Algebraic and Combinatorial Phylogenetics

Dates

from June 19 to July 7, 2017

Duration

3 weeks

We will organize some contributed talks sessions during the course weeks (1st and 3rd weeks).
See schedule.

Workshop

Workshop on Algebraic and combinatorial phylogenetics, 26-30 June, 2017

Venue

UPC, UPF and PRBB (Barcelona Biomedical Research Park)

Accomodation

List of BGSmath Research Groups involved with the proposal:

 

With the support of the Spanish Ministry of Economy and Competitiveness, through the ”María de Maeztu” Programme for Units of Excellence in R&D” (MDM‐2014‐0445).

Registration

The deadline for applying for financial support was February 20th 2017.

For registration and poster submission, fill in this form.

The only size restriction on a poster is that your poster display should not be larger than 1 width x 2 length meters.

If you have already registered, you can proceed with the payment following the links:

There will be a special issue of the Bulletin of Mathematical Biology on Algebraic Methods in Phylogenetics. Participants of the BGSMonth are invited to submit their works. For more details, click here.

The deadline for registration is May 31st, 2017.

Please, be aware that Barcelona is really crowded in summer, so please book your accommodation as soon as possible.
Here there is a list of possible hotels and residences that may help.

Presentation

There is an increasing demand on the visualization of the interplay between mathematics and other sciences. The interaction between mathematics and biology has had an explosion since the genomic era of this millenium when sequencing of genomes has become possible and computers are filled with biological data. This BGSMath monthly program is the chance to make this interplay visible even from what is usually known as “pure mathematics” point of view and to benefit from the top level bioinformatics community in Barcelona. Phylogenetics is the study of ancestral relationships among species. Its interest relies not only on the study of the evolutionary processes that led to the living (current?) species, but also on the direct relation to genomics (comparative genomics) and in emerging fields such as traceability of cancer cells.

This program does not only look for interdisciplinary applications of mathematics, but it also seeks for intradisciplinary interactions. Although it is more or less known that statistics, probability, computation, differential equations and algorithmics play an important role in biology, biostatistics and bioinformatics, it is probably less evident that areas like combinatorics, geometry and algebra can also interact with biology. Combinatorics has always been an important part of phylogenetics, specially since the use of networks has shown to be relevant in this field. Algebra and geometry have showed up in phylogenetics via the new discipline “algebraic statistics”.

Program Contents

We propose the organization of a month devoted to the study of combinatorial and algebraic tools used in phylogenetics.

Over the last ten years a tremendous progress have been observed in the study and design of mathematical models and phylogenetic reconstruction methods. A huge part of this development is due to algebra and combinatorics. To summarize this progress and communicate it to a wider mathematical audience it is important to organize a program where mathematicians (working in algebra, combinatorics, geometry, computation, algorithmics, probability, or statistics) and biologists can present the main achievements in this field.

The main aim of this program is twofold: to awake the interest of mathematicians in the applied research in biology, and to bring together mathematicians from different disciplines. The program will therefore be both inter- and intra- disciplinary.
We propose the organization of two courses, one focused on combinatorial aspects of phylogenetics and the other more algebraically oriented. The program will be concluded with a workshop.

We believe that this offers a good opportunity for those PhD students and postdocs who do research in related areas without any previous knowledge of phylogenetics, and, at the same time, for senior researchers who are interested in opening the range of applications of their research and learning new tools and approaches.

Both courses would be taught by leading figures in these research fields, which have confirmed their participation: Mike Steel (University of Canterbury, Christchurch NZ), Arndt von Haeseler (Center for Integrative Bioinformatics Vienna) and Piotr Zwiernik (Universitat Pompeu Fabra).

Objectives

The objectives of the intensive program are several:
• Introduce the algebraic and combinatoric tools used in phylogenetics to PhD students, postdocs and senior researchers working in these areas.

• Spread and explain mathematical tools among bioinformaticians.

• Get to know the results achieved recently in phylogenetics, with special emphasis on the diversity of mathematical and statistical tools that could be used.

• Strengthen ties between different research groups in similar topics here and outside of Catalonia.

• Increase the interaction between bioinformaticians and mathematicians working in Barcelona.

• Attract new PhD students to this interdisciplinary field.

• Create an interdisciplinary working group in Barcelona with researchers working in different fields

Planning and schedule

Week 1 

Course by Mike Steel and Arndt von Haeseler on Phylogenetics and combinatorics:

Lecture 1  Introduction to phylogenetics (Arndt); Basic combinatorics of discrete trees (Mike)
Lecture 2 Continuous phylogenies and distance-based reconstruction (Arndt); Phylogenies based on discrete characters (Mike)
Lecture 3  Evolution on a tree (part one) (Arndt); Tree shape and random discrete phylogenies (Mike)
Lecture 4  Evolution on a tree (part 2) (Ardnt); Evolution of trees (Mike)
Lecture 5 Supertrees and Supermatrices: (Ardnt); Phylogenetic networks (Mike)

https://sites.google.com/view/acphyl2017/week-1?authuser=0

Week 2

Workshop on Algebraic and combinatorial phylogenetics

Week 3

Course by Piotr Zwiernik course on Semialgebraic statistics, latent tree models, and phylogenetics:

Lecture 1: Trees, tree metric and tree spaces
Lecture 2: Latent tree graphical models
Lecture 3: Tree inference and estimation
Lecture 4: Parameter estimation
Lecture 5: Special submodels

https://sites.google.com/view/acphyl2017/week-3?authuser=0

 

 

Teachers

During this Monthly Program we will have the opportunity to participate in a course given by:

 

  • Mike Steel. He is the director of the Biomathematics Research Centre in New Zealand and one of the top researchers in phylogenetics. An indicator of his relevance is his h-index which is 55 (according to Google Scholar), 40 (Scopus) and 13 (MathSciNet). In his work he uses tools from combinatorics, probability, topology. Moreover he is an excellent and experienced speaker.

 

  • Arnd von Haeseler leads one of the top bioinformatics teams in Europe and he is the director of the Center for Integrative Bioinformatics Vienna. His team has developed one of the most used phylogenetic programs, IQ-tree. The high quality of his research and publications is confirmed by his h-index, which is 45 (according to Scopus).

 

  • Piotr Zwiernik works on the mathematical aspects of statistical models and, luckily, he is at Universitat Pompeu Fabra since January 2016. He has recently written the book “Semialgebraic statistics and latent tree models” (2015) and is the perfect speaker for emphasizing the role of algebra in phylogenetics.