13 PhD opportunities

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FAIRification of multi-Omics data to link databases and create knowledge graphs for plant-based fermented foods
MSCA-DN-2022 Joint-Doctorates
Apply for your PhD in the FAIROmics project - FAIRification of multiOmics data to
link databases and create knowledge graphs for fermented foods.
Job description
Title: DC1, PhD fellowship in Microbial ecology - Deciphering the role of bacterial-fungal interactions
in plant-based fermented food.
Researcher profile: Doctoral candidate.
Research field: Microbial ecology.
Type of contract: Temporary.
Job status: Full-time.
Duration: 36 months.
Application deadline: 15/05/2024 23:59 - Europe/Brussels.
Envisaged job starting date: October 2024.
How to apply: submit your application form through this link.
Hiring organisation and offer posting contact details
Organisation: French National Institute for Agriculture, Food, and Environment (INRAE).
Number of positions available: 1.
Country: France.
Address: : UMR SayFood, 22 place de l’agronomie, 91120 Palaiseau, France.
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: French National Institute for Agriculture, Food, and
Environment - INRAE (PhD title delivered by the Université Paris-Saclay) and Helmholtz Centre for
Environmental Research - UFZ (PhD title delivered by the University of Leipzig).
Offer description
In brief:
We are looking for 1 Doctoral Candidate (DC) to join our project at multiple sites in the EU with a
master’s degree in microbiology or microbial ecology interested in deciphering the role of bacterial-
fungal interactions in plant-based fermented food using multi-omics data.
The FAIROmics project has received funding from the European Union's Horizon Europe research and innovation programme
under the Marie Skłodowska-Curie grant agreement N°101120449.
Copyright and legal notice:
“Funded by the European Union. Views and opinions expressed are, however, those of the author(s) only and
do not necessarily reflect those of the European Union or the European Research Executive Agency. Neither the
European Union nor the granting authority can be held responsible for them”.
“DCR (University of Reading) is funded by the UK Research and Innovation”.
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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. However, they are not always reusable because they are difficult
to find and access and because databases are not systematically interoperable.
Objectives:
The objective of the proposed PhD project is to understand and predict the mechanisms involved in
the fermentation process of plant-based foods. This project will explore both intra- and inter-domain
interactions, using bacterial-fungal interactions in fermented food as model. Synthetic ecology will be
used to design simplified communities able to ferment plant-based food and insure organoleptic
quality of the product. A selection of microorganisms adapted to the plant-based matrix will done based
on current knowledge and using multiple criteria. Using publicly available metabarcoding, genomics
and metagenomics datasets of plant-based fermented food, taxa of interest will be selected for further
exploration of their metabolic potentials in relation to the composition of the matrix. Therefore,
synthetic communities will be defined for their functional potentialities (e.g. proteolytic, lipolytic,
flavouring, debittering, texturing, appetising). Microcosm-scale experiments will be set up to monitor
over time the fermentation process as well as to collect physicochemical (substrate degradation, pH,
moisture, oxygen) and multi-omics (transcriptomics, metabolomics) data combined with stable isotope
probing (SIP) to decipher the mechanisms of these interactions. By adding or excluding members of
these communities, the importance of the bacterial-fungal interactions will be highlighted, with a focus
on the identification of potential cross-feedings and synergy in the process of carbohydrate, fatty acid
and protein degradation during the food matrix fermentation as well as a focus on the role of fungal
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highways. For instance, at the microscale, the formation of a niche for fermentation on the fungal
hyphae can be explored.
Expected results:
All the datasets will be generated according to FAIR principles and thus, available to create knowledge
graphs within the FAIROmics framework. This PhD project aims to develop stable and efficient
communities for plant-based fermented food production but also to better understand the synergy
between bacteria and fungi during plant-based fermentation processes.
Location and planned secondment:
The PhD student will be located at INRAE in Palaiseau, France, for 24 months. The secondment will be
done at the Helmholtz Centre for Environmental Research – UFZ, Leipzig, Germany, under the
supervision of Dr. Lukas Y. Wick for a 12-month period.
Enrolment in Doctoral degree:

1st-degree awarding organisation: University of Paris-Saclay (UPSaclay), https://www.universite-paris-
saclay.fr/en
2nd-degree awarding organisation: University of Leipzig, Germany, https://www.uni-leipzig.de/en
Required skills/qualifications
• Master's degree in microbiology or microbial ecology or related field.

• Knowledge in microbial ecology, microbial interactions, community ecology.
• Knowledge in bacterial and/or fungal metabolism and physiology.
• Experience in (meta)genomic and/or metabolomic data analysis.
• Computational skills: R (preferred) or any other language suitable for data analysis.
• Curiosity, Creativity and Autonomy.
• Critical and independent mind.
• Self-driven personality able to work both independently and in a team.
• Prepared to work in an interdisciplinary environment.
Eligibility criteria
• Any nationality
• Doctoral Candidate (DC): The applicant must not have been awarded a doctoral degree.
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• 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.
* 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
Dr. Vincent Hervé (M) is a researcher at the French National Institute for Agriculture, Food, and
Environment (INRAE). He is a microbial ecologist working on microbial diversity (taxonomic and
functional), microbial interactions and the contribution of microorganisms to ecosystem functioning.
Recently his work has focused on fermented food.
Dr. Eric Dugat-Bony (M) is a researcher at the French National Institute for Agriculture, Food, and
Environment (INRAE). He is a microbial ecologist working on the effect of biotic (e.g. bacteriophages)
and abiotic (e.g. NaCl content) factors on the microbial ecosystems involved in food fermentation. His
favourite model ecosystem is the cheese surface.
Dr. Pascal Bonnarme (M) is a Research Director at SayFood, team Food Microbial Communities
(CoMiAl), specialising in microbial metabolism and fermented foods.
Dr. Lukas Y. Wick (M) leads the ‘Bioavailability’ group at the Dept. of Applied Microbial Ecology at the
Helmholtz Centre for Environmental Research UFZ in Leipzig, Germany. His interest relates to the bio-
physical and ecological drivers of microbial activity in natural and built environments, and he is an
expert on bacterial-fungal interactions and mycosphere processes.
Host institutions description
The French National Institute for Agriculture, Food, and Environment (INRAE) is a public research
establishment bringing together a working community of 12,000 people, with 268 research, service and
experimental units, located in 18 centres throughout France. INRAE is one of the world leaders in
agricultural and food sciences, plant and animal sciences. Its research aims to develop solutions for
multi-performance agriculture, high-quality food and sustainable management of resources and
ecosystems. The SayFood UMR (Paris-Saclay Food and Bioproduct Engineering Research Unit) aims to
contribute to product-process innovation that takes into account the constraints of upstream
production, consumer needs and expectations, and environmental issues.
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The Helmholtz Centre for Environmental Research - UFZ, Germany, is a centre in the Helmholtz
Association of National Research Centres with ca. 1100 people. It is one of the world’s leading research
centres in the field of environmental research, enjoying high social recognition. It demonstrates ways
in which sustainable use of our natural resource base is possible for the benefit of both humankind and
the environment. The Department of Applied Microbial Ecology Microbiology investigates complex
microbial communities and their importance for the reliability of microbial ecosystem services. This
knowledge finds its application in the development of ecologically inspired biotechnological
approaches.
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
The selection process is based on the merits of providing equal opportunity and will be in agreement
with the European Code of Conduct for the Recruitment of Researchers.
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
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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. The European Project Manager
will communicate the successful candidates to the Consortium and Partner
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Job description
Title: DC2, PhD fellowship in plant-based food fermentation genomics.
Research field: Food Microbiology, Fermentation, Genomics.
Envisaged job starting date: September 2024.
Hiring organisation and offer posting contact details:
Organisation: NIZO Food Research BV.

