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Functional Genomics and Systems Biology

17-26 June 2015

Wellcome Trust Genome Campus, Hinxton, Cambridge

Application deadline: 13 February 2015

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 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.

Programme

RNAi
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.

Microarrays
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, low amount and single cell (using microfluidics) cDNAlibraries for the IlluminaMiSeq and HiSeq2500 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.

Protein Interactions
Quantitative mass spectrometry is a central technology in current proteomics. Participants will get an overview of proteomics methods and will conduct affinity purification mass spectrometry (AP-MS) to characterise native protein complexes. This will include experimental training in biochemistry techniques including a mammalian tandem affinity purification method (TAP).Shotgun proteomics will be used to analyse the sample and instruction on analysing mass spectrometry data will be provided. This will be complemented with computational approaches for visualising protein interaction networks and integration with other data sources.

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.

Course instructors

Ioannis Ragoussis (McGill University and Génome Québec Innovation Centre, Canada)
Andrew Fraser (University of Toronto, Canada)
Tom Freeman (The Roslin Institute, Edinburgh, UK)
Anton Enright (European Bioinformatics Institute, Hinxton, UK)
Jyoti Choudhary (Wellcome Trust Sanger Institute, Hinxton, UK)

Confirmed guest speakers

Bernd Bodenmiller (Institute of Molecular Biology, University of Zurich, Switzerland)
Amy Caudy (Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Canada)
Andreas Heger (MRC Functional Genomics Unit, University of Oxford, UK)

Feedback from the 2014 course

“This has been a fantastic course! Thank you very much! :) The knowledge gained during the last week has changed the way I think about my research plans and I now feel equipped to enter the world of functional genomics!”
“I am very thankful to wellcome trust and instructors for such a nice course. This training is going to help me a lot during my Phd”
“I could have not expected anything better. Thank you to all of you!”
“I was very nervous about attending this course as it is so intensive, but the support and knowledge of the trainers and assistants was fantastic. There was also a good mix of dry and wet lab experience”

How to apply

Prerequisites
Applicants should be postdoctoral scientists, senior PhD students or clinician scientists engaged in relevant research. Applicants with molecular biology and/or some cell culture experience will be particularly welcome.

Cost
The course tuition fees are subsidised by The Wellcome Trust for scientists based in academic institutions from anywhere in the world. This is a residential course and there is a fee of £1045 towards board and lodging for non-commercial applicants. The fee for commercial applicants is £6300.

Bursaries
Limited bursaries are available for non-commercial applicants (up to 50% of the course fee) and are subject to open competition. If you would like to apply for a bursary, please complete the bursary section of the online application form (see below for application process).

Applications
Application forms for this course can now be completed online. If you have any problems with the online application process, please email us.

Please note: Applications must be supported by a recommendation from a scientific sponsor. This can be your supervisor or head of department. A request for a supporting statement will be sent to your nominated sponsor automatically during the application process. Applicants must ensure that their sponsor provides this supporting statement by the application deadline.

Deadlines
Application deadline: 13 February 2015.

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