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