Country: The Netherlands.
Address: Kernhemseweg 2, Ede, NL.
Please note that this PhD position will lead to the award of a double diploma from Wageningen
University and Research in The Netherlands and the National and Kapodistrian University of
Athens in Greece.
Offer description
In brief:
We are looking for a Doctoral Candidate (DC) to join our project at multiple sites in Europe with a
master’s degree in Food Microbiology / Molecular Microbiology / Analytical Chemistry /
Biotechnology / Biochemistry / Bioinformatics who is interested in new concepts to develop safe
innovative plant-based fermented foods based on genome mining of starter bacteria.
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sciences.
Scientific context:
Objectives:
The main objective of this research project is to rationally design mixed bacterial cultures to ferment
plant protein-based ingredients with desirable outcomes. This will be based on predictions derived from
available data sets on individual lactic acid bacteria (LAB) strains (with available sequenced genomes)
and favourable fermentation outcomes upon growth on different plant-based substrates. Strain
capabilities relevant to the preservation and safety of plant-based products will be determined. The
performance of mixed cultures to ferment plant-protein-based ingredients regarding the formation of
favourable flavour compounds, removal of unwanted chemical contaminants (e.g. off-flavours,
mycotoxins), and acid formation and preservation effect (suppressing the growth of spoilers and
pathogens) will be verified. Linking of functional properties of strains and genomic traits with
fermentation outcomes will support the design of novel fermented foods.
Expected results:
The project is expected to generate a model to predict outcomes of different plant protein-based
fermentations using mixed cultures of lactic acid bacteria with respect to flavour formation, removal of
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unwanted compounds, and preservation capacity. This allows for steering relevant fermentation
outcomes based on key gene functions and fermentative capacity of LAB strains on different plant-
based substrates.
Location and planned secondments:
National and Kapodistrian University of Athens, 8 months: metabolomics analyses of metabolites

in plant matrices upon fermentation.
University of Reading, 3 months: physiological evaluation of key gene expression in selected lactic
acid bacteria.
1st-degree awarding organisation: Wageningen University, Wageningen,

Netherlands, https://www.wur.nl/en/wageningen-university.htm
2nd-degree awarding organisation: National and Kapodistrian University of Athens,
Greece, https://en.uoa.gr/
Required skills/qualifications:
• Master’s degree in Food Microbiology / Molecular Microbiology / Analytical Chemistry /

Biotechnology / Biochemistry / Bioinformatics with demonstrable affinity for microbiology and
data science.
• Knowledge of and experience in working in a microbiological or biochemical laboratory.
• Affinity with complex data analysis and interpretation.
• Affinity with genome-based data analyses is favoured.
• Excellent planning and analytical skills.
• Open collaborative communication style with attention to the team.
• Excellent writing and presentation skills.
• Quality-driven.
• Proactive attitude with a strong sense of responsibility.
• Fluent spoken and written communication in English.
• Any nationality
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(B2).
Supervisors team
The supervisors team at NIZO consists of Dr. Marjon Wells-Bennik, Dr. Herwig Bachmann and Dr. Eric
Hester. Supervision from Wageningen University and Research is provided by Professor Marcel
Zwietering. Supervision at NKUA is provided by Assistant Professor Marilena Dasenaki and Associate
Professor Vasilis Valdramidis. At UREAD, Associate Professor Kimon-Andreas Karatzas will be the
supervisor.
Within NIZO, comprehensive knowledge is available on fermentation characteristics of starter culture

strains when grown on dairy and plant substrates in relation to development of flavour and controlling
food safety and quality. The lead supervisor is Principal Scientist Dr. Marjon Wells-Bennik. She has a
background in food microbiology (including functional genomics expertise) and is a visiting scientist at
Wageningen University. She initiated various consortium projects with multiple academic and industrial
stakeholders, including a recent project on “Microbial contaminants in plant-based protein ingredients”.
Since 2002, she has supervised 8 PhD students; 2 are ongoing, and 6 obtained their degrees. She has
published over 70 research articles and filed two patents. She can transfer fundamental knowledge to
more applied research. Co-supervisors at NIZO are Dr. Herwig Bachmann (extensive expertise in
fermentation, dairy and dairy-alternative technology) and Dr. Eric Hester (senior bioinformatician/data
scientist).
At Wageningen University and Research (WUR) supervision will be provided by Prof. Dr. M.H.
Zwietering who is the Head of the Food Microbiology group (FHM) and has a background in modelling.
His group investigates aspects of food safety, food spoilage and fermentation.
At the Kapodistrian University of Athens (Department of Chemistry), supervision is provided by

Associate Professor Dr. Vasilis Valdramidis and Assistant Professor Dr. Marilena Dasenaki. Dr.
Valdramidis holds a Ph.D. degree in Chemical Engineering from the Catholic University of Leuven,
Belgium and a primary degree in Agriculture (Food Science and Technology) from the Aristotle
University of Thessaloniki (Greece). He published around 100 manuscripts in peer-reviewed journals
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and chapters in books. He supervised eight post-doctoral researchers and more than 10 Ph.D.s (as main
or co-supervisor). Dr. Dasenaki’s research focuses on the study of food metabolomics using cutting-
edge mass spectrometric techniques and advanced chemometric tools, and she has published more
than 45 peer-reviewed papers and four book chapters.
At the University of Reading (UREAD), supervision is provided by Associate Professor Dr Kimon A.

G. Karatzas. He heads the Food Microbiology group in the Department of Food & Nutritional Sciences,
University of Reading. His scientific outputs include more than 55 articles in high-impact journals, one
international patent and various chapters in books. Currently, his group comprises 6 PhD students, and
previously, he successfully supervised 9 PhD students as the main PI and 12 as Co-PI and nine
postdoctoral researchers and visiting scientists. He has a longstanding experience in microbial
physiology of stress and molecular biology and more than 22 years of experience in food fermentations.
The student will benefit from the knowledge that has been built up in the domain of this project and
be supervised by experienced staff in the field of food microbiology, fermentation, and bioinformatics
at NIZO and WUR. In addition, the student will greatly benefit from the chemical analytical and
predictive modelling capabilities at NKUA and access to molecular biology expertise at UREAD.
Moreover, collaboration will be set up on semantic data mining at the start of the project, and the use
of artificial intelligence to train and improve models for rational predictions of favourable fermentation
outcomes.
The student in this project will be appointed at NIZO. NIZO (https://www.nizo.com/) is a leading
company in contract research for better food and health with one of the most advanced R&D centres
in the world. NIZO has state-of-the-art research facilities and laboratories, highly skilled experts and
comprehensive expertise on bacteria, proteins and processing. NIZO’s focus is on the development and
application of innovations for the global food industry and related markets. This includes cheese
research, development and production, and development of plant-based alternatives. With 75 years of
experience with starter cultures and food safety and quality control and with up-to-date new
technologies, including genomics approaches, NIZO brings the latest food technologies to life. NIZO is
continuously looking for new ways of improving food products and, at the same time, quality of life.
The degree awarding institutions for the student in this project will be and the National and
Kapodistrian University of Athens (NKUA).
WUR (https://www.wur.nl/en.htm) is an internationally leading education and research organisation in

