tools that use java for user interface and for implementing statistical analysis. We develop the user interface using Java, and we carry out the statistical analysis using the libraries of the R statistical package.
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
A. Publications in the filed of computational biology, or other areas related to biology:
1. 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)
2. Integrative Analysis of Normal Long Integenic Non-Coding RNAs in Prostate Cancer
Pushpinder Bawa, Sajna Zackaria, Mohit Verma, Saurabh Gupta, R Srivatsan, Bibha Chaudhary and Subhashini Srinivasan.
PLOS ONE, 10(5): e0122143 DOI:10.1371/journal.pone.0122143 (2015)
3. 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, 2, 21–33 (2012).
4. From data repositories to potential biomarkers: application to prostate 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, 102, 1111–1116 (2012)
5. Maintaining patents protecting biologics or small molecular drugs
Ganesan Marimuthu, Sangita Kumari, Muthukrishnakumar Kandasamy, Srivatsan Raghunathan and Gayatri Saberwal
Nature Biotechnology, 30, 50–53 (2012)
6. 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., 7: 647–662 (2008)
B. Publications in the field of astrophysics
1. Observations on muon multiplicity distribution with the GRAPES-2 experiment at Ooty for studies on the mass composition of cosmic rays at PeV energies.
S.K. Gupta, N.V. Gopalakrishnan, A.V. John, D.K. Mohanty, S.D. Morris, K.C. Ravindran, K. Sivaprasad, B.V. Sreekantan, R. Srivatsan and S.C. Tonwar.
Physical Review D 68, 052005 (2003)
2. Optimization of the number of soft X-ray arrays and detectors for the SST-1 tokamak by the tomographic method.
A. K. Chattopadhyay, C.V.S. Rao, and R. Srivatsan.
Review of Scientific Instruments, 74 (4), (2003).
3. Detection and Tracking of IPS disturbances using Interplanetary Scintillation.
Balasubramanian, V., Srivatsan, R., Janardhan, P. and Ananthakrishnan, S.
Bull. Astro. Soc. India, 26, 225 (1998)
4. IPS Observations of the Solar Wind at 327 MHz – A comparison with Ulysses
Janardhan, P., Balasubramanian, V., Ananthakrishnan, S and Srivatsan, R.
Bull. Astr. Soc. India, 24, 645 (1996)
5. On the nature of Compact components of Radio Sources at 327 MHz.
Balasubramanian, V., Janardhan, P. and Srivatsan, R.
Bull. Astr. Soc. India, 24, 829 (1996)
6. An episode of Ultra-high energy radiation from Gamma ray source Geminga: GRAPES I Observations at Ooty during 1984–1987.
S.K. Gupta, B.V. Sreekantan, R. Srivatsan, and S.C. Tonwar.
Physical Review. D. 48, 3463 (1993)
7. Evidence for the time variability of PeV energy flux from Cygnus X-3 : Ooty observations during the period 1984–1987
S.C. Tonwar, S.K. Gupta, M.R. Rajeev, B.V. Sreekantan, and R. Srivatsan.
Astrophysical Journal 390, 273–279 (1992)
8. Detection of Ultra-high energy radiation from Scorpius X-1 : Ooty observations during 1984-1987
S.C. Tonwar, N.V. Gopalakrishnan, S.K. Gupta, M.R. Rajeev, B.V. Sreekantan and R. Srivatsan.
Physical Review Letters. 67, 2248–2251 (1991)
9. New results from Ooty EAS array for cosmic ray sources at PeV energies: CYG X-3, Crab pulsar and SCO X-1.
S.C. Tonwar, S.K. Gupta, N.V. Gopalakrishnan, M.R. Rajeev, R. Srivatsan and B.V. Sreekantan.
Nuclear Physics B (Proc. Suppl.) 14A, 226–234 (1990)
10. Episodic emission from HERCULES X-1 at energies greater than 100 TeV: Observations with Ooty Extensive Air Shower array during 1986.
S.K. Gupta, M.R. Rajeev, B.V. Sreekantan, R. Srivatsan and S.C. Tonwar
Astrophysical Journal, 354, L13–L16 (1990)
11. Evidence for pulsed emission from the Crab Pulsar at PeV energies: Ooty Observations during 1984-87.
S.K. Gupta, M.R. Rajeev, B.V. Sreekantan, R. Srivatsan and S.C. Tonwar.
Astronomy and Astrophysics, 245, 141–144 (1990)
Education and experience
I obtained by PhD in astrophysics from the Tata Institute of Fundamental Research, Mumbai. I continued in astrophysics research at the Institute for Plasma Research, Gandhinagar and the National Centre for Radio Astrophysics, Pune before doing a post-doc in the US. Subsequently I turned to biology and worked at Strand Life Sciences in Bangalore. I moved to IBAB in 2011 and have initiated a unique teaching programme here. A new research programme is now in a consolidation phase.