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@kuleuven.be) or Philippe Lemey (philippe.lemey@kuleuven.be). -- Guy Baele, PhD. Department of Microbiology and Immunology Evolutionary and Computational Virology Section Rega Institute - KU Leuven Herestraat 49, 3000 Leuven, BELGIUM