life sciences with more than 10,000 students (of which 25% are from abroad). WUR participates through
the laboratory of Food Microbiology, FHM (www.wur.nl/fhm) and is headed by Prof. M.H. Zwietering.
FHM aims to understand the behaviour of food-associated microbes to assure the quality and safety of
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food. The research areas range from eco-physiology to risk assessment and genomics of food-
associated microorganisms in food supply chains and aspects of food safety, food spoilage and
fermentation are investigated. FHM has fully equipped microbiological labs both for fermentation
research and for food safety research.
The Department of Chemistry (DoC) of the NKUA will be involved in the project. DoC has expertise,
state-of-the-art infrastructure and facilities available for performing research in the areas of food
science, food chemistry, environmental chemistry and water diagnostics. It also has expertise in the
coordination and implementation of research and development activities, dissemination, and
exploitation activities with national mainly stakeholders, e.g., the Hellenic Food Authority, and private
food companies that export all around the world. The key facilities of the Department of Chemistry of
NKUA include cutting-edge high-resolution mass spectrometric systems (LC-TIMS-TOF/MS, LC-
QTOF/MS, GC-APCI-QTOF/MS) used for the HRMS analysis of the molecular ‘fingerprint’ of foodstuff
following advanced target and non-target screening workflows. Additionally, there is full access to
applied microbiological analysis for bacteria and fungal contaminants as well as techniques for
mycotoxin identification.
We offer

• Each DC will undergo individual training at individual institutes according to the PCDP
description.

Selection process
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will communicate the successful candidates to the Consortium and Partners.
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Job description
Title: DC3, PhD fellowship in Multi-omics data production during olive fermentation.
Organisation: National and Kapodistrian University of Athens.

Country: Greece.
Address: Panepistimiopolis Zographou, 15771 Athens.
a stay in each of these organisations: the National and Kapodistrian University of Athens (NKUA),
Greece and the Wageningen University (WU), Netherlands.
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 (Food Chemistry, Analytical Chemistry, Biotechnology, Food
Microbiology) interested in multi-omics data production and comprehensive compositional
understanding during olive fermentation.
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sciences.
Scientific context:
Objectives:
The main objectives of this research project are to study microbial communities and to design plant-
based food production, to explore fermented foods and to produce multi-omics data during olive
fermentation. Metagenomics and transcriptomics coupled with metabolomic approaches will be used
to comprehensively characterise the impact of microbiome on the chemical composition of table olives
and other plant-based substrates and define the dynamic changes in key metabolites, determining their
nutritional and sensory qualities during the fermentation process. Metagenomics, transcriptomics and
metabolomics data will be produced according to the FAIR principles, using cutting-edge analytical
methodologies and advanced chemometric techniques.
Expected results:
The analysis of the metabolomics, metagenomics and transcriptomics data will result in the
identification of the microbial communities, microbes, metabolites and functional genes and their role
in olive fermentation. Elucidating the metabolic pathways underlying the production of the quality- and
flavour-determining components can lead to the optimisation of the fermentation process and to the
effective monitoring of food quality changes.
The PhD student will mainly be located at NKUA in Athens, Greece for 27 months. Two secondments
are planned :
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• One in NIZO Research Company in Ede, Netherlands for 3 months to verify the growth, the acid
production and the volatile production of L. plantarum strains on different plant-based
substrates.
• One in the University of Reading, United Kingdom for 6 months to do shotgun sequencing and
meta-transcriptomics.

1st-degree awarding organisation: National and Kapodistrian University of Athens, https://en.uoa.gr/
2nd-degree awarding organisation: Wageningen University, https://www.wur.nl/en/wageningen-
university.htm
• Master's Degree in Food Chemistry, Analytical Chemistry, Biotechnology, Food Microbiology.

• Strong background in advanced analytical techniques (Mass Spectrometry, NMR) and omics
approaches.
• Previous experience in data analysis programming and statistical skills.
• Team player and having a collaborative attitude.
• Knowledge of bioinformatics will be considered an asset.
• Networking and communication skills in a multicultural and multidisciplinary environment.
• Willingness to travel abroad for the purpose of research, training and dissemination.
• Any nationality
(B2).
Supervisors team
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The supervisor's team will be composed of Assistant Professor Marilena Dasenaki and Associate
Professor Vasilis Valdramidis from NKUA, Associate Professor Kimon-Andreas Karatzas from
UREAD, Dr Marjon Wells-Bennik from NIZO and Professor Marcel Zwietering from Wageningen
University. All of them have ample experience in Food Chemistry and Food Microbiology and have
supervised numerous PhD students.
Dr. Marilena Dasenaki (F) is an Assistant Professor at the Laboratory of Food Chemistry of the National
and Kapodistrian University of Athens. Her research activity focuses on the study of food metabolomics
using cutting-edge mass spectrometric techniques and advanced chemometric tools. Overall, Dr
Dasenaki’s research has been published in 45 peer-reviewed papers and four book chapters, attracting
more than >1100 citations, with an h-index of 18, and her work has been presented at several
international scientific conferences.
Dr. Vasilis Valdramidis (M) is an Associate Prof at the National and Kapodistrian University of Athens
(Department of Chemistry). He holds a Ph.D. degree in Chemical Engineering from the Catholic
University of Leuven, Belgium and a primary degree in Agriculture (Food Science and Technology) from
the Aristotle University of Thessaloniki (Greece). He has about 100 publications in peer-reviewed
Journals and chapters. He supervises/-ed eight post-doctoral researchers and more than 10 Ph.D.s (as
main or co-supervisor) and acted as external examiner of several PhD Thesis across Europe.
Dr. Kimon A. G. Karatzas (M) is a Faculty member (Associate Professor in Food Microbiology) of the
Department of Food & Nutritional Sciences, University of Reading. His scientific outputs include more
than 55 articles in high-impact journals (h-index of 23 based on SCOPUS), one international patent and
various chapters in books. He is also a member of the ASM and SGM and the Editorial Board of Microbial
Physiology and Metabolism, Frontiers in Microbiology and of the journal Foods. Currently, his group
comprises 6 PhD students (2 will complete their studies in a few months) while he is co-supervisor of 3
more PhD students. In the past, he successfully supervised 9 PhD students as main PI and twelve as Co-
I and nine postdoctoral researchers and visiting scientists. He has long experience in microbial
physiology of stress and molecular biology and more than 22 years of experience in food fermentations.
He conducted one of the first studies looking at the probiotic properties of isolates from fermentations
of olives which is highly relevant to this project. He also has long experience in the fermentation of
traditional products; he has conducted the first work of analysing the microbiota and using starter
cultures for the production of lafun, a traditional casava-fermented Nigerian product. He also has a
strong collaboration with various relevant companies and other scientists in the area.
Dr. Marjon Wells-Bennik (F) is a Principal Scientist at NIZO with extensive expertise in food
microbiology, including fermentation and safety of plant-based dairy alternatives. She initiated various
consortium projects with multiple academic and industrial stakeholders, including a recent project on
“Microbial contaminants in plant-based protein ingredients”. Since 2002 she has supervised 8 PhD
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students; 2 are ongoing and 6 obtained their degree. She has published over 70 research articles and
filed two patents. She can transfer fundamental knowledge to more applied research. (FTE: 0.1)
Dr. M.H. Zwietering (M) is the Head of WU-FHM which groups two personal professors, two associate
professors and one assistant professor and approximately 30 scientists that aim to understand the
behaviour of food-associated microbes to ensure the quality and safety of food. The research areas go
from genomics and eco-physiology to risk assessment of food-associated microorganisms in food
supply chains. Both aspects of food safety, food spoilage and fermentation are investigated.
In The National and Kapodistrian University of Athens (NKUA), officially founded on April 14th, 1837,
is the first University not only of Greece but both the Balkan peninsula and the Eastern Mediterranean
region. The main sources of funding of NKUA are European, international and national funds, like for
example, the Partnership Agreement (PA) for the Development Framework, 2014-2020 (European
Structural and Investment FundESIF), Horizon 2020, as well as partnerships with public and private
sector bodies, the provision of services to legal entities and individuals, grants and donations. The Dept
of Chemistry (DoC) will be involved in the project. DoC has expertise, state-of-the-art infrastructure and
facilities available for performing research in the areas of food science, food chemistry, environmental
chemistry and water diagnostics. It also has expertise in coordinating and implementing research and
development activities, dissemination, and exploitation activities with national mainly stakeholders, e.g.,
the Hellenic Food Authority, and private food companies that export worldwide. The key facilities of the
Department of Chemistry of NKUA include cutting-edge, high-resolution mass spectrometric systems
(LC-TIMS-TOF/MS, LC-QTOF/MS, GC-APCI-QTOF/MS) used for the HRMS analysis of the molecular
‘fingerprint’ of foodstuff following advanced target and non-target screening workflows. Additionally,
there is full access to applied microbiological analysis for bacteria and fungal contaminants as well as
techniques for mycotoxin identification.
Wageningen University is an internationally leading education and research organisation in life

