workshop on viral evolution and molecular phylogenetics of viruses

Brian Foley btf at lanl.gov
Tue May 4 04:05:48 EST 2004


Dear Sir/Ms,

Please find below the program and
application instructions for the one-week Aug 30 - Sep 3.2004 "10th Workshop
on Viral Evolution and Molecular Epidemiology"
(http://www.kuleuven.ac.be/aidslab/program.htm).

This interactive learning-workshop for scientists and students working in
the fields of virology, epidemiology, bioinformatics and evolution has been
organized for 9 consecutive times by the Rega Institute at the Katholieke
Unversiteit Leuven by Professor Annemieke Vandamme and has gained a wide
respect for its high quality faculty and hands-on approach to learning.

Regular teachers include Annemie Vandamme, Marco Salemi, Vincent Moulton,
Oliver Pybys and many other experts of the field. They will bring the
absolutely latest information of the field to the workshop.

In 2003 the workshop was held at Stanford University, USA and in 2004 it
will take place in Helsinki, Finland, organized jointly by the Rega
Institute, the Finnish National Public Health Institute and the University
of Helsinki.

Application to the workshop is now open at the website mentioned above. The
workshop is divided into one-week parallel "Basic" and "Advanced" modules
that both have a limit of 20 participants. The basic level module is
targeted towards scientists not familiar with phylogenetic analysis, and the
advanced module towards those that have some experience of basic
phylogenetic analysis. Both modules are taught in a computer class with
multiple assistant teachers and ample parctical exersises and interactive
learning possibilities.

Participation is by application only, and there is a peer-review of
applications. The deadline for applications is May 15 and applications must
be done using the web-form or by email using a form found on the web-page
(Please DO NOT send unstructured applications to this address or Professor
Vandamme by
email. We will not have the possibility to respond to them).
People chosen to attend the workshop will be notified by early June.

In the attachment a pdf-file with further information and direct web-links
to the site are included

The complete faculty and program of the course are also listed below.

I hope you found this message interesting, if it was sent to you in error, I
apologize for the inconvenience.

- Mika Salminen
###################################
Laboratory Director, Ph.D., Doc.
HIV-laboratory
Department of Infectious
Disease Epidemiology
National Public Health Institute
Helsinki
FINLAND
####################################

10th Workshop on Viral Evolution and Molecular Epidemiology

Advanced Course 30.8.-3.9.2004

SUNDAY 29.8

Arrivals

MONDAY 30.8

Welcome address and practical instructions

Understanding molecular evolution. Theoretical Lecture.
Marco Salemi - 2h

Statistical inference in phylogenetics and population genetics. Theoretical
Lecture.
Oliver Pybus - 1 h

Lunch

Construction and Interpretation of Phylogenetic trees. Theoretical Lecture.
Marko Salemi - 1 h.

Construction & Interpretation of Phylogenetic trees using Dambe, Mega, Paup
& Mr Bayes. Practical session.
Marko Salemi - 2 h

Free computer time w. teachers available

TUESDAY 31.8

Phylogenetic analysis using the split-decomposition method. Theoretical
session Vincent Moulton - 1,5 h.

Phylogenetic analysis using the split-decomposition method. Practical
session
Vincent Moulton - 1.5 h.

Lunch

Plenary Lecture: Tracking and identifying micro-organisms in the era of
Bioterrorism
Åke Lundqvist - SMI/Karolinska Institute BSL-4 Facility - 1h

Student's session I - 2h

Free computer time w. teachers available

WEDNESDAY 1.9

Testing evolutionary hypythesis: PAUP* and MODELTEST.
Marco Salemi - 2 h

Student's session II - 1,5h

Lunch

Likelihood methods using TREE-PUZZLE. Theoretical background.
Heiko Schmidt - 1,5 h.

Likelihood methods using TREE-PUZZLE. Practical session.
Heiko Schmidt - 1,5 h.

Free computer time w. teachers available

THURSDAY 2.9

Detecting recombination in viral sequences. Theoretical lecture.
Mika Salminen - 1 h.

Detecting recombination in viral sequences. Practical session using SIMPLOT
Mika Salminen - 1,5 h.

Plenary Lecture: Viral Zoonooses
Olli Vapalahti - 1h

Lunch

Investigating natural selection and adaptation in viral gene sequences.
Theoretical background.
Oliver Pybus - 1,5 h

Practical session using CODEML and MacClade.
Oliver Pybus - 1,5 h

Free computer time w. teachers available

FRIDAY 3.9

Inferring population history from DNA data.
Mary Kuhner - 2,5 h.

Plenary Lecture: Influenza virus evolution.
To be announced - 1h

Lunch

Estimating evolutionary rates and epidemiological history from viral gene
sequences. Theoretical background
Andrew Rambaut - 1,5h.

