Job description
Title: DC5, PhD in integrative bioinformatics and systems biology - From sequence to strain-specific phenotypes.
Researcher profile: Doctoral candidate.
Type of contract: Temporary.
Job status: Full-time.
Duration: 36 months.
Application deadline: CLOSED.
Envisaged job starting date: October 2024.
How to apply: It is not possible to apply to this project anymore.
Hiring organisation and offer posting contact details
Organisation: Vrije Universiteit Amsterdam.
Number of positions available: 1
Country: Netherlands.
Address: O2 Building, De Boelelaan 1108, 1081HZ Amsterdam, The Netherlands.
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.
Offer description
In brief:
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 (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.
FAIROmics project:
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.
Scientific context:
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, but not always reusable because they are difficult to find and access and because databases are not systematically interoperable.
Objectives:
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.
Expected results:
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.
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) for two months to apply methods to in-house data.
Enrolment in Doctoral degree
1st-degree awarding organisation: Vrije Universiteit Amsterdam, https://vu.nl/en
2nd-degree awarding organisation: University of Bologna, https://www.unibo.it/en/homepage
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.
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 3 years immediately prior to the date of selection in the same appointing international organisation.
* EXCLUDED: short stays such as holidays, compulsory national services such as mandatory military service and procedures for obtaining refugee status under the General Convention.
- Language: Applicants must demonstrate fluent reading, writing and speaking abilities in English (B2).
Supervisors team
Vrije Universiteit Amsterdam:
- Prof. Bas Teusink, professor in systems biology, co-leader of the Systems Biology Lab and Scientific Director of the Amsterdam Institute of Molecular and Life Science. The Systems Biology Lab houses expertise in molecular systems biology, with a focus on the regulation of cellular metabolism. It combines theoretical, computational and quantitative experimental approaches. Teusink is an expert in cellular physiology, genome-scale metabolic modelling and resource allocation, with food microbiology as a key application area. He will supervise the mechanistic aspects of the project.
- Dr. Douwe Molenaar, associated professor is an expert in microbiology, bioinformatics and multivariate statistics. He will supervise the data-driven part of the project and act as a daily supervisor.
Universita di Bologna:
Prof. Daniel Remondini, professor in physics and specialised in the application of mathematical models in Biology, such as Network Theory for the study of Complex Systems, and the development of innovative algorithms for the analysis of high dimensional biological data.
Host institutions description
The Systems Biology Lab houses both experimental and computational expertise, and is part of the Amsterdam Institute of Molecular and Life Science, offering expertise in relevant disciplines such as protein structure modelling and AI applications in biochemistry. The VU University offers bachelor and master teaching in the life sciences with a strong emphasis on the inter-disciplinarity of modern biology, with a strong focus on bioinformatics, systems biology, imaging, and multi-omics technologies in the priority areas of Health and Life Sciences and Science for Sustainability.
The research group in UNIBO has been active for almost 20 years in the modelling and analysis of biological processes and high-throughput data. The group applies and develops bioinformatics and statistical analysis algorithms, as well as network-based approaches to complex systems. This expertise has also been applied in clinical and industrial contexts in relation to the development of automated diagnostic and classification tools. Network theory, Statistical Mechanics, Machine Learning and Deep Learning are among the tools used for these purposes.
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.
Selection process
- Candidates apply for a position using the online application form.
- 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.
- 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.
- 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).
- The best candidates will be chosen by the main supervisors. The European Project Manager will communicate the successful candidates to the Consortium and Partners.