sciences with more than 10,000 students (of which 25% are from abroad). WU participates through the
Laboratory of Food Microbiology, FHM (www.wur.nl/fhm). WU-FHM is headed by Prof. M.H. Zwietering
and groups two personal professors, two associate professors and one assistant professor and
approximately 30 scientists that aim to understand the behaviour of food-associated microbes to
ensure the quality and safety of food. The research areas go from genomics and eco-physiology to risk
assessment of food-associated microorganisms in food supply chains. Both aspects of food safety, food
spoilage and fermentation are investigated. Wageningen University has fully equipped microbiological
labs both for fermentation research and for food safety research (MLII).
We offer
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description.

Selection process
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Job description
Title: DC5, PhD fellowship in integrative bioinformatics and systems biology - From sequence to
strain-specific phenotypes.
Research field: Systems biology, bioinformatics, explainable AI, data analysis.
Organisation: Vrije Universiteit Amsterdam.

Number of positions available: 1
Country: Netherlands.
Address: O2 Building, De Boelelaan 1108, 1081HZ Amsterdam, The Netherlands.
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:
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:
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sciences.
Scientific context:
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.
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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.
1st-degree awarding organisation: Vrije Universiteit Amsterdam, https://vu.nl/en

2nd-degree awarding organisation: University of Bologna, https://www.unibo.it/en/homepage
• 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.
• Any nationality
(B2).
Supervisors team
The Vrije Universiteit Amsterdam:

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• 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.
The 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.
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

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description.

Selection process
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Job description
Title: DC6, PhD fellowship in Improving Predictive Power: Addressing Identifiability Challenges in
Microbial Community Models.
Organisation: Spanish Council for Scientific Research, IIM-CSIC.

Country: Spain.
Address: IIM-CSIC, C/Eduardo Cabello, N6, 36208, Vigo.
a stay in each of these organisations: the University of Vigo (UVIGO), Spain and the University of
Leuven (KUL), Netherlands.
Offer description
In brief:
We are looking for 1 Doctoral Candidate (DC) to join our project at two sites in the EU (Spain and
Belgium) with a master’s degree in a relevant discipline (Applied mathematics, Systems Biology,
Bioengineering, or similar) interested in the dynamic modelling of microbial communities.
FAIROmics project:
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sciences.
Scientific context:
Objectives:
We seek a highly motivated and skilled Doctoral Candidate (DC) to join the Bioprocess and Biosystems
Engineering (Bio2Eng) group at IIM-CSIC (months 1 to 18), whereafter the PhD research will be
continued at the Chemical & Biochemical Process Technology & Control (BioTeC+) group at KU
Leuven/Campus Gent (months 19-36). The major aim is to develop theoretical methods and software
tools to address the challenges of modelling microbial communities. The candidate will work on
exploring and developing (1) identifiability analysis methods specifically devoted to ecological models
and (2) novel model-based optimal experimental design (OED) methods with special emphasis on those
accounting for biological variability. The candidate will combine ecological and coarse-grained models,
identifiability, and OED concepts to define dynamic models that are able to characterise ecological
interactions in microbial communities. Models obtained will be tested using data obtained in previous
projects and within parallel studies within FAIROMICS. Methods developed will be released as open-
source tools.
Expected results:
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• Novel methods for the structural identifiability analysis of ecological models.
• Novel methods for model-based experimental design accounting for biological variability.
• Software tools to facilitate the application of developed theoretical and numerical methods.
The Doctorate Candidate will spend 18 months at IIM-CSIC in Vigo (Spain), whereafter the research will
be continued for another 18 months at the BioTeC+ group of KU Leuven/Campus Gent (Belgium). KU
Leuven/BioTeC+ is a multidisciplinary team at the interface of in silico systems biology and in vitro
experimental predictive microbiology. Collaboration with the wet lab research is envisaged via
experimental data exchange.
1st-degree awarding organisation: University of Vigo, https://www.uvigo.gal/en

2nd-degree awarding organisation: KU Leuven, https://www.kuleuven.be/english/kuleuven/index.html
• Master's Degree in (Applied) Mathematics, Engineering including Computational Engineering,

Mathematical Engineering, Biosystems Engineering, Control Engineering, or a related field.
• Background in mathematical modelling.
• Background in numerical methods.
• Strong programming skills in Python or MATLAB.
• Excellent communication and interpersonal skills.
• Ability to work independently and as part of a team.
• Any nationality
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(B2).
Supervisors team
The Biosystems and Bioprocess Engineering Group at IIM-CSIC (bio2eng.csic.es) focuses on

understanding and designing biological systems and bioprocesses at different scales. Our research has
wide-ranging applications, including industrial biotechnology and food processing. The Applied
Systems Biology team, led by Dr. Eva Balsa-Canto, is where the Doctorate Candidate will work. The
team uses hybrid-mechanistic modelling to study biosystems like microbial communities or microbial
metabolism and to design novel bioprocesses of interest in the food and biotechnological industry. The
team has significant experience in developing theory and methods related to model identification:
structural and practical identifiability, sensitivity analysis, parameter estimation, model-based optimal
design, dynamic optimisation and inverse optimal control. We not only develop theoretical concepts,
but we also create practical solutions such as software tools to facilitate the application of our research
results.
Our research institute is located in the vibrant coastal city of Vigo, situated in Galicia, on the northwest
coast of Spain. Vigo is a place where land and sea meet, offering picturesque beaches, fresh seafood,
and a lively maritime culture.
The vision of BioTeC+ (Chemical & Biochemical Process Technology &

