Projects
Identification of transcription factor binding sites;
Advisor: Dr. Raj Bhatnagar
Numerous methods exists for de-novo indentification of TFBS. However, no method
works well with mammalian genomes where the transcription regulatory networks
are more complicated. We are developing an efficient search technique coupled
with powerful statistical measures.
Identification of co-factors of transcription factors;
Collaborator: Dr. Anil Jegga
Most of the transcription factors work in concert with other transcription
factors. Searching for these co-factors in the neighborhood of putative
binding sites gives more confidence in the prediction of novel sites.
Further, it allows one to understand the complex mechanism by which
transcription factors interact to selectively regulte transcription.
Analysis of transcriptional mechanism of miRNA;
Collaborator: Dr. Anil Jegga
microRNA are key pieces in the jigsaw puzzle of the gene regulatory system. Very
small in size (21-23 nucleotides), they provide post-transcriptional control
of gene regulation. They have been discovered relatively recently; the scope
of their role is yet to be fully understood.
Identification of synteny and analysis of genome rearrangement;
Collaborator: Dr. Jarek Meller
The evolutionary relatedness of two species may be measured by calculating
the relative perturbation of order of synteny blocks (blocks of conserved gene
order). However, the process of identification of synteny is highly sensitive
to the choie of parameters. We are developing tools for assessing
the role of parameters as well as proposing stable measures for genome
rearrangement.
Mining maximal bicliques with bias;
Collaborator: Barrington Young
Bipartitie graphs are an intrinsic part of a wide variety of problems. In such
cases, the maximal bicliques brings out useful relationships in the data. We
have developed an algorithm for mining maximal bicliques which works better
than all the current algorithms. Further, our algorithm may only discover the
bicliques that meet users specified bias.
