Joint EMBL-EBI Wellcome Trust Advanced Course on Computational Molecular Evolution

Date:

 Monday 13 - Friday 24 April 2015

Venue: 

European Bioinformatics Institute (EMBL-EBI) - Wellcome Genome Campus, Hinxton, Cambridge,  CB10 1SD, United Kingdom

Application deadline: 

Friday 14 November 2014

Participation: 

Open application with selection

Contact: 

Yvonne Thornton

Registration fee: 

£1625

Registration closed

Overview

This 2-week advanced course aims to provide graduate and postgraduate researchers with the theoretical knowledge and practical skills to carry out molecular evolutionary analyses on sequence data.

The need for effective and informed analysis of biological sequence data is increasing with the explosive growth of biological sequence databases. A molecular evolutionary framework is central to many Bioinformatics approaches used in these analyses, e.g. de novo gene finding from genomic sequences.

Additionally, explicit use of molecular evolutionary and phylogenetic analyses provide important insights in their own right, e.g. analysis of adaptive evolution in viruses providing clues to their interaction with host immune systems.

This course will offer a unique opportunity for direct interaction with some of the world-leading scientists and authors of famous analysis tools in evolutionary bioinformatics (John Huelsenbeck, Olivier Gascuel, Nick Goldman, Bruce Rannala, Alexandros Stamatakis, Ziheng Yang, etc).

Audience

Preference will be given to applicants who:

  • are doctoral candidates in the early to middle stages of their thesis research
  • already have some familiarity with phylogenetic methods (i.e. have already used some of the relevant tools)
  • have already collected/assembled molecular sequence datasets to analyze in their work
  • have experience working in a Unix/Linux command-line environment

Syllabus, tools and resources

During this course you will learn about: 

  • Data retrieval and assembly
  • Next Generation Sequencing technologies*
  • Alignment techniques
  • Phylogeny reconstruction
  • Hypothesis testing
  • Analysis of selection
  • Analysis of divergence times
  • Population genetics approaches
  • Parallel cothiputing

The course will cover sessions on analysis of both protein and nucleotide sequences, including NGS data.

*Please note: The course focuses on NGS analyses for molecular evolution and does not include tutorials on the traditional DNA-seq or RNA-seq data processing (QC, read mapping, SNP calling, assembly etc).

Outcomes

After this course you should be able to:
  • Identify and retrieve molecular sequence data
  • Compare methods for molecular evolutionary analyses, and their strengths and weaknesses
  • Construct hypotheses and apply appropriate tests to answer evolutionary questions
  • Discuss some major challenges and developments in the field