Control) (www.cit.kuleuven.be/biotec) (PI Prof. Jan F.M. Van Impe) is to consolidate and strengthen
both its international research position and its societal impact by focusing on a carefully selected
number of research areas and application domains in applied chemistry/chemical and biological
process engineering. At present, these application domains can be characterised by the keywords
industrial biotechnology, closing the waste/water cycle, and public health. These constitute the pillars
(columns) (bio)chemical reactions & reactors, (biological) waste(-water) treatment systems, and
predictive microbiology/microbial risk assessment within BioTeC’s research matrix. This broad range of
application domains is supported by our long-standing systemic (systems and control) approach
towards applied chemistry/chemical and biological process engineering. The research areas (i) systems
theory, systems biology and analysis, process model identification (including optimal experimental
design), (ii) process monitoring, and (iii) optimisation and model-based control characterise the
transversal rows in the research matrix. These rows constitute the longstanding fundament of BioTeC’s
research covering and underpinning all application domains (pillars).
KU Leuven/BioTeC+ runs a state-of-the-art L2 accredited laboratory for experimental predictive

microbiology research, as well as high-end computing facilities. Our five postdocs and 14 PhD
researchers are involved in numerous international research projects and networks, including six
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ongoing EU projects. As a most international and inclusive team, we look forward to welcome you to our
campus in the vibrant city of Gent, Belgium!
The Spanish National Research Council (CSIC) is the largest public research organisation in Spain and
one of the most important in the European Research Area (ERA). It is the main player in the Spanish
Science, Technology, and Innovation System and is currently made up of over 13,200 people. These
individuals are distributed between the CSIC Corporate Organization, 121 research institutes, and three
national centres located throughout Spain, as well as an institute in Rome. The CSIC conducts research
in three core areas: Society, Life, and Material, which cover most academic disciplines. In March 2021,
the CSIC was among the institutions awarded the 'HR Excellence in Research Award'. The DC will be
enrolled in the “Mathematical Methods and Numerical Simulation in Engineering and Applied Sciences”
Doctorate program offered by the University of Vigo.
KU Leuven boasts a rich tradition of education and research that dates back six centuries and received
the European HR Excellence in Research Award based on its current policy and a comprehensive action
plan. The university’s basic research orientation has always been and will remain fundamental research.
At the same time, the university remains vigilantly open to contemporary cultural, economic and
industrial realities, as well as to the community’s needs and expectations. In the Times Higher Education
ranking, KU Leuven is ranked as the 12th European university, while in the Reuters Top 100 of the
World’s most innovative institutions, KU Leuven is listed as the first European university for the fourth
year in a row. KU Leuven strives for an inclusive, respectful and socially safe environment. We embrace
diversity among individuals and groups as an asset. Open dialogue and differences in perspective are
essential for an ambitious research and educational environment. In our commitment to equal
opportunity, we recognise the consequences of historical inequalities. We do not accept any form of
discrimination based on, but not limited to, gender identity and expression, sexual orientation, age,
ethnic or national background, skin colour, religious and philosophical diversity, neurodivergence,
employment disability, health, or socioeconomic status. The DC will be enrolled in the Arenberg
Doctoral School via the Faculty of Engineering Technology.
We offer

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description.

Selection process
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Job description
Title: DC7, PhD fellowship in identifying and controlling of key regulatory mechanisms for differential
responses and metabolic shifts in microorganism populations.
Research field: (bio)process modelling, (bio)process control, systems biology.
Organisation: CSIC - Insititute for Integrative Systems Biology (I2SysBio).

Country: Spain.
Address: Carrer del Catedràtic Agustín Escardino Benlloch, 46980 Paterna, Valencia.
a stay in each of these organisations: The CSIC - Insititute for Integrative Systems Biology (I2SysBio),
Spain and the University of Paris-Saclay (UPSaclay), France.
Offer description
In brief:
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.
FAIROmics project:
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sciences.
Scientific context:
Objectives:
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.
Expected results:
• List of the identified key regulators and variables for control of the microorganism population.
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• 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.
The PhD student will mainly be located at the CSIC - Insititute for Integrative Systems Biology (I2SysBio)
site in Valencia for 20 months. A secondment at the UMRSayFood - INRAE/AgroParisTech is also
planned for a duration of 16 months.
1st-degree awarding organisation: Universitat Politècnica de València https://www.upv.es/index-

en.html
2nd-degree awarding organisation: Université Paris-Saclay https://www.universite-paris-saclay.fr/en
• Master’s degree in engineering, physics, systems biology, applied mathematics or biology with
a strong theoretical/computational component, not later than 30 Sept 2024. You should NOT
have any kind of PhD degree. 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).
• Networking and good communication skills (writing and presentation skills).
• Any nationality
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(B2).
Supervisors team
The supervisor team is composed of Irene Otero-Muras (I2SysBio), Cristian Trelea and Emmanuel
Bernuau (AgroParisTech). The PhD candidate will benefit from the research experience in dynamic
modelling and automatic control in CSIC-I2SysBio and APT. Both partners develop complementary tools
for model analysis, parameter identification, and multi-objective dynamic optimisation and have
extensive experience with theory and applications of automatic control to biological processes.
Specifically, at CSIC-I2SysBio, the DC will benefit from the expertise in advanced mathematical analysis
and control of biomolecular systems (including regulation, signalling and metabolism), whereas at APT,
the DC will develop theoretical and computational tools for dynamic system control during
fermentation/ripening processes.
Institute for Integrative Systems Biology: The Spanish National Research Council (CSIC-Agencia
Estatal Consejo Superior de Investigaciones Científicas) https://www.csic.es/en/csic is an autonomous,
multi-disciplinary public research body affiliated to the Spanish Ministry of Science and Innovation. The
CSIC has its own legal structure and is represented throughout the Spanish territory with a total of 105
centres/institutes. CSIC is the first Spanish organisation in the Framework Program of the European
Union by number of projects and economic return. The I²SysBio https://www.uv.es/i2sysbio is a joint
research institute involving Universitat de València (UV) and CSIC. I²SysBio Scientific Programs focus on
research into the structure, function, dynamics, evolution, and manipulation of complex biological
systems.
AgroParisTech is a school of engineering in the field of life sciences https://www.agroparistech.fr/en,

part of the Paris-Saclay University. The DC will be hosted at the Paris-Saclay Food and Bioproduct
Engineering Research Unit (SayFood). This lab’s research interests are physical, biochemical and
microbiological processes that govern the food and non-food transformations of bioproducts. SayFood
is a joint research unit between AgroParisTech and INRAE national research institute on agriculture,
food and environment https://www.inrae.fr/en.
We offer

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description.

