Dr Chris Needham, Research Fellow, School of Computing, University of Leeds

I am an RCUK Research Fellow, working on various tasks related to computational modelling of biological systems. I have a particular interest in modelling gene regulatory networks from microarray data.

I am part of the BioSystems research group in the School of Computing and work closely with the Bioinformatics group in the Faculty of Biological Sciences. I am involved in the new Leeds Biomedical and Health Research Centre (BHRC) and cross-displinary research across the University, in particular Math-Biology (see the MathBiol wiki for on campus users - details of the monthly seminar programme and other activities).

Learning gene regulatory networks

Gene regulatory networks govern the functional development and biological processes of cells in all organisms. Genes regulate each other as part of a complex system, of which it is vitally important to gain an understanding. For example, discovery of the complete gene regulatory networks in humans would allow the identification of genes which cause disease, and could be used for drug discovery to identify genes interacting with compounds of interest. Similarly in plants knowledge of the gene regulatory networks would allow the development of stress (drought/salt/temperature) resistant crops. MORE >>

Information about other Bioinformatics work undertaken can be found on the protein function prediction page.

I am part of a White Rose Network MICROSYST - looking at the systems biology of bacterial adaptations to stress.

Machine Learning

I have a strong interest in Machine Learning, Artifical Intelligence and Statistics and their application to Biology. I have a Computer Vision background and am part of the Vision group. I gave a tutorial at ISMB2006 on Bayesian networks which developed into a PLoS Education article:

Needham, C J; Bradford, J R; Bulpitt, A J; Westhead, D R. A Primer on Learning in Bayesian Networks for Computational Biology. PLoS Computational Biology, vol. 3, pp. e129. 2007. doi:10.1371/journal.pcbi.0030129

Collaborations, studentships, visitors and outreach

I am actively looking for Biologists to collaborate with, particularly to reverse engineer gene regulatory networks from dynamic time series data. I am happy to hear and talk to prospective PhD students interested in this area, and would welcome overseas visitors to Leeds to work with for a week/month (funding opportunities exist to support this).

Earlier research activities

I worked on a BBSRC E-Science project Protein function prediction and classification using uncertainty, which aimed to investigate the use of Bayesian networks to integrate information, express relationships and make inferences or predictions on biological problems, motivated by data generation in genomics and proteomics.

In my first post-doc position, I undertook research as part of the CogVis Project to study the design of Cognitive Vision Systems. The system developed to learn protocols from perceptual observations won the BCS Machine Intelligence Prize.

Previous PhD research within the School was undertaken in the Computer Vision Group to automatically track and model the behaviour of sports players during a game. Details can be found on his thesis overview page: Tracking and modelling team game interactions. I have also worked with ProZone Ltd. who specialise in Football Match Analysis.

Publications

A dynamically generated up to date list of publications is available.

Personal

Guides and stuff

A Camera Calibration example using the Tsai Camera Calibration software, and example software (TsaiCal C++ Class) allowing multiple cameras to be used in an application. A brief guide to using our video capture machines, making a DVD, the hi-res screen, Matlab, and the Matlab compiler. Example programs to get to grips with pointers in C++. A clustering/vector quantization example. Fitting Gaussians to data. Online Error Calculations for binary classifiers.

Contact Details

email:       chrisn@comp.leeds.ac.uk
tel:            +44 113 343 5767
fax:           +44 113 343 5457
room:        7.23 E C Stoner
address:   School of Computing, The University of Leeds, Leeds, LS2 9JT