Practical session using TIPDATE and GENIE.
Andrew Rambaut - 1,5h.

SATURDAY 4.9

Departures

Basic Course 30.8.-3.9.2004

SUNDAY 29.8

Arrivals

MONDAY 30.8

Welcome address and practical instructions

Fundamentals of molecular evolution. Theoretical Lecture.
Annemie Vandamme - 2h

Alignment algorithms. Theoretical Lecture.
Annemie Vandamme - 1h

Lunch

Methods for construction of phylogenetic trees - I. Theoretical Lecture.
Annemie Vandamme - 1h

Methods for construction of phylogenetic trees - II. Theoretical Lecture.
Annemie Vandamme - 1h

Database homology searching. Practical computer session.
Mark van Ranst - 1,5h
Free computer time w. teachers available

TUESDAY 31.8

Markov models in Molecular phylogeny. Theoretical Lecture.
Marco Salemi - 2h

Sequence alignments - I. Practical computer session using Bioedit, Clustal
and Mega
Philippe Lemey - 1,5 h

Lunch

Plenary Lecture: Tracking and identifying micro-organisms in the era of
Bioterrorism
Åke Lundqvist - SMI/Karolinska Institute BSL-4 Facility - 1h

Student's session I - 2h

Free computer time w. teachers available

WEDNESDAY 1.9

Construction and interpretation of phylogenetic trees - Practical computer
session using Phylip and Mega
 Philip Lemey - 2h

Student's session II - 1,5h

Lunch

Data exploration using DAMBE. Theoretical lecture.
Xuhua Xia - 1,5 h

Data exploration using DAMBE. Practical session.
Xuhua Xia - 1,5 h

Free computer time w. teachers available

THURSDAY 2.9

Phylogenetic analysis of proteins. Theoretical session.
F. Opperdoes 1 h

Phylogenetic analysis of proteins. Practical session.
P. Lemey/ F. Opperdoes 1 h

Plenary Lecture: Viral Zoonooses
Olli Vapalahti - 1h

Lunch


Detecting recombination in viral sequences.
Theoretical lecture.
Mika Salminen

An integrated UNIX environment for molecular phylogenetic analyses.
Theoretical session.
Tulio de Oliveira - 1h

Practical computer session using GDE.
Tulio de Oliveira - 1 h

 Free computer time w. teachers available

FRIDAY 3.9

Maximum likelihood and bayesian methods in Molecular phylogeny.
Marco Salemi - 2,5 h

Plenary Lecture: Influenza virus evolution.
To be announced - 1h

Lunch

Practical use of phylogenetic analysis. Students Datasets

SATURDAY 4.9

Departures

Faculty:
Anne-Mieke Vandamme Ph.D. Professor in Evolutionary Genetics
Katholieke Universiteit Leuven, Belgium.
Mika Salminen Ph.D.
Docent in Virology, Laboratory Director, Department of Infectious Disease
Epidemiology, National Public Health Institute (KTL), Helsinki, Finland
Philippe Lemey Research Associate
Rega Institute for Medical Research, Leuven, Belgium.
Fred Opperdoes Professor in Biochemistry
International Institute of Cellular and Molecular Pathology and Universitè
Catholique de Louvain, Belgium.
Åke Lundqvist M.D., Ph.D.
Laboratory Director, Swedish Institute for Infectious Disease Control (SMI),
Centre fo Microbiological preparedness,Stockholm, Sweden
Marc Van Ranst M.D., Ph.D.
Professor in Bioinformatics at the Katholieke Universiteit Leuven, Belgium.
Xuhua Xia Ph.D., Biology Department, University of Ottawa, Ontario, Canada.
Olli Vapalahti M.D., Ph.D.
Professor of Zoonotic Virology, Department of Virology, Haartman Institute,
Faculty of Medicine and Division of Microbiology and Epidemiology, Faculty
of Veterinary Medicine, University of Helsinki, Finland
Marco Salemi Ph.D.
Postdoctoral fellow, Dept. Ecology and Evolutionary Biology, University of
California at Irvine.
Heiko Schmidt Ph.D.
Postdoc at the John-von-Neumann Institute for Computing (NIC), Jülich,
Germany
Andrew Rambaut Ph.D.
Postdoctoral Scientist at the Department of Zoology, University of Oxford,
Oxford, UK.
Vincent Moulton Ph.D.
Professor of Bioinformatics, The Linnaeus Centre for Bioinformatics, Uppsala
University, Uppsala, Sweden.
Tulio de Oliveira
Ph.D. Research Associate, Nelson Mandela School of Medicine, University of
KwaZulu-Natal, Durban, South Africa
Oliver Pybus Ph.D., Postdoctoral Scientist at the Department of Zoology,
University of Oxford, Oxford, UK.
Mary Kuhner Ph.D., Professor at the Genetocs Department, University Of
Washington, Seattle, Washington.





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