Selection process
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Job description
Title: DC9, PhD fellowship in the design of Information Extraction Tools to characterise molecules
produced or degraded by microbes and applications to plant-fermented food ecosystems.
Research field: Artificial Intelligence, Natural Language Processing and Bioinformatics.
Organisation: INRAE Jouy-en-Josas,

Country: France.
Address: 78352 Rue de la Manufacture, 78350 Jouy-en-Josas.
Contact email: fairomics-dc10@inrae.fr
a stay in each of these organisations: The University of Paris-Saclay (UPSaclay), France and the
University of Szeged (USZ), Hungary.
Offer description
In brief:
master’s degree in a relevant discipline (Master’s degree in engineering, physics, systems biology,
applied mathematics, biotechnology) interested in Modelling, analysis and control of biological systems
in the context of microbial fermentations.
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FAIROmics project:
sciences.
Scientific context:
Objectives:
The PhD project aims to develop information extraction (IE) methods to automatically produce a
knowledge graph about microbe biology involved in plant-based food transformation or preservation.
The knowledge graph will formalise the molecules produced and degraded by microorganisms in the
fermentation process.
The IE methods will involve named-entity recognition, entity normalisation with respect to semantic
references and relationship extraction. They will be based on the most recent deep learning approaches
that train language models using few or no training examples by transfer learning or exploiting existing
structured information, i.e. knowledge bases and ontologies for distant or weak learning by including
relevant information according to the needs of the FAIROmics dedicated use cases (e.g. NCBI Taxonomy
for taxa, FoodEX2 for food, ChEBI for molecules, KEGG for pathways). Existing annotated corpora will
serve as a starting point for training (e.g. CHEMDNER, Pathway Curation, Bacteria Biotope).
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The project will rely on existing tools and resources on microbe biology developed by MaIAGE partners
(e.g. Omnicrobe application*, Ontobiotope ontology*, extraction workflow).
Expected results:
The PhD student will design and evaluate original machine-learning-based methods for extracting
information on plant-based fermentation metabolism from text. The models and software will be
available to the scientific community in an open-source license. The extracted knowledge will feed a
publicly available knowledge graph of microbial properties. The results will be published in the major
NLP venue and relevant bioinformatics journals.
The PhD student will be mainly located at the INRAE site in Jouy-en-Josas for 24 months and at the
Szeged University for a 12-month secondment.
1st-degree awarding organisation: University Paris-Saclay, https://www.universite-paris-saclay.fr/

2nd degree awarding organisation: University of Szeged, https://u-szeged.hu/english
• Master's degree or equivalent in AI, NLP and ML.

• Strong background in AI and NLP acquired at the Master's level. Significant work experience or
training in biology is a plus.
• Solid computer development skills.
• Applicants must demonstrate an openness to learn new things, versatility, creativity, problem-
solving skills, and attention to detail.
• Any nationality
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(B2).
Supervisors team
French team:
Two MaIAGE teams will be involved in the PhD supervision: the Bibliome team* and the StatInfOmics
team*:
• Robert Bossy (Bibliome): Natural Language Processing and application to microbiology,

software engineering.
• Claire Nédellec (Bibliome): Natural Language Processing and application to microbiology,
knowledge representation and ontology.
• Hélène Chiapello (StatInfOmics): Microbial bioinformatics, omics data.
• Sandra Dérozier (StatInfOmics): Microbial bioinformatics, software engineering.
Hungarian team :
• Vidács Lázló: Artificial intelligence, natural language processing, software engineering.

• Balázs Nagy: Artificial intelligence, natural language processing, software engineering.
INRAE is Europe’s top agricultural research institute and the world’s number two centre for the
agricultural sciences. Its scientists are working towards solutions for society’s major challenges. RU1404
MaIAGE gathers mathematicians, computer scientists, bioinformaticians and biologists to tackle
problems from biology, agronomy and ecology. Our research concerns processes at various levels,
ranging from molecular, cellular or multicellular levels to organisms, populations, and entire
ecosystems.
The University of Szeged (USZ) is recognised as a top research institution in Hungary, boasting a
diverse student body of over 21,000, including more than 4,000 international students from 115
countries. Led by László Vidács, the Applied Artificial Intelligence Research Group is dedicated to
advancing cutting-edge AI research. We specialise in diverse AI applications, from natural language
understanding to image processing. Our tailored machine learning and deep learning solutions address
real-world challenges in many domains, including medical imaging diagnostics, forensic text analysis,
and program source code processing.
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We offer

description.

Selection process
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Job description
Title: DC10, PhD fellowship in Artificial Intelligence-based tools for information retrieval from text
documents - Automatic information extraction from scientific publications and other sources to build
knowledge graph.
Research field: Applied Physics, Computer Science, Data Analysis, Machine Learning, Artificial Intelligence.
Organisation: Department of Physics and Astronomy, Bologna University.

Country: Italy.
Address: Viale Berti Pichat 6/2, 40127 Bologna.
a stay in each of these organisations: the University of Bologna (UNIBO), Italy and the University of
Szeged (USZ), Hungary.
Offer description
In brief:
master’s degree in a relevant discipline (Physics, Computer science, Mathematics, Statistics, Engineering
or related fields) interested in learning and developing AI-assisted tools for information extraction from
domain-specific scientific texts (journals, books, etc.) related to novel food engineering, microbial
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catalogues, fermentation, and other relevant processes. The information acquired and related semantic
analysis will be utilised to build knowledge graphs and more general ontologies.
FAIROmics project:
sciences.
Scientific context:
Objectives:
The candidate will learn AI algorithms mainly related to Natural Language Processing and information
embedding (eg word2vec, Transformer Networks, G-retriever) and connection of topics and keywords
(e.g. through Network Diffusion processes), and within the context of FAIRomics will apply for specific
case studies:
• Development of AI-assisted tools to enhance the yield of the research team in literature search
and processing.
• Automatic and semi-automatic information extraction from domain-specific scientific texts
(journals, books, etc.) related to novel food engineering, fermentation, and other relevant
processes.
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• Demonstrate the efficacy of the developed system, focusing on a carefully selected pool of
previously collected articles and books. The information acquired and semantic analysis will be
utilised to build knowledge graphs and more general ontologies, which will be used to enhance
the method's performance and expand the knowledge base of domain-specific databases such
as microbe collection catalogues.
Expected results:
Expected is a prototype AI tool that can process a pool of documents by automatically analysing their
text and retrieving topic-specific information in terms of key concepts and named elements and finding
the connection among them. This supports the building of a knowledge graph and/or, more generally,
an ontology according to the domain defined by the documents. The extracted information can be
used, on the one hand, to find related documents or identify parts of documents for a set of user-
specified concepts. On the other hand, extracted and processed information in terms of a knowledge
graph can be used to incorporate new data into existing knowledge bases and data catalogues. Possibly,
the developed tools will also be applied in other related contexts, e.g. social networks.
The first secondment will occur at the Department of Software Engineering, University of Szeged
HU (Prof. Laszlo Vidacs), Month 14 (18 months), to develop automatic and semi-automatic information
extraction and processing to build knowledge graphs and ontologies.
The second secondment will occur at the Department of Computer Science, University Paderborn
DE (Prof. Axel-Cyrille Ngonga Ngomo), Month 28 (2 months), to learn about state-of-the-art
knowledge-driven data science methods.
1st-degree awarding organisation: Alma Mater Studiorum – University of Bologna, Bologna

IT, https://www.unibo.it/en/homepage
2nd-degree awarding organisation: University of Szeged, Szeged HU, https://u-szeged.hu/english
• Master's degree in Physics, Computer science, Mathematics, Statistics, Engineering or related

fields, giving access to PhD school and NOT to have any kind of PhD degree. Although
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appreciated, previous research experience (which must be no longer than four years) is not
mandatory.
• Good skills in programming high-level languages like Python, R, and Matlab (not mandatory but
highly recommended for network tools development and usage).
• Any nationality
(B2).
Supervisors team
The lead supervisor is D. Remondini, full professor at the Department of Physics and Astronomy at
Alma Mater Studorium – Bologna University. He works 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, biomedical and virological data (multiple
omics, NGSeq, Neuroimaging, text data) with Machine Learning and AI techniques. He actually leads a
group with 4 PhD students (1 ITN PhD student) 3 PostDoc Students, and 3 Research Assistants, with
>50 Undergraduate and Master Thesis students in Physics. The Co-supervisor is E. Giampieri (Assistant
Professor), with expertise in scientific computing, data management analysis and modelling, and
supervisor of >20 Undergraduate and Master Thesis students in Physics.
The Hungarian team is composed of Vidács László and Balázs Nagy, professors in artificial intelligence,
natural language processing, and software engineering.

