Functional Genomics and Systems Biology

This intensive laboratory and computer-based training course introduces participants to genome-wide analysis of gene function, including hands-on experience in performing RNAi, expression profiling using different platforms and yeast 2-hybrid analyses.

Practical demonstrations of the latest Solexa high throughput sequencing techniques applied on cDNA sequencing will also be included in the programme. Laboratory work will be complemented by training in state-of-the-art approaches to data analysis and interpretation through the use of a range of bioinformatics and systems biology tools, including R, Bioconductor, GeneSpring, network analysis and pathway modelling. Particular emphasis will be placed upon the integration of complementary approaches to ask specific biological questions.

The course will include seminars by distinguished international speakers who will present cutting-edge research in functional genomics and systems biology.

Programme
RNAi
RNAi has recently emerged as one of the most powerful tools for examining gene function. Different RNAi technologies will be compared both for RNAi in mammalian cells in culture and in C. elegans in vivo. Participants will carry out a high-throughput RNAi screen, and this will illustrate many of the theoretical considerations in designing such large-scale RNAi experiments. We will also illustrate how RNAi can be combined with microarray analysis to identify pathway targets.

Expression profiling
Practical guidance will be given in the use of commercial (e.g. Affymetrix and Illumina) and spotted oligo microarray platforms for the analysis of gene expression including miRNAs.This will involve the use of different RNA and miRNA labelling strategies, hybridisation and image analysis.Participants will be given training in aspects of microarray data analysis and interpretation using a range of commercial and academic software tools.

Practical instruction will also include microarray and RNAi data validation by quantitative PCR methods.Finally, there will be the opportunity to discuss the theoretical considerations for microarray fabrication, experimental design and the relative merits of different expression profiling platforms, including emerging technologies.

Yeast two-hybrid analysis
Yeast two-hybrid analysis will be used as an approach to identifying novel protein-protein interactions. Experiments will include the construction of baits, library screening, and analysis of clones to minimise artefacts.

Bioinformatics
This will provide an overview and discussion of current bioinformatics resources most relevant to functional genomics investigations.These will include microarray data storage and standards, genome browsers, gene/protein annotation and pathway analysis.

Systems biology
The course will cover integration of data into interaction and regulatory networks and systems biology approaches to mining and modelling of these data.

Informal tutorials from academic groups and commercial organisations will complement the laboratory sessions.

Course instructors
Andrew Fraser (The Wellcome Trust Sanger Institute, Hinxton, UK)
Tom Freeman (Division of Pathway Medicine, Edinburgh, UK)
David Markie (Dunedin School of Medicine, New Zealand)
Ioannis Ragoussis (Wellcome Trust Centre for Human Genetics, Oxford, UK)
Anton Enright (European Bioinformatics Institute, Hinxton, UK)

Guest speakers
Eran Segal (Weizmann Institute of Science, Israel)
Rickard Sandberg (Karolinska Institute, Sweden)
Chris Ponting (MRC Functional Genomics Unit, Oxford, UK)

Cost
This is a residential course, without exception, and there is a fee of £975 towards board and lodging for academic applicants. The fee for commercial (non-academic) applicants is £5725. The course tuition fees are subsidised by The Wellcome Trust for scientists based in academic institutions from anywhere in the world.

Bursaries
Limited bursaries are available for academics (50 per cent of fee) and are subject to open competition.

Applications
Applicants will be required to complete an application form containing their CV together with a 300-word outline of the relevance of the course to their research. Please note that documentation supporting their application will be required from the applicant's supervisor/head of department.

Bursaries for Wellcome Trust Advanced Courses
The Wellcome Trust subsidises all courses and workshops, so there are no tuition fees. The ‘course fee' for the UK courses (held at Hinxton) covers on-site accommodation and food for the duration of the course. Bursaries are available to assist with UK course fees, but not travel costs. We are committed to building scientific capacity in developing countries and are expanding the number of courses and workshops run outside of the UK (‘overseas' courses). There is no fee for these courses and bursaries are available for travel, sustenance and accommodation. Please see below for full details.

UK Courses (held at the Wellcome Trust Genome Campus in Hinxton)
A limited number of bursaries are available for each course. These are awarded by the selection committee according to merit. The bursary usually covers 50 per cent of the course fee, though in exceptional circumstances an application for the total course fee may be considered. Where there are many bursary applications, the selection committee may issue smaller amounts. We cannot assist with travel costs. All bursary requests to attend UK courses must be accompanied by a bursary application form. This must be completed and signed by your scientific sponsor (supervisor or head of department) and include justification for the bursary. Applicants will be notified of a bursary award along with their place on the course, usually within one month of the application deadline. We will reject incomplete applications. Both the application form and sponsor's letter must be received before the application deadline. The decision of the selection committee is final.

Overseas courses (held outside the UK)
A number of bursaries are available for each overseas course. These are awarded by the selection committee according to merit. There is no course fee.The bursary will cover travel, accommodation and sustenance. The maximum award for travel (in economy/second class) will be £750. All likely travel costs must be detailed in the overseas bursary application form, which must accompany all bursary requests for courses held outside of the UK. We will notify you of the chosen hotel and sustenance award if successful. The selection committee may judge that a partial award should be granted. We will reject incomplete applications. Both the application form and sponsor's letter must be received before the application deadline.