Please allow me to bring the following PhD position, in algorithmic aspects of phylogenetic
network construction, to your attention. The PhD position will be based at the Department
of Knowledge Engineering (DKE) at the University of Maastricht, in the Netherlands.
We are looking for a student with a strong algorithmic background to work on a number of
novel combinatorial optimization problems emerging in this field. Topics such as
approximation algorithms, fixed parameter tractability, graph theory and (mixed integer)
linear programming will figure heavily in this project.
Full details can be found on the following page. This is also the page through which
candidates can apply for the position. Please include a letter of motivation, a CV and
two references, and indicate how soon you could begin (we have a preference for
as soon as possible). Finally, please note that the closing date for applications is
rather tight (25th May) although this might be extended in the coming days.
http://www.academictransfer.com/employer/UM/vacancy/9663/lang/en/
For your convenience I include some details of the project below. In the event of queries
about this position please do not hesitate to contact me directly.
Kind regards,
Steven Kelk
Department of Knowledge Engineering (DKE)
University of Maastricht
E: steven.kelk@maastrichtuniversity.nl
W: http://skelk.sdf-eu.org
T: +31 (0)43 3882019
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A rooted phylogenetic network is a rooted directed acyclic graph where the leaves are bijectively labeled by a set X of taxa (e.g. species) and all edges are directed away from the root. Such a network represents a hypothesis of how the set X is believed to have evolved from a single common ancestor, the root. The use of a directed acyclic graph, rather than just a tree, allows us to model not only speciation events (vertices with indegree at most one and outdegree at least two) but also reticulation events (vertices with indegree at least two) such as horizontal gene transfer, hybridization and recombination. See the book "Phylogenetic Networks: Concepts, Algorithms and Applications" by Huson, Rupp and Scornavacca for an introduction. The recent presentation "Algorithmic aspects of phylogenetic network construction" (downloadable from the website http://skelk.sdf-eu.org) also offers some background.
The overall challenge is to generate a plausible hypothesis for what the "real" network looked like, given only information derived from the set X of taxa. Although there has been a great deal of research conducted into the corresponding problem on trees, the field of phylogenetic networks is still very young, both in a modeling sense (what is the best way to model these complicated biological phenomena?) and in an algorithmic sense (given a model, how can we efficiently compute the optimum network?)
We are looking for a PhD student to work on the algorithmic side of the story. The student will employ techniques from combinatorial optimization and operations research to develop algorithms that can efficiently construct optimal phylogenetic networks. Topics such as approximation algorithms, fixed parameter tractability, graph theory and (mixed integer) linear programming will figure heavily in this research.
The student will be based at the Department of Knowledge Engineering (DKE) at Maastricht University in the Netherlands, where the research will be embedded within the Networks and Strategic Optimization research cluster of DKE. There will be collaboration with researchers in Amsterdam (CWI/VU).
The phd fellow should have a strong Masters-level background in mathematics, computer science, operations research or a related discipline. Experience with biology or bioinformatics is by no means essential, although the student should at least be open to understanding the basics of the real-world biological issues that motivate these mathematical questions. Candidates must be comfortable with writing and speaking in English.
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