FAIROmics – PhD fellowship in identifying and controlling of key regulatory mechanisms for differential responses and metabolic shifts in microorganism populations.

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.

Application deadline: 15/05/2024 23:59 – Europe/Brussels.

Envisaged job starting date: October 2024.

Hosting organisation: Insititute for Integrative Systems Biology (I²SysBio), Valencia, Spain.

Planned secondment: One in UMRSayFood – INRAE/AgroParisTech, France is for a duration of 16 months.

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 University of Valencia (UPV), Spain and the University of Paris-Saclay (UPSaclay), France.

Offer description:

We are looking for one Doctoral Candidate (DC) to join our project at multiple sites in the EU with a master’s degree in a relevant discipline (Master’s degree in engineering, physics, systems biology, applied mathematics, biotechnology) interested in (Modeling, analysis and control of biological systems in the context of microbial fermentations).

The objectives of the project is to elucidating key genes, enzymes and proteins responsible for differential metabolic and cellular responses using model-based analysis techniques:

• Identifying the key regulators and most suitable variables for control of the fermentation/ripening process.
• Conceptualisation and formulation of the control problems to be addressed in order to drive the microorganism population to a desired state in order to meet the a priori desired product-specific control and optimisation objectives (including the control of key metabolic shifts) in the presence of uncertainty and molecular noise.
• Developing methods and software tools for the control and optimisation of gene regulation and metabolism of microorganism populations during the fermentation/ripening process.

The expected results of the project are:

• List of the identified key regulators and variables for control of the microorganism population.
• Definition of the control problems to be addressed in order to drive the microorganism population to a desired state.
• Methods and tools for model-based feedback control of the microbial population under molecular noise.

Required skills/qualification:

• Master’s degree in engineering, physics, systems biology, applied mathematics or biology with a strong theoretical/computational component, not later than 30 Sept 2024. Previous research experience (which must be no longer than four years) although appreciated, is not mandatory.
• Educational background and previous research experience relevant to the chosen position.
• Good numerical/computational skills.
• Ability to communicate with different disciplines (from experimental biology to computational and theoretical mathematics).
• Willingness to travel abroad.

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.