FAIROmics – PhD fellowship in integrative bioinformatics and systems biology – From sequence to strain-specific phenotypes.

About the Project

Plant-based dairy and meat alternatives have grown in popularity in recent years for various reasons, including sustainability and health benefits, as well as lifestyle trends and dietary restrictions. However, plant-based food products can be nutritionally unbalanced, and their flavour profiles may limit their acceptance by consumers. Microorganisms have been used in making food products for millennia. However, the diversity of microbial communities driving plant-based fermentations, as well as their key genetic and phenotypic traits and potential synergies among community members, remain poorly characterised. Many data exist, but they are spread into different literature (scientific and grey) or, in the best case, in different databases. However, they are not always reusable because they are difficult to find and access and because databases are not systematically interoperable.

The FAIROmics initiative, an interdisciplinary research programme, will gather universities, research centres and private companies to enable the FAIRification of omics data and databases interoperability and develop knowledge graphs for data-driven decision-making to rationally design microbial communities for imparting desirable characteristics to plant-based fermented foods in the context of open science and its regulations. The FAIROmics training programme aims to develop doctoral candidates’ skills at the interface between artificial intelligence, life sciences, humanities, and social sciences.

Title: DC5, PhD fellowship in integrative bioinformatics and systems biology – From sequence to strain-specific phenotypes.

Hosting organisation : Vrije Universiteit Amsterdam (VUA), https://vu.nl/en

Please note that this PhD position will lead to the award of a double diploma after the completion of a stay in each of these organisations: The Free University of Amsterdam (VUA), Netherlands and the University of Bologna (UNIBO), Italy.

Applications Deadline 15/05/2024 23:59 – Europe/Brussels.

Envisaged job starting date: October 2024.

Location and planned secondments:

The PhD student will mainly be located at VUA in Amsterdam for 22 months. Two secondments are planned :

• One at UNIBO in Bologna for 12 months for the training and development of hybrid mechanistic/AI methods.
• One at Chr. Hansen in Hoersholm (Denmark) to apply methods to in-house data for two months.

We are looking for one Doctoral Candidate to join our project at multiple sites in the EU with a master’s degree in a relevant discipline (Systems biology, bioinformatics, explainable AI, data analysis) interested in combining genomic and phenotypic data with biochemical knowledge to develop models that can predict relevant phenotypes from genotypes.

The project aims at developing models to improve the prediction of strain-specific phenotypes. The models will handle different levels of granularity and combine genomic information, mechanistic knowledge (enzyme signatures, promoter architecture, context methods such as operon structures or co-expression, thermodynamic data) and phenotypic data with artificial intelligence and machine learning techniques. Phenotypic data will include data from available strain collections with sequenced strains and information on their phenotypic behaviour, as well as data from strains screened within FAIROmics for activities during plant-based fermentations.

DC5 will deliver insight into to what extent integration of mechanistic knowledge and experimental data with AI/ML methods can lead to reliable predictions of variation in traits from variations in sequences. In the process, we will develop an inventory of relevant features and mechanisms and associated databases (or links thereto), methods and predictive models.

Required skills/qualifications:

• A Master’s degree in a relevant field, such as (bio)physics, systems biology, bioinformatics or computer science (with a good understanding of biology).
• Strong in, and affinity with, the use of computational methods in biological contexts.
• Good at problem-solving.
• Independent but willing to ask for help.
• Curious and communicative.

We offer:

• A comprehensive, interactive and international training programme covering the broader aspects and interface between life science, data science, artificial intelligence and humanities and social sciences, as well as transferable skills.
• An enthusiastic team of professionals to co-operate with.
• Personal Career Development Plan (PDCP) to prepare young researchers for their future careers.
• Each DC will undergo individual training at individual institutes according to the PCDP description.
• An attractive compensation package in accordance with the MSCA-DN programme regulations for doctoral candidates. The exact salary will be confirmed and will be based on a living allowance of 3400€/month (correction factor to be applied per country) + mobility allowance of 600€/month. Additionally, researchers may also qualify for a family allowance* of 660€/month, depending on the family situation. Taxation and social (including pension) contribution deductions based on national and company regulations will apply.

*family = be married/be in a relationship with equivalent status to a marriage recognised by the legislation of the country or region where it was formalised/have dependent children who are being maintained by the researcher.

Eligibility criteria:

• Any nationality
• Doctoral Candidate (DC): The applicant must not have been awarded a doctoral degree.
• Mobility rule: The DC must not have resided or carried out main activity (work, studies, etc.) in the country of their host organisation for more than 12 months* in the three years immediately prior to the date of selection in the same appointing international organisation.
• Language: Applicants must demonstrate fluent reading, writing and speaking abilities in English (B2).

* EXCLUDED: short stays such as holidays, compulsory national services such as mandatory military service and procedures for obtaining refugee status under the General Convention.

Recruitment process:

1. Candidates apply for a position using the online application form (ACCESSIBLE HERE).
2. The FAIROmics Project Manager provides a first screen of the written applications to check the eligibility of the candidate and forwards the eligible applications to the DC supervisors.
3. The DC supervisors will select the best candidates based on CV, academic records, recommendation and motivation letters and adequate skill set. To better assess the best candidate, the shortlisted candidates might be asked to write an abstract of provided scientific documents relevant to the research subject.
4. The selected applicants will be interviewed through an online meeting by the Selection Committee (two main supervisors and two representatives of a beneficiary or associated partner, with at least one person external to the DC’s project).
5. The best candidates will be chosen by the main supervisors.

For more information about the offer, the project and the recruitment process, please visit our website.