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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

 

 Organizing Committee

 

Co-chairs

 

Members

 

 Visitors and Participants

 

 

 Overview

 

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.


 Activities


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

08:30am - 08:50am

Registration

08:50am - 09:00am

Opening Remarks

 

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 ---

 

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

08:30am - 09:00am

Registration

 

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 ---

 

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

08:30am - 09:00am

Registration

 

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 ---

 

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

08:30am - 09:00am

Registration

 

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 ---

 

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

08:30am - 09:00am

Registration

 

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 ---

 

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.


 Venue

 

 

Organizing Committee · Visitors and Participants · Overview · Activities · Venue

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