- Jolt Factorization of Nonlinear Symplectic Maps (Sole investigator). Sponsored by National Board for Higher Mathematics (1996-1999).
- Applications of Lie Algebraic Techniques to Accelerator Physics (Sole Investigator). Sponsored by Department of Science and Technology (1997-2000).
- Establishment of Indian S&T Server and Internet School (Co-Investigator). Sponsored by Department of Scientific and Industrial Research (1998-2001).
- Evolution of specialization and organization in economic systems (Principal Investigator). Sponsored by Department of Science and Technology (2000-2003).
- Funding of Nonlinear Studies Group at IISc (Co-Investigator). Sponsored by Indian Space Research Organisation (2001-2006).
- Programme on analytics and numerics of non-linear systems (Co-Investigator). Sponsored by Defence Research and Development Organisation (2001-2004).
- Causality measures and VAR modelling of time series (Sole Investigator). Sponsored by Defence Research and Development Organisation under the IISc-DRDO Engineering Mathematics Programme (2001-2003).
- A high- resolution study of loess/dunal deposits of Gujarat: Pilot project (Co-Principal Investigator). Sponsored by Department of Science and Technology (2001-2002).
- Kalman filtering and nonlinear causality measures (Sole Investigator). Sponsored by Defence Research and Development Organisation under the Engineering Mathematics Programme (2003-2005).
- Indo-French cyber university project at IISc (jointly with Prof. N. Balakrishnan). Sponsored by Ministry for Human Resources Development (2003- ).
- Enabling infrastructure for projects in computational mathematics (Principal Investigator). Sponsored by Defence Research and Development Organisation (2004-2007).
- Experimental and computational studies on neurobiological systems (Co-Investigator). Sponsored by Department of Biotechnology (2005-08).
- Characterisation of quaternary sediment from lower reaches of Narmada with special reference to climate variability and cultural evolution (Co-investigator).
Sponsored by Department of Science and Technology (2005-2008). - Effect of noise on causality and a new denoising algorithm (Sole Investigator). Sponsored by Defence Research and Development Organisation under the Engineering Mathematics Programme (2005-2006).
- Autonomous navigation using Brain-Machine Interface (Principal Investigator). Sponsored by Defence Research and Development Organisation (2006-2009).
- Block coherence and non-parametric Granger causality (Sole investigator). Sponsored by Defence Research and Development Organisation under the Engineering Mathematics Programme (2006-2009).
- Mathematics Initiative at the Indian Institute of Science (Principal investigator). Sponsored by Defence Research and Development Organisation (2007-2010).
- DST Centre for Mathematical Biology (Principal Investigator). Sponsored by the Department of Science and Technology (2007-2013).
- Indian Institute of Science Mathematics Initiative (Principal Investigator). Sponsored by the Department of Science and Technology (2007-2012).
- DST IRHPA Centre for Neuroscience at IISc (Co-Investigator). Sponsored by the Department of Science and Technology (2010-2015).
- Indo-US Virtual Institute for Mathematical and Statistical Sciences (Principal Coordinator). Sponsored by the Indo-US S&T Forum (2012-2014).
- National Mathematics Initiative at IISc (Convener). Sponsored by the Department of Science and Technology (2012-2017).
- Indo-French Centre for Applied Mathematics (Director). Sponsored by the Department of Science and Technology (2013-2016).
- DST Centre for Mathematical Biology Phase II (Principal Investigator). Sponsored by the Department of Science and Technology (2013-2018).
- Tata Trust Grant on Alzheimer’s Research (Co-Investigator). Sponsored by Tata Trusts (2014-2020).
- Indo-French Centre for Applied Mathematics Phase II (Director). Sponsored by the Department of Science and Technology (2018-2022).