- 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
- 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
Improved site prediction using DWMs (work in progress)
- 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
- Planned for the future: extending the approach of Sigma to
protein sequences and protein-coding DNA sequences.
- Developmental biology
VijayRaghavan's group (NCBS, Bangalore) on mesoderm development
in Drosophila (which substantially motivated the development
demonstrated the extreme complexity of the regulation of the founder
cell determining gene duf (a.k.a. kirre).
- Evolution of centromeres in yeast
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
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