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Workshop on Phylogenetics for Infectious Diseases - with a focus on DNA viruses
(10 - 14 October 2011)
Organizing Committee · Visitors and Participants · Overview · Activities · Venue
Co-chairs
- Vincent T. K. Chow (National University of Singapore)
- Swee Hoe Ong (Genome Institute of Singapore)
- Gavin J. Smith (Duke-NUS Graduate Medical School Singapore)
- Julian W. Tang (National University Hospital)
- Von Bing Yap (National University of Singapore)
Members
- Alexei Drummond (University of Auckland)
- Tommy Lam (University of Oxford)
- Philippe Lemey (Katholieke Universiteit Leuven)
- Marc Suchard (University of California at Los Angeles)
The aim of this workshop is to discuss how to improve the analysis of evolutionary and epidemiological aspects of viruses (mainly focusing on their genomic sequences) and the infections they cause, using mathematical tools. The main focus will be on DNA viruses (e.g. varicella zoster virus, human papillomaviruses, adenoviruses, etc.) though RNA viruses, such as influenza and HIV are also included. The invited speakers/participants are an inter-disciplinary mixture of specialists in virology, epidemiology and mathematical modelling (phylogenetics/statistics). By the end of the workshop, the participants should have a better understanding of alternative and possibly newer mathematical approaches to analyse such viral gene sequence data.
The style of the workshop will mainly be discussion-based, whereby various invited speakers will present their work and the audience will be encouraged to be interactive, i.e. to query/suggest/debate how any particular hypothesis can be tested in a better way, or how any analytical approach may be improved. The workshop hopes to foster greater collaboration between the various specialists in different disciplines. It is planned that an IMS lecture series publication will be produced after the workshop.
Monday,
10 Oct 2011 |
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08:30am - 08:50am |
Registration |
08:50am - 09:00am |
Opening Remarks |
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Chair: Julian W. Tang, National University Hospital |
09:00am - 10:00am |
DNA viruses and phylogenetics Julian W. Tang, National University Hospital |
10:00am - 11:00am |
Overview: some potential problems (Part I): DNA vs RNA genomes (alignment, tree construction, recombination) Philippe Lemey, Katholieke Universiteit Leuven, Belgium |
11:00am - 11:30am |
--- Coffee Break --- |
11:30am - 12:30pm |
Some modeling issues in phylogenetics Von Bing Yap, National University of Singapore |
12:30pm - 02:30pm |
--- Lunch --- |
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Chair: Marc Suchard, University of California at Los Angeles, USA |
02:30pm - 03:30pm |
Phylogenetic analysis applied to bacterial DNA genomes - epidemiological applications Jennifer Gardy, BC Centre for Disease Control, Canada |
03:30pm - 04:00pm |
--- Coffee Break --- |
04:00pm - 05:00pm |
Overview: some potential problems (Part II): DNA vs RNA genomes (model selection, molecular clock, coalescent inference) Alexei Drummond, University of Auckland, New Zealand |
Tuesday,
11 Oct 2011 |
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08:30am - 09:00am |
Registration |
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Chair: Vincent T. K. Chow, National University of Singapore |
09:00am - 10:00am |
The phylogenetics of human papillomaviruses Hans-Ulrich Bernard, University of California at Irvine, USA |
10:00am - 11:00am |
The phylogenetics of varicella zoster virus: contagion at the Raffles hotel in 1899 and beyond Charles Grose, University of Iowa, USA |
11:00am - 11:30am |
--- Coffee Break --- |
11:30am - 12:30pm |
Network models in phylogenetics David Welch, Penn State University, USA |
12:30pm - 02:30pm |
--- Lunch --- |
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Chair: Alexei Drummond, University of Auckland, New Zealand |
02:30pm - 03:30pm |
Estimating selection pressures: DNA vs RNA genomes Sergei L. Kosakovsky Pond, University of California at San Diego, USA |
03:30pm - 04:00pm |
--- Coffee Break --- |
