[BBC] PhD position in Leuven (computer science / statistics)

[Guy Baele]

The Laboratory of Clinical and Epidemiological Virology (Rega Institute 
- KU Leuven; https://rega.kuleuven.be/cev/ecv/) is looking for a 
motivated PhD student to perform research in a multidisciplinary team. 
This constitutes an exciting opportunity to work on computational and 
statistical methods in molecular evolution with applications in 
infectious diseases.

Research group

The Evolutionary and Computational Virology Laboratory at the Division 
of Clinical and Epidemiological Virology (Rega Institute, KU Leuven) 
focuses on the evolutionary processes that shape viral genetic 
diversity. This encompasses large-scale epidemic processes, such as 
population growth and spatial dispersal (a popular topic in 
phylogeographic and phylodynamics research), as well as small-scale 
transmission histories and within-host evolutionary processes, including 
adaptation and recombination. It is our objective to gain better 
insights into these evolutionary and population genetic processes and to 
clarify how they relate to epidemic and disease dynamics. To this aim we 
plan to focus on statistical and computational developments to analyze 
the increasing amount of data brought about by massive sequencing 
studies, mainly in a framework of Bayesian phylogenetic inference, for 
which our research group holds a strong track record. We also aim to 
explore the applicability of novel models and statistical inference 
tools, developed as part of our research, in different fields of research.

Project

This project focuses on new developments in a popular Bayesian 
phylogenetic inference framework (BEAST: 
https://github.com/beast-dev/beast-mcmc) and its applications to 
important evolutionary problems, with a particular focus on infectious 
diseases.

The project involves the development of an integrated web system and 
database that allows users to register, upload and retrieve sequence 
data to and from the database. Each user will be able to determine the 
sharing policy for the data he/she has provided. Such a system should be 
easily distributed so that other research groups can deploy it on their 
own server(s) and put it to use without technical interventions. 
Further, this system will interface with the BEAST software package to 
analyze the sequence data in an efficient manner. The candidate is 
expected to design and implement such a system and determine an 
appropriate strategy to properly distribute the developed system as an 
easily installed/deployed software package.

Additionally, multiple parallelization ideas will be implemented in the 
BEAST software package. BEAST is mostly written in Java, with its 
high-performance computational library, known as BEAGLE, being 
implemented in C/C++. The goal is to develop and implement efficient 
parallelization strategies from both a computational and a statistical 
perspective. The computational aspect entails the implementation of 
popular routines typically used in computer architecture, whereas the 
statistical aspect entails the development and adaptation of novel 
transition kernels in a Bayesian phylogenetic inference framework.

Profile

The candidate for this PhD position should have a strong quantitative 
background, and preferably holds a master's degree in computer science / 
informatics (or equivalent through experience), with an interest in 
statistics/mathematics and (bio)informatics. The candidate hence needs 
to be experienced in an object-oriented programming language such as 
Java or C/C++. The candidate should be sufficiently proficient in 
English, motivated to work in a team and publish his/her findings, and 
willing to travel.

Offer

The candidate will be able to perform research in a dynamic and 
multidisciplinary team (computer scientists, data analysts and 
evolutionary biologists), housed in the brand new facilities of the Rega 
institute at the University hospital campus, and guided by prolific 
supervisors. KU Leuven is one of the top universities in Europe and 
leads the Reuters ranking of Europe’s most innovative universities for 
the second year in a row.

The targeted starting date will be October 1st 2017 and the candidate 
should obtain his/her master’s degree by that time. All applicants are 
expected to submit a motivation letter, overview of their study results 
and two references (with their contact details).

Additional information, as well as the application procedure, can be 
found here:
https://icts.kuleuven.be/apps/jobsite/vacatures/54182826

Please use the university’s job portal when applying for this position. 
For more information, contact Guy Baele (guy.baele at kuleuven.be) or 
Philippe Lemey (philippe.lemey at kuleuven.be).


-- 
Guy Baele, PhD.
Department of Microbiology and Immunology
Evolutionary and Computational Virology Section
Rega Institute - KU Leuven
Herestraat 49, 3000 Leuven, BELGIUM

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