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The project will occur at the Laboratory of Applied Physics and Systems Biophysics, Department of
Physics and Astronomy (DIFA) of the Alma Mater Studiorum - University of Bologna, Italy. DIFA
is one Department of the Science School and one of the most scientifically productive Physics
Departments in Italy. DIFA has a large computing facility, available to the Biophysics group (14-core
HPC, 2 GPU server with >1TB RAM and 2 nVidia A100, mirrored storage server with >100 Tb storage),
and to the whole Department (OPH HPC facility, >200 cores). Prof. Daniel Remondini is the director of
the lab, with specific expertise in biomedical data analysis (Machine Learning, Deep Learning), complex
network theory and its applications to BioMedicine. Dr Enrico Giampieri has specific expertise in
scientific computing, including networks, stochastic processes and statistics in High-Performance
Computing environments. All the lab members are involved in several national and EU projects
(Precision Medicine, Epidemiology, Public Health, Food Production).
The University of Szeged (USZ) is recognised as a top research institution in Hungary, boasting a
diverse student body of over 21,000, including more than 4,000 international students from 115
countries. Led by László Vidács, the Applied Artificial Intelligence Research Group is dedicated to
advancing cutting-edge AI research. We specialise in diverse AI applications, from natural language
understanding to image processing. Our tailored machine learning and deep learning solutions address
real-world challenges in many domains, including medical imaging diagnostics, forensic text analysis,
and program source code processing.
We offer

description.

Fermented Multi
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FAIROmics
Selection process
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Job description
Title: DC11, PhD fellowship in Network-based algorithms for Knowledge Graph construction and
analysis and application to the Omnicrobe knowledge graph.
Research field: Applied Physics, Computer Science, Data Analysis, Machine Learning, Artificial
Intelligence.
Organisation: Department of Physics and Astronomy, Bologna University.

Country: Italy.
Address: Viale Berti Pichat 6/2, 40127 Bologna.
a stay in each of these organisations: the University of Bologna (UNIBO), Italy and the University of
Paris-Saclay (UPSaclay), France.
Offer description
In brief:
master’s degree in a relevant discipline (Physics, Computer science, Mathematics, Statistics, Engineering
or related fields) interested in learning and developing Network and Machine Learning tools for the
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analysis and construction of Knowledge Graphs related to bacterial communities used for food
processing.
FAIROmics project:
sciences.
Scientific context:
Objectives:
To understand the network structure of Knowledge Graphs to develop and test algorithms for their
characterisation and optimisation. In particular, spectral approaches based on the network Laplacian
operator and techniques for node embedding derived from AI (eg DeepWalk, node2vec, Transformer
Networks or Autoencoders) will be tested, providing an interpretation of KG elements useful for
manifold learning or geometric deep learning. Moreover, network analysis theory, such as community
structure characterisation or identification of key elements (nodes, links, pathways), will be studied and
applied to the available cases.
In the FAIROmics project framework, the nodes of the graph represent biological entities, e.g. bacteria,
food matrix, food ingredient, metabolites, genes, the function of these genes, etc. The edges represent
relationships between these entities, e.g. bacteria growing in the food matrix. Moreover, the entities are
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themselves linked to reference classes, defined in knowledge graphs such as ontologies (e.g. bacteria
taxa in NCBI taxonomy, food matrix in FoodEx2).
Specific data will be analysed and produced within the FAIRomics project, and as a starting case study
the Omnicrobe knowledge graph, containing bacteria habitats and phenotypes, will be analysed to
characterise element similarity at different levels (nodes, paths, modules, communities), allowing to
check network structure, possible inconsistencies, missing or hidden relationships.
Expected results:
It is expected to get a deeper comprehension of Knowledge Graph structures and how to query and
manipulate them. This should allow them to improve their understanding and usability, for example by:
1) identifying hidden relationships through link imputation and analysis of node embedding
similarity;
2) extracting possible relevant outliers or anomalies (regarding ontologies/nodes and/or
relationships/links) corresponding to wrong elements within KGs;
3) clustering of KG elements through network community algorithms;
4) identify "knowledge modules" through network diffusion algorithms. The developed Network
tools are also useful in a wide range of contexts, from biological networks (e.g. Protein
interaction, Gene regulation, Microbial community ecology) to Social networks (structure and
dynamics of social networks, sentiment analysis, node classification, etc.).
The secondment will occur in INRAE MaIAGE (DrProf. H. Chiapello) at Month 14 (12 months period) to
apply the developed algorithms to the Omnicrobe Knowledge Graph
https://maiage.inrae.fr/fr/node/2694 in which ground truth information is available, in order to train
and test the models and tools designed for the analysis of FAIROmics KG.
1st-degree awarding organisation: Alma Mater Studiorum – University of Bologna, Bologna

IT https://www.unibo.it/en/homepage
2nd-degree awarding organisation: University Paris- Saclay https://www.universite-paris-saclay.fr/en
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• Master's degree in Physics, Computer science, Mathematics, Statistics, Engineering or related
fields, giving access to PhD school and NOT to have any kind of PhD degree. Although
appreciated, previous research experience (which must be no longer than four years) is not
mandatory.
• Good skills in programming high-level languages like Python, R, and Matlab (not mandatory but
highly recommended for network tools development and usage).
• Any nationality
(B2).
Supervisors team
The lead supervisor is D. Remondini, full professor at the Department of Physics and Astronomy at Alma
Mater Studorium – Bologna University. He works 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, biomedical and virological data (multiple
omics, NGSeq, Neuroimaging, text data) with Machine Learning and AI techniques. He actually leads a
group with 4 PhD students (1 ITN PhD student) 3 PostDoc Students, and 3 Research Assistants, with
>50 Undergraduate and Master Thesis students in Physics. The Co-supervisor is E. Giampieri (Assistant
Professor), with expertise in scientific computing, data management analysis and modelling, and
supervisor of >20 Undergraduate and Master Thesis students in Physics.
During the secondment at INRAE-Paris Saclay University, two MaIAGE teams will be involved in the PhD
supervision: the StatInfOmics team (https://maiage.inrae.fr/en/statinfomics) and the Bibliome team
(https://maiage.inrae.fr/en/bibliome):
• Hélène Chiapello (StatInfOmics): Microbial bioinformatics, omics data;