Programme

Time Topic Trainer
Day 1 - Monday 13th April 
12:30 Registration and Lunch  
13:30 An introduction and overview of the course  Laura Emery 
14:00 How to interpret molecular phylogenetic trees and sequence alignments Aidan Budd, Adrian Friday and Laura Emery   
15:15  Tea/coffee break
15:45 How to interpret molecular phylogenetic trees and sequence alignments Aidan Budd, Adrian Friday and Laura Emery  
17:30 Tea/coffee break 
18:00 How to interpret molecular phylogenetic trees and sequence alignments Aidan Budd, Adrian Friday and Laura Emery  
19:30 Dinner 
Day 2 - Tuesday 14th April 
07:30 Breakfast  
08:30 How to interpret molecular phylogenetic trees and sequence alignments  Aidan Budd, Adrian Friday and Laura Emery  
10:15 Tea/coffee break 
10:45 How to interpret molecular phylogenetic trees and sequence alignments  Aidan Budd, Adrian Friday and Laura Emery 
12:30 Lunch 
13:30 Dataset Assembly & sequence alignment  Stephen Smith and Ben Redelings  
15:15 Tea/coffee break 
15:45 Dataset Assembly & sequence alignment  Stephen Smith and Ben Redelings 
17:30 Tea/coffee break 
18:00 Keynote lecture 1 Martin Embley 
19:00 Break 
19:30 Dinner 
Day 3 - Wednesday 15th April 
07:30 Breakfast  
08:30 Dataset Assembly & sequence alignment  Stephen Smith and Ben Redelings  
10:15 Tea/coffee break 
10:45 Dataset Assembly & sequence alignment  Stephen Smith and Ben Redelings   
12:30 Lunch 
13:30  Dataset Assembly & sequence alignment  Stephen Smith and Ben Redelings   
15:15 Tea/coffee break 
15:45 Dataset Assembly & sequence alignment  Stephen Smith and Ben Redelings   
17:30 Tea/coffee break
18:00 Practical   
19:30 Dnner 
Day 4 - Thursday 16th April 
07:30 Breakfast 
08:30 An introduction to NGS technologies  Adam Leache and Alexandros Stamatakis  
10:15 Tea/coffee break 
10:45 An introduction to NGS technologies  Adam Leache and Alexandros Stamatakis   
11:00 Phylogeny-reconstruction methods Oliver Gascuel, Brian Moore and Maria Anisimova
12:30  Lunch 
13:30  Fre time/ Optional tour of sequencing centre    
15:15 Tea/coffee break 
15:45 Phylogeny-reconstruction methods Oliver Gascuel, Brian Moore and Maria Anisimova 
17:30 Tea/coffee break  
18:00 Practical  
19:30 Dinner 
Day 5 - Friday 17th April 
07:30 Breakfast  
08:30 Phylogeny-reconstruction methods Oliver Gascuel, Brian Moore and Maria Anisimova  
10:15 Tea/coffee break 
10:45 Phylogeny-reconstruction methods Oliver Gascuel, Brian Moore and Maria Anisimova  
12:30  Lunch 
13:30  Phylogeny-reconstruction methods Oliver Gascuel, Brian Moore and Maria Anisimova  
15:15 Tea/coffee break 
15:45 Phylogeny-reconstruction methods Oliver Gascuel, Brian Moore and Maria Anisimova  
17:30 Tea/coffee break 
18:00 Practical  
19:30 Dinner 
Day 6 - Saturday 18th April 
07:30 Breakfast  
08:30 Parallel computing phylogenetics  Alexis Stamatakis
10:15 Tea break
10:45 Parallel computing phylogenetics Alexis Stamatakis
12:30 Bus to Cambridge
19:00 Bus back to campus
19:30 Dinner
Day 7 - Sunday 19th April 
07:30 Breakfast  
08:30 Phylogeny-reconstruction methods Oliver Gascuel, Brian Moore and Maria Anisimova  
10:15 Tea/coffee break 
10:45 Phylogeny-reconstruction methods Oliver Gascuel, Brian Moore and Maria Anisimova  
12:30  Lunch 
13:30  Phylogeny-reconstruction methods Oliver Gascuel, Brian Moore and Maria Anisimova  
15:15 Tea/coffee break 
15:45 Phylogeny-reconstruction methods Oliver Gascuel, Brian Moore and Maria Anisimova  
17:30 Tea/coffee break 
18:00 Practical  
19:30 Dinner 
Day 8 - Monday 20th April 
07:30 Breakfast  
08:30 Hypothesis testing in phylogenetics Maria Anisimova, Asid Tamuri
10:15 Tea/coffee break 
10:45 Hypothesis testing in phylogenetics Maria Anisimova, Asid Tamuri
12:30  Lunch 
13:30  Keynote Lecture 3 John Huelsenbeck
15:00 Free time
19:30 Dinner 
Day 9 -Tuesday 21st April 
07:30 Breakfast  
08:30 Hypothesis testing in phylogenetics Maria Anisimova and Asif Tamuri   
10:15 Tea/coffee break 
10:45 Hypothesis testing in phylogenetics Maria Anisimova and Asif Tamuri     
12:30  Lunch 
13:30  Hypothesis testing in phylogenetics Maria Anisimova and Asif Tamuri  
15:15 Tea/coffee break 
15:45 Hypothesis testing in phylogenetics Maria Anisimova and Asif Tamuri  
17:30 Tea/coffee break 
18:00 Keynote lecture 4 Tanja Stadler
19:00 Break   
19:30 Dinner   
Day 10 - Wednesday 22nd April 
07:30 Breakfast  
08:30 Estimating divergence times  Jeff Thome and Tracy Heath  
10:15 Tea/coffee break 
10:45 Estimating divergence times  Jeff Thome and Tracy Heath   
12:30  Lunch 
13:30  Coalescent model and inference from population data  Bruce Rannala  
15:15 Tea/coffee break 
15:45 Coalescent inference of population sizes ad divergence times  Adam Leache and Ziheng Yang  
17:30 Tea/coffee break 
18:00 Optional MrBayes tutorial  
19:30 Dinner 
Day 11 - Thrusday 23rd April 
07:30 Breakfast   
08:30 Species tree estimation Bruce Rannala and Adam Leache 
10:15 Tea/coffee break  
10:45 Species tree estimation Bruce Rannala and Adam Leache  
12:30 Lunch  
13:30 Species delimitation  Bruce Rannala and Adam Leache 
15:15 Tea/coffee break  
15:30 Species delimitation  Bruce Rannala and Adam Leache 
17:30 Break  
19:30 Course Dinner Restaurant  
Day 12 - Friday 24th April 
07:30 Check out by 10:00 
08:00 Breakfast 
09:00 Q & A session / TAs free for analysis of trainees own data  
10:15 Tea/coffee break  
10:45 Q & A session / TAs free for analysis of trainees own data  (Feedback)  
12:30 Lunch  
European Bioinformatics Institute (EMBL-EBI)
Wellcome Genome Campus Hinxton Cambridge CB10 1SD United Kingdom

