Dear colleague, As some of you might know I am currently looking for a PhD student to work = with me on algorithmic aspects of phylogenetic networks. I am still at the = stage of informally asking around within my academic network to see if anyb= ody knows of any strong candidates. If you do know of somebody then please = do not hesitate to get in touch, or to bring him/her into contact with me. For your convenience I have provided some details of the project below, fee= l free to forward this on to anyone you think might be interested. Formal r= ecruitment procedures will start in due course. Kind regards, Steven Kelk Department of Knowledge Engineering (DKE) Maastricht University Netherlands ---------------------------------- PhD position available in algorithmic aspects of phylogenetic networks Summary: For this PhD position I'm looking for a student with a strong algo= rithmic background to work with me on a number of novel combinatorial optim= ization problems emerging from the field of phylogenetic networks. Topics s= uch as approximation algorithms, fixed parameter tractability, graph theory= and (mixed integer) linear programming will figure heavily in this project= . Steven Kelk, March 27th 2011. 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 ed= ges 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, a= llows us to model not only speciation events (vertices with indegree at mos= t one and outdegree at least two) but also reticulation events (vertices wi= th indegree at least two) such as horizontal gene transfer, hybridization a= nd recombination. See the book =93Phylogenetic Networks: Concepts, Algorith= ms and Applications=94 by Huson, Rupp and Scornavacca for an introduction. The overall challenge is to generate a plausible hypothesis for what the = =93real=94 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 t= hese complicated biological phenomena?) and in an algorithmic sense (given = a model, how can we efficiently compute the optimum network?) I am looking for a PhD student to work with me on the algorithmic side of t= he story. The student will employ techniques from combinatorial optimizatio= n and operations research to develop algorithms that can efficiently constr= uct optimal phylogenetic networks. Topics such as approximation algorithms,= fixed parameter tractability, graph theory and (mixed integer) linear prog= ramming will figure heavily in this research. For this reason the student should primarily have a strong background in ma= thematics, computer science or operations research. 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 iss= ues that motivate these mathematical questions. The student will primarily be based with me at the Department of Knowledge = Engineering (DKE) at Maastricht University in the Netherlands, where the re= search will be embedded within the Networks and Strategic Optimization rese= arch cluster of DKE. There is potentially also an option for the student to= spend a part of his or her time at a second university at the Netherlands,= but this option is still under scrutiny. If you know of any good candidates for this position please don=92t hesitat= e to put them in touch with me. The beginning date is flexible but sooner i= s preferred over later and in any case the project should definitely be und= erway by the end of 2011. Please note that this document should not be considered a formal notificati= on of the position opening; this will follow in due course and be published= via the usual channels. Thanks for your help, Dr. Steven Kelk Department of Knowledge Engineering (DKE) Maastricht University Postbus 616 6200 MD Maastricht Netherlands Email: steven.kelk@maastrichtuniversity.nl Web: http://skelk.sdf-eu.org Telefoon: +31 (0)43 38 82019