04:00pm - 05:00pm |
Bayesian analysis: DNA vs RNA genomes Marc Suchard, University of California at Los Angeles, USA |
Wednesday,
12 Oct 2011 |
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08:30am - 09:00am |
Registration |
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Chair: Sergei L. Kosakovsky Pond, University of California at San Diego, USA |
09:00am - 10:00am |
Pyrosequencing and phylogenetics for influenza surveillance Yi-Mo Deng, WHO Collaborating Centre for Reference and Research on Influenza, Australia |
10:00am - 11:00am |
Temporal, spatial and genetic clustering of norovirus outbreaks Patrick K. C. Tang, BC Centre for Disease Control, Canada |
11:00am - 11:30am |
--- Coffee Break --- |
11:30am - 12:30pm |
Combinatorial approaches for studying viral evolution and transmission Niranjan Nagarajan, Genome Institute of Singapore |
12:30pm - 02:30pm |
--- Lunch --- |
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Chair: Philippe Lemey, Katholieke Universiteit Leuven, Belgium |
02:30pm - 03:30pm |
Current statistical/computational challenges and developments in phylogenetic techniques (Part I) Alexei Drummond, University of Auckland, New Zealand |
03:30pm - 04:00pm |
--- Coffee Break --- |
04:00pm - 05:00pm |
Current statistical/computational challenges and developments in phylogenetic techniques (Part II) Marc Suchard, University of California at Los Angeles, USA |
Thursday,
13 Oct 2011 |
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08:30am - 09:00am |
Registration |
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Chair: Hans-Ulrich Bernard, University of California at Irvine, USA |
09:00am - 10:00am |
Sequence and phylogenetic analyses of dengue and enteroviruses from asia Vincent T. K. Chow, National University of Singapore |
10:00am - 11:00am |
Problems and limitations of the phylogenetics of influenza viruses Gavin J. Smith, Duke-NUS Graduate Medical School Singapore |
11:00am - 11:30am |
--- Coffee Break --- |
11:30am - 12:30pm |
Phylogenetic diffusion models: from cross-species transmissions to phylogeography Philippe Lemey, Katholieke Universiteit Leuven, Belgium |
12:30pm - 02:30pm |
--- Lunch --- |
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Chair: Gavin J. Smith, Duke-NUS Graduate Medical School Singapore |
02:30pm - 03:30pm |
XMRV - a modern phylogenetic controversy? Stéphane Hué, University College London, UK |
03:30pm - 04:00pm |
--- Coffee Break --- |
04:00pm - 05:00pm |
Phylogeographic study of avian influenza virus Tsan Yuk (Tommy) Lam, University of Oxford, UK |
Friday,
14 Oct 2011 |
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08:30am - 09:00am |
Registration |
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Chair: Niranjan Nagarajan, Genome Institute of Singapore |
09:00am - 10:00am |
Development of a comprehensive pathogen detection microarray Charlie Wah Heng Lee, Genome Institute of Singapore |
10:00am - 11:00am |
Selective processes driving evolution in tropical bacterial pathogens Patrick Boon Ooi Tan, Genome Institute of Singapore |
11:00am - 11:30am |
--- Coffee Break --- |
11:30am - 12:30pm |
Structured meta-population dynamics and the persistence of seasonal H3N2 influenza A viruses in east and southeast asia Justin Bahl, Duke-NUS Graduate Medical School Singapore |
12:30pm - 02:30pm |
--- Lunch --- |
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Chair: Charles Grose, University of Iowa, USA |
02:30pm - 03:30pm |
A clinical perspective - are phylogenetic analyses of viral infections useful Paul A Tambyah, National University of Singapore |
03:30pm - 04:00pm |
--- Coffee Break --- |
04:00pm - 05:00pm |
Joint analysis of phylogenetic and epidemiological histories of rapidly evolving viruses Denise Kühnert, University of Auckland, New Zealand
BEAST 2 for viral phylogenetics Remco Bouckaert, University of Auckland, New Zealand |
Students and researchers who are interested in attending these activities are requested to complete the online registration form.
The following do not need to register:
- Those invited to participate.
Organizing Committee · Visitors and Participants · Overview · Activities · Venue
