Functional Genomics and Systems Biology

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 and 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.

Feedback from the 2015 course:

“Very well run course. Professional, competent, and approachable
instructors made the learning environment less formal and facilitated
useful discussions. Course assistants were helpful with labs/analysis.
The research interests of participants were broad, and I was able to
learn new things about other areas.”
“Thanks for making this course such a wonderful experience!”
“Great course great instructors!”
“The hands-on practice in both wet & dry lab are very useful and help
to understand the whole pipeline.”

The programme will include lecture and practical
laboratory/computer-based sessions covering the following topics:

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) cDNA
libraries for the Illumina  MiSeq 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

Guest speakers
Marc-Emmanuel Dumas Imperial College London, UK
Donal O’Carroll University of Edinburgh, UK

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 is subsidised by the Wellcome Genome Campus
Advanced Courses and Scientific Conferences Programme. This is a
residential
course and there is a fee of £1065 towards board and lodging
for non-commercial applicants. Please contact us for the commercial fee.

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

Please note: Applications
must be supported by a
recommendation from a scientific or clinical sponsor (e.g. 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. Applications without a supporting
statement cannot be considered.

Deadlines
Deadline for Applications: Closed

Bursaries
Advanced Courses are subsidised for non-commercial
applicants from anywhere in the world. Additional, limited bursaries are
available (up to 50% of the course fee) and are awarded on merit. If you
would like to apply for a
bursary, please complete the bursary section
of the online application
form.

Please note that both the applicant
and sponsor are required to provide
a justification for the
bursary as part of the application.

Bursary terms and conditions

UK Courses (held at the Wellcome Genome Campus, Hinxton,
Cambridge)
A
limited number of bursaries are available for each course. These are
awarded by the selection committee according to merit. The bursary
covers a maximum of 50% 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 to attend UK
courses.

Overseas Courses (held outside of the UK)
A
limited number of bursaries are available for each course. These are
awarded on merit to cover travel, accommodation and sustenance. The
maximum award for travel (economy class) will be £750.

Bursaries can be applied for as part of the course application form.
Applicants
will be notified of a bursary award along with their place on
the
course, usually within one month of the application deadline. The
decision of the selection committee is
final.