[BBC] PhD or post-doc position in the Laboratory of Clinical and Epidemiological Virology (Rega Institute - KU Leuven)

[Guy Baele]

The Laboratory of Clinical and Epidemiological Virology (Rega Institute 
- KU Leuven) is looking for a motivated PhD student or postdoctoral 
researcher with a background in bioinformatics/computer science to 
perform research in a multidisciplinary team. The candidate for this 
position should have a strong quantitative background, and preferably 
hold a master's degree (with distinction/cum laude) and/or PhD in 
computer science / (bio-)informatics (or equivalent through experience). 
The candidate hence is preferably experienced in an object-oriented 
programming language such as Java, although KU Leuven offers courses in 
object-oriented programming (among others) which the candidates can take 
if necessary. The candidate should be sufficiently proficient in 
English, motivated to work in a team and publish his/her findings, and 
willing to travel.

Full description at KU Leuven's job site: 
https://www.kuleuven.be/personeel/jobsite/jobs/55574468?hl=en&lang=en
Apply here: http://www.kuleuven.be/eapplyingforjobs/light/55574468

Project description

This project focuses on new developments in a popular Bayesian 
phylogenetic and phylodynamic inference framework (BEAST: 
https://github.com/beast-dev/beast-mcmc) and its applications to 
important evolutionary problems, with a particular focus on infectious 
diseases. BEAST is mostly written in Java, with its high-performance 
computational library, known as BEAGLE, being implemented in C/C++ with 
CUDA C and C++, the C/C++ interface to the CUDA parallel computing 
platform. The first part of the project involves the continued 
development of an online Bayesian phylodynamic inference approach that 
allows incorporating novel data into an ongoing analysis. As such, the 
current implementation of such an approach in BEAST 
(https://arxiv.org/abs/2002.00245) will need to be extended towards more 
complex models with varying dimensionality and evaluated in terms of its 
statistical and computational performance. Other approaches to increase 
the performance of Bayesian phylodynamic inference can also be 
investigated, such as through parallelization (and interfacing with the 
BEAGLE library) and the design of novel transition kernels (e.g. 
Hamiltonian Monte Carlo) aimed at exploring (posterior) distributions of 
interest in a more efficient manner.

In a second part of the project, useful software applications that 
complement Bayesian phylogenetic and phylodynamic inference will need to 
be designed and implemented. The main goal is to focus on assessing and 
interpreting the exploration of tree space, and think of useful and 
easy-to-interpret visualizations to do so. Novel approaches to 
visualizing the results of phylodynamic analyses altogether, along with 
the associated uncertainty on all parameters of interest and 
accompanying metadata, are also an important aspect of the position, 
with our group having previous experience in this area (for example, in 
developing SPREAD and SpreaD3). To this end, web-based applications can 
also be developed, and knowledge of JavaScript and/or Python is also 
considered a plus. The topics proposed are not carved in stone however, 
and we are certainly open to exploring new ideas and concepts.

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 Gasthuisberg University hospital campus, and guided by 
prolific supervisors. The candidate will be able to contribute to the 
continued development of the BEAST software package - used by many 
researchers in the fields of phylogenetics, phylodynamics and molecular 
evolution - and collaborate with top researchers in the field. 
Additionally, at the Division of Clinical and Epidemiological Virology, 
the candidate will be able to interact with several top researchers in 
the field of epidemiology, virology and metagenomics, and work on 
important infectious disease problems from an evolutionary perspective.


The targeted starting date will be June/July 1st 2020, although both 
earlier and later starting dates can be negotiated, and the candidates 
should obtain his/her master’s and/or PhD 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). Funding 
is available for 4 years to perform a PhD, and between 2-3 years in case 
a post-doctoral researcher is selected. The position will remain open 
until a suitable candidate has been selected.


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

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