Award details

A systems approach to candidate gene and pathway identification

Reference	BBS/E/C/00004941
Principal Investigator / Supervisor	Dr Mansoor Saqi
Co-Investigators / Co-Supervisors
Institution	Rothamsted Research
Department	Rothamsted Research Department
Funding type	Research
Value (£)	972,812
Status	Completed
Type	Institute Project
Start date	01/04/2008
End date	31/03/2012
Duration	48 months

Abstract

This project will develop integrated bioinformatics approaches for identifying new genes and pathways implicated in a range of biological processes relevant to plant pathology and crop science. This work will in part build on earlier research into data integration and graph-based analysis methods that have been used in the development of the ONDEX data integration framework for systems biology applications. Research efforts will be directed in the following areas: 1. Methods and software for integrating new sources of biological information including gene function, biochemical pathway, protein structure, gene network and other information (including that extracted from biological literature through text mining) will be developed in response to requirements derived from the biological applications to be studied. 2. Comparative genome analysis and visualisation methods will be developed to exploit the information from model organisms that have more complete genome and pathway information. These methods will be applied to the prediction of new candidate gene and pathway functions from partially or newly sequenced crop, pest and pathogen genomes. 3. Machine learning approaches (including graphical data analysis, data mining and visualisation) will be developed to extract new biological insights from integrated datasets with the aim of identifying novel interactions at the gene and pathway level for the purpose of predicting new gene function, annotation of emerging genomes and other 'omics resources. 4. Specialist databases of gene function (e.g. PHI-base) will be further developed in collaboration with biologists as resources for the research community and to underpin research in the above areas.

Summary

unavailable

Committee	Closed Committee - Engineering & Biological Systems (EBS)
Research Topics	Crop Science, Plant Science, Systems Biology, Technology and Methods Development
Research Priority	X – Research Priority information not available
Research Initiative	X - not in an Initiative
Funding Scheme	X – not Funded via a specific Funding Scheme

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