Functional Genomics and Systems Biology

Course summary

This intensive laboratory and computer-based training course introduces participants to a wide range of post-genome techniques including practical experience in performing RNAi experiments, expression profiling using the latest platforms, yeast 2-hybrid analyses and hands on experience with sample preparation procedures for Illumina high throughput sequencing. 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 resources and systems biology tools, including R, Bioconductor, network analysis (e.g. BioLayout Express3D) 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.
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RNAi has recently emerged as one of the most powerful tools for examining gene function. Participants will carry out a high-throughput RNAi screen in C.elegans and this will illustrate many of the theoretical considerations in designing such large-scale RNAi experiments. Different RNAi methodologies will be discussed both for C. elegans in vivo and RNAi in mammalian cells in culture. We will also illustrate how RNAi can be combined with microarray analysis to identify pathway targets.

Practical guidance will be given in the use of commercial microarray platforms for the analysis of gene expression. This will involve participants working through the labelling of series of RNA samples, and their hybridisation to arrays. Participants will be given training in many aspects of microarray data analysis and interpretation using a range of commercial and academic software tools. Finally, there will be the opportunity to discuss the theoretical considerations for microarray experimental design and the relative merits of different expression profiling platforms, including emerging sequencing technologies.

Next generation sequencing
Labwork will involve the preparation and quality control of directional small, total and polyA RNA libraries for the Illumina HiSeq2000 genome analyser. Raw data will be collected and analysed using sequence alignment methods during the course. Further statistical, differential expression and data mining procedures will be applied.

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.

Computational Systems Biology
An overview and discussion of current bioinformatics resources most relevant to functional genomics investigations will be provided. These will include information on using genome browsers, gene/protein annotation, microarray data repositories, protein-protein interaction data, and pathway analysis. The course will also provide instruction on the 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 (University of Toronto, Canada)
Tom Freeman (The Roslin Institute, 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)

2012 Guest speakers (2013 speakers TBC shortly)

Ido Amit (Weizmann Institute of Science, Israel)
Joshua Levin (Broad Institute of MIT and Harvard, USA)
Bret Pearson (University of Toronto, Canada)
Derek Stemple (Wellcome Trust Sanger Institute, UK)
Julian Knight (Wellcome Trust Centre for Human Genetics, Oxford, UK)
James Watson (European Bioinformatics Institute, Hinxton, UK)

19 Jun - 28 Jun 2013
United Kingdom
meeting website