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- Computational regulatory genomics
- PhyloGibbs-MP, a successor
to PhyloGibbs (originally developed with E D Siggia and E van
Nimwegen), an ab initio motif-finder with the following
features:
- Takes account of phylogenetically related sequence and scores it via an evolutionary model
- Self-assesses the significance of its predictions via samplign
- Predicts cis-regulatory modules as well as regulatory sites
- Makes use of "informative priors"
- Outputs GBrowse-compatible annotations
- and more...
- Going beyond the position weight matrix: a simple generalisation of the PWM to include dinucleotides. Improved site prediction using DWMs (work in progress)
- PhyloGibbs-MP, a successor
to PhyloGibbs (originally developed with E D Siggia and E van
Nimwegen), an ab initio motif-finder with the following
features:
- Multiple sequence alignment
- Sigma, an alignment program for intergenic (non-coding) DNA, was developed to meet the needs of PhyloGibbs (in particular, to avoid spurious alignment of unrelated sequence)
- Its successor, Sigma-2, based on an evolutionary model; manuscript, including extensive benchmarks against several other widely-used programs, accepted in BMC Bioinformatics.
- Planned for the future: extending the approach of Sigma to protein sequences and protein-coding DNA sequences.
- Developmental biology
- Collaboration with K VijayRaghavan's group (NCBS, Bangalore) on mesoderm development in Drosophila (which substantially motivated the development of PhyloGibbs-MP). The results demonstrated the extreme complexity of the regulation of the founder cell determining gene duf (a.k.a. kirre).
- Evolution of centromeres in yeast
- Collaboration with Kaustuv Sanyal's group (JNCASR, Bangalore) on centromeres in Candida species. We found that the evolution of centromeric DNA in C. dubliniensis seems to be highly accelerated compared to the rest of the genome, while centromeres in C. albicans and C. dubliniensis appear to have unusual features that puts them in an intermediate category between "point" and "regional" centromeres. Work is in progress on C. tropicalis. This work was a motivated for the improved sequence alignment program Sigma-2.
Older research: exactly solvable systems, and magnetic ordering and frustrated spin systems. (With B Sriram Shastry, my PhD advisor, and Antoine Georges, my first postdoc advisor.) I don't really follow this field any more, but the papers are listed on the publications page.