Department of Statistics

R a h u l     S a t i j a

I am a DPhil student in the Department of Statistics at University of Oxford under the joint supervision of Prof. Jotun Hein and Dr. Lior Pachter. My work focuses on using probabalistic alignment methods to improve the quality of alignment in cis-regulatory regions while simultaneously annotating putative regulatory elements, such as transcription factor binding sites.

1. Improving and annotating multiple alignments
   We are currently designing a multiple alignment software package which integrates experimental information in order to improve the alignment accuracy in cis-regulatory regions.  

2. Combining Statistical Alignment and Phylogenetic Footprinting
   Alignment-based phylogenetic footprinting is a popular and effective comparative genomics technique for detecting conserved elements in multiple genomes. While previous approaches assume a single precalculated alignment in the footprinting analysis, we have developed a method that performs both analyses simultaneously. As a result, our conserved element predictions are robust to alignment error and uncertainty. Our method is implemented in the Java software package BigFoot and is described in the publications listed below.
   
   R. Satija, I. Miklos, A. Novak, R. Lyngsoe and J. Hein. BigFoot: Bayesian Alignment and Phylogenetic Footprinting with MCMC. BMC Evolutionary Biology. In Press.
   
   R. Satija, L. Pachter and J. Hein. Combining statistical alignment and phylogenetic footprinting to detect regulatory elements. Bioinformatics (2008)
   

3. Genome-wide prediction of conserved elements
   We are currently implementing a combined alignment and footprinting tool to simultaneously re-align full genomes and output a predicted list of conserved elements.
   
   

Department Address:

Department of Statistics
1 South Parks Road
Oxford OX1 3TG, UK
Tel: +44 1865 285365
Fax: +44 1865 272595

College Address:

Balliol College
Broad Street
Oxford OX1 3BJ, UK

 Email: satija (at) stats.ox.ac.uk