At EMBL-EBI, we manage the world’s public biological data and make it freely available to the scientific community via a range of services and tools, perform basic research and provide professional training in bioinformatics. Set on the beautiful Wellcome Genome Campus near Cambridge in the UK, we support scientists throughout the world in seeking solutions to challenges in healthcare, agriculture and the environment.

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In association with

How to apply

Registration is now closed.

Prerequisites
Preference will be given to applicants who:

  • are doctoral candidates in the early to middle stages of their thesis research
  • already have some familiarity with phylogenetic methods (i.e. have already used some of the relevant tools)
  • have already collected/assembled molecular sequence datasets to analyze in their work
  • have experience working in a Unix/Linux command-line environment

Cost
The course is subsidised by the Wellcome Trust. The course is residential and there is a charge of £1625 towards board and lodging for non-commercial applicants.The fee for commercial applicants is £3200.

Bursaries
Limited bursaries are available for non-commercial applicants (up to 50% of 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.

Application deadline

14 November 2014

Number of places

30 places

Registration closed

Organisers

Laura Emery

Nick Goldman

Ziheng Yang - University College London, UK

Aidan Budd - EMBL, Germany

Alexandros Stamatakis - Heidelberg Institute for Theoretical Studies, Germany

Trainers

Martin Embley - University of Newcastle, UK

John Huelsenbeck - University of California, Berkeley, USA

Tanja Stadler - ETH Zurich

Ziheng Yang - University College London, UK

Alexandros Stamatakis - Heidelberg Institute for Theoretical Studies, Germany

Aidan Budd - EMBL, Germany

Adrian Friday - University of Cambridge, UK

Laura Emery - EMBL-EBI, UK

Stephen Smith - University of Michigan, Ann Arbor, USA

Ben Redelings - National Evolutionary Synthesis Center, North Carolina, USA

Adam Leache - Department of Biology & Burke Museum, University of Washington, USA

Olivier Gascuel - LIRMM-CNRS, Montpellier, France

Maria Anisimova - ETH Zurich, Switzerland

Brian Moore - University of California, Berkeley, USA

Asif Tamuri - EMBL-EBI, UK

Jeff Thorne - Genetics and Statistics Department, North Carolina State University, USA

Tracy Heath - University of California, Berkeley, USA

Bruce Rannala - Genome Center and Department of Evolution and Ecology, University of California, USA

Adam Leache - Department of Biology & Burke Museum, University of Washington, USA

Materials & attachments

Joint EMBL-EBI Wellcome Trust Advanced Course on Computational Molecular Evolution