JOB DESCRIPTION

Closed for Applications

Title

Early Stage Researcher (ESR1)  

PhD fellowship in multi-omics data mining through (dynamic) mechanistic models

Project Title

“E-MUSE Complex microbial ecosystems multiscale modelling: mechanistic and data driven approaches integration” MSCA-ITN-2020 European Training Network

Hosting Organization

STICHTING VU (VUA), established in DE BOELELAAN 1105, AMSTERDAM 1081 HV, Netherlands, VAT number: NL851029279B01

Researcher Profiles

ESRs

Research Field

Food microbiology, molecular microbiology, cheese process, flavour formation, process modelling

Application Deadline

15th April  2021, 23:59 - Europe/Brussels

Envisaged Job Starting Date

15.05.2021

Duration

The appointment will initially be for 1 year. After a satisfactory evaluation of the initial appointment, the contract will be extended for a duration of 2 years.

Contract Type

full-time employment (based on COVID-19 evolution and restrictions, possibility to start remotely, once situation allows the presence is required)

Remuneration

Remuneration according to Dutch PhD regulations minimal €2395 gross salary/month first year to €3061 in third year. Plus € 600 gross mobility allowance/month and €500 gross family allowance/month (if applicable).
Taxation and Social (including Pension) Contribution deductions based on National and company regulations will apply.

Objectives

In this project, we will develop tools and methods to integrate dynamic multi-level omics data with genome-scale mechanistic models in the context of microbial communities. With partners in the E-MUSE Network (KUL, UNIBO, USZ, CHRH) we will explore (1) the use of machine-learning approaches for feature selection (for example SVM, Random forest, Ensemble techniques, etc.) for model development and prioritisation; (2) conversely the use of the mechanistic models and Individual-based Model as prior knowledge to constrain the search space in data-driven approaches. We will integrate the data into dynamic constraint-based ecosystem models, and apply the tools and methods to the biological study cases, i.e. the cheese ripening case and the growth physiology of associated microbial species.

Expected Results

We expect to deliver tools (open source software) and methods (algorithms, modelling strategies) to use multi-omics data to generate insight in the relevant interactions inside and between microorganisms in complex dynamic ecosystems. We will provide insight in the usefulness of combining machine-learning and mechanistic modelling approaches. Finally, we will provide, in collaboration with the network partners, specific models and predictions that will lead to a better understanding of the biological use cases.

Planned Secondments

In total, 2 months will be spent at the Agencia estatal consejo superior de investigaciones cientificas in Spain (dynamic optimisation technologies), 2 months at the Katholieke Universiteit Leuven in Belgium (modelling aspects) and 3 months at the Institut national de recherche pour l’agriculture, l’alimentation et l’environnement in France and at the Chr. Hansen A/S in Denmark (biological data).

Enrolment in Doctoral degree

Vrije Universiteit Amsterdam (VUA) (https://www.vu.nl/en)

Requirements

Required Education Level

Master’s degree in systems biology, bioinformatics, (bio)physics, engineering or biology with a strong theoretical/computational component

Skills / Qualifications

•    Independence, curiosity, open-mindedness, ability to (learn to) communciate with different disciplines (experimental, computational, theoretical) and will to understand complex systems
•    educational background and previous research experience relevant for the chosen position
•    networking and communication skills in a multicultural and multidisciplinary environment
•    willingness to travel abroad for the purpose of research, training and dissemination

Specific Requirements

For the eligibility please check: Eligibility Criteria

Required Languages

English: B2, good oral and written communication skills in English are compulsory

Supervisors Team

Host Institution Description

The Vrije Universiteit Amsterdam (VUA) is a university in Amsterdam, Netherlands, founded in 1880, and ranked among the world's top 150 universities by four major ranking tables. The VUA is one of two large, publicly funded research universities in the city of Amsterdam (https://www.vu.nl/en/index.aspx). The host Systems Biology Lab is headed by prof Bas Teusink and Frank Bruggeman and searches for the organizational principles of cellular behaviour. It develops and combines computational and experimental approaches to investigate the mechanisms and fitness consequences of gene expression regulation, metabolic strategies and growth. Its research spans different levels of organization, from single cells to cell cultures and microbial communities, and aims for fundamental understanding and apply it to different areas of application, like food, health, and biotechnology.