Department of Statistics

A z i z     M i t h a n i

I am a DPhil student in the Department of Statistics at University of Oxford under the joint supervision of Prof. Jotun Hein and Dr. Gail Preston since October 2006. I am working on the models of network evolution specifically focusing on dynamics and evolution of nitrogen assimilations in plant pathogenic Pseudomonas.

I am also the Secretary of St Anne's College MCR.

My PhD thesis is focused on analysing the evolution of biological networks. At present I am working on the following two topics.

1. Modelling the evolution of metabolic networks. I have developed a stochastic model for the evolution of metabolic networks that models the evolution as discrete space continuous time Markov process. The model allows addition and deletion of reactions from the network under realistic assumptions and the restriction that only functional metabolisms are allowed.
   

2. Analysing metabolic networks. I have developed the software tool, Rahnuma, written in Java, that enumerates pathways between two or more metabolites and compares an arbitrary number of metabolisms. Rahnuma uses hypergraphs as underlying network representation. It uses deterministic depth-first graph traversal for metabolic pathway prediction.  I have used Rahnuma to analyse metabolic adaptation of plant pathogens belonging to genus Pseudomonas.

I am currently extending my stochastic model to analyse a set of metabolic networks related by a phylogeny. Making proper evolutionary analysis of networks is highly challenging due to the large number of possible networks and even larger number paths between networks. However, due to the increasing number of inferred networks in related organisms, such models are increasingly in demand. If time permits I also hope to apply my methods to other kinds of networks such as protein interaction networks, regulatory networks and signals transduction networks.

• Rahnuma: Hypergraph based tool for metabolic pathway prediction and network comparison. Bioinformatics 2009 25(14):1831-1832, doi: 10.1093/bioinformatics/btp269. Abstract

• A stochastic model for the evolution of metabolic networks with neighbor dependence. Bioinformatics 2009 25(12):1528-1535, doi: 10.1093/bioinformatics/btp262. Abstract

• Rahnuma: Hypergraph based Tool for Analysis and Comparison of Metabolic Pathways, Nitrogen 2007, July 2007. Poster

• Comparative Analysis of Nitrogen Assimilation Pathways in Pseudomonas using Hypergraphs, Nitrogen 2007, July 2007. Talk

• Comparative Analysis of Amino Acid Assimilation Pathways using Hypergraphs, MBPP 2007, September 2007. Talk

• Rahnuma: Hypergraph based Tool for Analysis and Comparison of Metabolic Pathways, American Society for Cell Biology Meeting, December 2007. Poster

• A stochastic model of metabolic network evolution, Network Biology Meeting, August 2008. Talk

Biological and social networks and their evolution is an active area of research in Oxford with comprehensive resources including umbrella of Oxford Centre for Integrative System Biology (OCISB) and Systems Biology Doctoral Training Centre (SysBio-DTC). Some key names working in this area include Tom Snijders, Gesine Reinert and David Fell. Further ideas for research in this and other exciting areas of computational and systems biology can be found on our group page.
 

Department Address:

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

College Address:

St Anne's College
Woodstock Road
Oxford OX2 6HS, UK

 Email: mithani (at) stats (dot) ox (dot) ac (dot) uk