Logic List Mailing Archive

PhD student position in algorithmic aspects of phylogenetic networks, Maastricht (The Netherlands)

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