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