DATA ANALYSIS AND VISUALISATION DESIGN FOR EMERGING INFECTIOUS DISEASES

DATA ANALYSIS AND VISUALISATION DESIGN FOR EMERGING INFECTIOUS DISEASES

Belgium 30 Nov 2021
KU Leuven

KU Leuven

State University, Browse similar opportunities

OPPORTUNITY DETAILS

State University
Area
Host Country
Deadline
30 Nov 2021
Study level
Opportunity type
Specialities
Opportunity funding
Full funding
Eligible Countries
This opportunity is destined for all countries
Eligible Region
All Regions

(ref. BAP-2021-460)

Last modification : Sunday, June 20, 2021
 

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 phylodynamic 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 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 visualization approaches, in order to facilitate interpretation and dissemination of our research.

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In a first part of the project, useful software applications that complement Bayesian phylogenetic and phylodynamic inference will need to be designed and implemented. In order to translate the phylodynamic output of our proposed models into tangible responses, the goal will be to develop a user-friendly, feature-rich, interactive and flexible web-based visualization platform that can easily be applied to different pathogens and enables sharing these visualisations as frictionlessly as possible. The web technology platforms to be used are not carved in stone and can be chosen provided they scale well with increasing amounts of data. Our research group has previous experience in this area, in the development of the SPREAD software package (https://doi.org/10.1093/bioinformatics/btr481) and its successor that makes use of Data-Driven Documents: SpreaD3 (https://doi.org/10.1093/molbev/msw082). Knowledge of recent web technologies (see the profile description) is hence considered a strong plus.

The second part of the project will involve becoming familiar with Bayesian phylogeographic reconstructions on various pathogens, but with an initial focus on rabies virus. While a previously hired PhD student will focus on developing novel models for phylogeographic inference, applying these models and comparing their inference results to one another constitutes an important responsibility within the current job description. A collection of useful data sets from different geographic regions will have to be established, and this for different pathogens, and will need to be carefully analysed alongside available metadata and current hypotheses on viral spread within the field of research. However, these types of analyses constitute only a starting point, and we certainly welcome novel ideas for analyses, model and/or application developments or interesting pathogens to study.

The candidate for this position should have a background in computer science and/or web design, and preferably hold a master's degree (with distinction/cum laude) and/or PhD in computer science / (bio-)informatics (or equivalent through experience). Take note that the specifics of the funded project do not allow senior post-doctoral researchers to be hired on a full-time basis (i.e. only PhD students or researchers that have recently obtained their PhD can be hired). The candidate is preferably experienced in one or more recent web technologies such as JavaScript, HTML, CSS, Python, Data-Driven Documents (https://d3js.org/), React (http://facebook.github.io/react/) and Node.js (http://nodejs.org) application. The candidate should be sufficiently proficient in English, motivated to work in a team and publish his/her findings, and willing to travel (when conditions allow for it). 

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 application suite - used by many researchers in the fields of phylogenetics, phylodynamics and molecular evolution, and consisting of a wide range of software tools - 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 October 1st 2021, although both earlier and later starting dates can be negotiated, and the candidate 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 junior post-doctoral researcher is selected. The position will remain open until a suitable candidate has been selected.

Please use the KU Leuven university job portal only when applying for this position. For more information, contact Prof. Dr. Guy Baele (guy.baele@kuleuven.be) and/or Dr. Simon Dellicour (simon.dellicour@ulb.be).

You can apply for this job no later than November 30, 2021 via the  online application tool 

KU Leuven seeks to foster an environment where all talents can flourish, regardless of gender, age, cultural background, nationality or impairments. If you have any questions relating to accessibility or support, please contact us at diversiteit.HR@kuleuven.be.

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