EMBO workshop on current challenges and problems in phylogenetics

Workshop theme

Phylogenetic trees and networks are central to modern molecular evolutionary biology, with applications ranging from the origin of viruses (e.g. HIV, influenza) to modelling plant and animal radiations. As biologists attempt to reconstruct larger slices of the 'tree of life' using increasingly complex data, and incorporating more accurate models of molecular evolution, mathematics (and its sister fields, statistics and computer science) is increasingly being seen as an essential tool.

This workshop will showcase some of the recent achievements, challenges and new problems that arise in using mathematical approaches to understand molecular evolution. Topics covered will include: phylogenomics, molecular epidemiology, genetic biodiversity and phylogeography, processes of reticulate evolution (such as horizontal gene transfer), haplotype mapping by perfect phylogeny, population genetics in phylogeny, and metagenomics.

In addition this workshop will launch (and set the agenda for) a 4-month workshop of collaboration and research at the Isaac Newton Institute for Mathematical Sciences in a program on Phylogenetics, which will bring mathematicians and biologists together to develop new approaches in molecular phylogenetics.

The application is closed

Timetable

Monday 3rd September 2007
08:30 to 09:55	Registration	No Room Required
09:55 to 10:00	David Wallace - Welcome	Room 1
10:00 to 11:00	Tandy Warnow Japan Atomic Energy Agency & University of Texas at Austin Computational and mathematical challenges involved in very large-scale phylogenetics	Room 1
11:00 to 11:30	Coffee	No Room Required
11:30 to 11:50	Daniel Huson Dendroscope - an interactive viewer for large phylogenetic trees	Room 1
11:50 to 12:10	Barbara Holland Massey University Appropriate models for heterogeneous multi-gene data sites	Room 1
12:10 to 12:30	Heng Li Incorporating speices phylogeny in the reconstruction of gene trees	Room 1
12:30 to 13:30	Lunch at Wolfson Court	No Room Required
14:00 to 15:00	Mark Pagel University of Reading Mixture models in phylogenetic inference	Room 1
15:00 to 15:30	Tea	No Room Required
15:30 to 15:50	Gabriele Margos University of Bath Multilocus sequence analysis of Borrelia burgdorferi s.l.	Room 1
15:50 to 16:10	Katherine St John City University of New York Comparing phylogenetic trees	Room 1
16:10 to 16:30	Benny Chor Phylogenetic reconstructions based on RNA secondary structure	Room 1
16:45 to 18:30	Welcome Wine Reception and poster session	No Room Required
18:45 to 19:30	Dinner at Wolfson Court (Residents only)	No Room Required

Tuesday 4th September 2007
09:00 to 10:00	Olivier Gascuel CNRS (Centre national de la recherche scientifique) Advances and limitations of maximum likelihood phylogenetics	Room 1
10:00 to 10:20	Stephen Willson Iowa State University Restrictions on meaningful phylogenetic networks	Room 1
10:20 to 10:40	Katharina Huber University of East Anglia Inference rules for super-network construction	Room 1
10:40 to 11:00	Sagi Snir Maximum parsimony on phylogenetic networks: some rigorous results	Room 1
11:00 to 11:30	Coffee	No Room Required
11:30 to 11:50	Dan Gusfield University of California, Davis Integer programming for phylogenetic computations	Room 1
11:50 to 12:10	Quartet compatability: new results and surprising counterexamples	Room 1
12:10 to 12:30	Andreas Brandstaedt On k-leaf powers	Room 1
12:30 to 13:30	Lunch at Wolfson Court	No Room Required
14:00 to 15:00	Gabriel Valiente Technical University of Catalonia Tripartitions in phylogenetic networks	Room 1
15:00 to 15:30	Tea	No Room Required
15:30 to 15:50	Fabio Pardi CNRS (Centre national de la recherche scientifique) Branch and bound construction of balanced minimum evolution optimal trees	Room 1
15:50 to 16:10	Tanja Gernhard Technische Universität München New analytical results for the speciation times in neutral models	Room 1
16:10 to 16:30	Ruriko Yoshida University of Kentucky Partitioning the sample space on five taxa for the neighbour joining algorithm	Room 1
18:45 to 19:30	Dinner at Wolfson Court (Residents only)	No Room Required

Wednesday 5th September 2007
09:00 to 10:00	Michal Kucera Reconstruction of phylogeny by stratophenetic tracing in the fossil record and its comparison with molecular data	Room 1
10:00 to 10:20	Mahendra Mariadassou Explicit bounds for the stability of maximum likelihood trees	Room 1
10:20 to 10:40	Dirk Metzler Insertion-deletion models for dequence evolution and Bayesian sampling methods for multiple alignment	Room 1
10:40 to 11:00	Elizabeth Allman University of Alaska Fairbanks Indentifiability of the GTR=gamma substitution model of DNA evolution	Room 1
11:00 to 11:30	Coffee	No Room Required
11:30 to 12:30	Likelihood calculations on the ancestral recombination graph	Room 1
12:30 to 13:30	Lunch at Wolfson Court	No Room Required
18:45 to 19:30	Dinner at Wolfson Court (Residents only)	No Room Required

Thursday 6th September 2007
09:00 to 10:00	David Posada Universidad de Vigo Model averaging in phylogenies	Room 1
10:00 to 10:20	Frederick Matsen University of California Glimpses from the strange world of phylogenetic mixtures	Room 1
10:20 to 10:40	Shlomo Moran Technion - Israel Institute of Technology Neighbor joining algorithms for inferring phylogenies via LCA-distances	Room 1
10:40 to 11:00	Ilan Gronau Technion - Israel Institute of Technology Reconstruction of phylogenetic trees with very short branches	Room 1
11:00 to 11:30	Coffee	No Room Required
11:30 to 11:50	Charles Semple University of Canterbury Nature reserve selection problems	Room 1
11:50 to 12:10	Andreas Spillner Ernst-Moritz-Arndt-Universität Greifswald Computing phylogenetic diversity for split systems	Room 1
12:10 to 12:30	Klaas Hartmann University of Canterbury Prioritising species for biodoversity conservation	Room 1
12:30 to 13:30	Lunch at Wolfson Court	No Room Required
14:00 to 15:00	Allen Rodrigo University of Auckland Big trees: challenges and opportunites in the phylogenetic analysis of large data sets	Room 1
15:00 to 15:30	Tea	No Room Required
15:30 to 15:50	Brent Charles Emerson University of East Anglia Mitochondrial DNA heteroplasmy and recombination in a reptilian secondary contact zone	Room 1
15:50 to 16:10	Mark Wilkinson Generalising from consensus to supertree methods	Room 1
19:30 to 23:00	Conference Dinner - Christ's College Dining Hall	No Room Required

Friday 7th September 2007
09:00 to 10:00	Ingo Ebersberger Center for Integrative Bioinformatics Vienna (CIBIV) Mapping human genetic ancestry	Room 1
10:00 to 10:20	Magnus Bordewich University of Durham Consistency of phylogenetic tree search algorithms based on the balanced minimum evolution principle	Room 1
10:20 to 10:40	Alice Lesser Uppsala Universitet Optimal and hereditarily optimal realisation of metric spaces	Room 1
10:40 to 11:00	Peter Humphries University of Canterbury Properties of the TBR metric	Room 1
11:00 to 11:30	Coffee	No Room Required
11:30 to 12:30	Stars, nets, and the "war on error": Six mathematical challenges	Room 1
12:30 to 12:35	Closing remarks	No Room Required
12:35 to 13:30	Lunch at Wolfson Court	No Room Required
18:45 to 19:30	Dinner at Wolfson Court (Residents only)	No Room Required

Speakers

Elizabeth Allman University of Alaska Fairbanks
Magnus Bordewich University of Durham
Andreas Brandstaedt
Benny Chor
Ingo Ebersberger Center for Integrative Bioinformatics Vienna (CIBIV)
Brent Charles Emerson University of East Anglia
Olivier Gascuel CNRS (Centre national de la recherche scientifique)
Tanja Gernhard Technische Universität München
Ilan Gronau Technion - Israel Institute of Technology
Dan Gusfield University of California, Davis
Klaas Hartmann University of Canterbury
Barbara Holland Massey University
Katharina Huber University of East Anglia
Peter Humphries University of Canterbury
Daniel Huson
Michal Kucera
Alice Lesser Uppsala Universitet
Heng Li
Gabriele Margos University of Bath
Mahendra Mariadassou
Frederick Matsen University of California
Dirk Metzler
Shlomo Moran Technion - Israel Institute of Technology
Mark Pagel University of Reading
Fabio Pardi CNRS (Centre national de la recherche scientifique)
David Posada Universidad de Vigo
Allen Rodrigo University of Auckland
Charles Semple University of Canterbury
Sagi Snir
Andreas Spillner Ernst-Moritz-Arndt-Universität Greifswald
Katherine St John City University of New York
Gabriel Valiente Technical University of Catalonia
Tandy Warnow Japan Atomic Energy Agency & University of Texas at Austin
Mark Wilkinson
Stephen Willson Iowa State University
Ruriko Yoshida University of Kentucky

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EMBO workshop on current challenges and problems in phylogenetics

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