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• Sandra Dérozier (StatInfOmics): Microbial bioinformatics, software engineering;
• Robert Bossy (Bibliome): Natural Language Processing and application to microbiology, software
engineering;
• Claire Nédellec (Bibliome): Natural Language Processing and application to microbiology,
knowledge representation and ontology.
The project will occur at the Laboratory of Applied Physics and Systems Biophysics, Department of
Physics and Astronomy (DIFA) of the Alma Mater Studiorum - University of Bologna, Italy. DIFA
is one Department of the Science School and one of the most scientifically productive Physics
Departments in Italy. DIFA has a large computing facility, available to the Biophysics group (14-core
HPC, 2 GPU server with >1TB RAM and 2 nVidia A100, mirrored storage server with >100 Tb storage),
and to the whole Department (OPH HPC facility, >200 cores). Prof. Daniel Remondini is the director of
the lab, with specific expertise in biomedical data analysis (Machine Learning, Deep Learning), complex
network theory and its applications to BioMedicine. Dr Enrico Giampieri has specific expertise in
scientific computing, including networks, stochastic processes and statistics in High-Performance
Computing environments. All the lab members are involved in several national and EU projects
(Precision Medicine, Epidemiology, Public Health, Food Production).
The secondment will take place at INRAE MaIAGE. INRAE is Europe’s top agricultural research institute
and the world’s number two centre for the agricultural sciences. Its scientists are working towards
solutions for society’s major challenges. RU1404 MaIAGE gathers mathematicians, computer scientists,
bioinformaticians and biologists to tackle problems from biology, agronomy and ecology. Our research
concerns processes at various levels, ranging from molecular, cellular or multicellular levels to
organisms, populations, and entire ecosystems.
We offer

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Selection process
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Job description
Title: DC12, PhD fellowship in applied mathematics - Optimal Transportation to improve databases
integration.
Research field: applied mathematics, statistics, physics, biostatistics, bioinformatics or computer
science.
Organisation: Université Toulouse III - Paul Sabatier.

Country: France.
Address: 118 route de Narbonne, 31062 Toulouse, CEDEX 9.
a stay in each of these organisations: The University of Toulouse III - Paul Sabatier (UT3), France and
the University of Bologna (UNIBO), Italy.
Offer description
In brief:
master’s degree in a relevant discipline (applied mathematics, statistics, physics, biostatistics,
bioinformatics or computer science) interested in biological applications.
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FAIROmics project:
sciences.
Scientific context:
Objectives:
• Improve database interoperability.

• Contribute to the development of methods based on optimal transportation.
• Apply developments to database integration.
• Characterise, test and validate database fusion process with synthetic data generation
approaches.
Expected results:
The expected results are, first, a thorough comparison between optimal transportation and other
approaches usually used for database integration. This comparison will mainly be oriented to practical
applications, but theoretical works are still to be done and could also be addressed in this project
(depending on the candidate who will be selected). Another expected result is the extension of the tools
already available in the R package OTrecod to address more problems of database integration and
missing data imputation issues.
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The PhD student will mainly be located in the UNI3 at Toulouse, France for 22 months. Two
secondments are planned :
• One in the University of Szeged (USZ) for two months with Lazlo Vidacs to confront optimal
transportation approaches to machine learning methods.
• One at UNIBO in Bologna for 12 months with prof. Daniel Reomndini to learn and apply
techniques of manifold learning (useful to characterise the integrated data structure) and
synthetic data generation (to validate and extend the integrated datasets obtained through
optimal transportation approaches).
1st-degree awarding organisation: University Toulouse III – Paul Sabatier, https://www.univ-

tlse3.fr/home
2nd-degree awarding organisation: Alma Mater Studiorum Universitá di Bologna,
https://www.unibo.it/en/homepage
• A Master's or engineering degree in applied mathematics, statistics, biostatistics, bioinformatics

or computer science.
• Experienced user of the statistical software R, and at least basic knowledge in one other
programming language (Python, …) and database management system.
• Experience with real, multivariate data analysis and biological data would be a plus.
• Interest in biology, biological processes and the complexity of living.
• Educational background and previous research experience relevant to the chosen position.
• Any nationality
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(B2).
Supervisors team
Université Toulouse III - Paul Sabatier:
In Toulouse, the PhD will be part of the Statistics and Optimisation team. This team covers a spectrum
from theory to applications. A big part of applications is oriented to biology with many collaborations
with INRAE and INSERM. The PhD will be supervised by Sébastien Déjean (statistics, omics data
analysis), Philippe Saint Pierre (biostatistics, machine learning) and Nicolas Savy (biostatistics,
probability, machine learning).
Universita di Bologna:
In Bologna, Prof. Daniel Remondini is a full professor and head of the Biophysics Group at the
Department of Physics and Astronomy UNIBO. He has worked for more than 20 years on the analysis
and modelling of biological data in medicine (multi-omics, imaging, text and symbolic strings), applying
Network Theory, Machine Learning and Artificial Intelligence methods. Prof. Remondini teaches in
Biomedical Courses (Physics for Medicine and Biotechnology, School of Specialization in Medical
Physics) and on Applied Physics Master Course (Complex Networks, Pattern Recognition).
Prof. Enrico Giampieri is an associated professor in the Biophysics Group at the Department of
Specialized, Diagnostic, and Experimental Medicine, collaborating with prof. Remondini since 2008. He
has been working for more than ten years on the analysis of biomedical complex systems (bayesian
statistics, machine learning, computer vision, stochastic processes). Prof. Giampieri teaches in
Biomedical Courses (Physics for Medicine and radiologic imaging specialists) and on Applied Physics
Master Course (Software and computing methods for applied physics).
The University Toulouse III - Paul Sabatier is an educational leader in France's Occitanie region. It
offers a broad array of programs in the sciences, technology, and health. The Institute of Mathematics
(IMT) federates the mathematics community of the Toulouse area. It is composed of 6 main teams that
cover a very broad spectrum of mathematics ranging from theoretical aspects to applications.
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The research group in UNIBO has been active for almost 20 years in 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

description.
Selection process
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Job description
Title: DC13, PhD fellowship in explainable machine learning techniques to support the design of plant-
based fermented food products – Development of a serious game to support the design of plant-
based fermented food products.
Research field: Computer science, Applied mathematics.
Hiring organisation and offer posting contact details
Organisation: Paderborn University.

Country: Germany.
Address: : Warburgerstrasse 100, 33098 Paderborn.
a stay in each of these organisations: The Paderborn University and the French National Institute
for Agriculture, Food, and Environment - INRAE (PhD title delivered by the Université Paris-Saclay).
Offer description
In brief:
We are looking for a Doctoral Candidate (DC) to join our project at multiple sites in the EU with a
master’s degree in computer science, applied mathematics or similar interested in the use of knowledge
representation in food sciences.
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FAIROmics project:
sciences.
Scientific context:
Objectives:
DC13 will collect, integrate and fuse knowledge about plant-based fermented food necessary to design,
implement and evaluate a serious game on plant-based food synthesis. The knowledge to harmonise
will cover several areas: technical (raw material used, microbial consortia, formulation, processing…),
consumer (sensory and hedonic properties, expectations…), environmental (impact on climate change,
resource use, ecosystems…) and more widely sustainability (e.g. stakeholder expectations for social
aspects and prices for economic aspects). A representative case study will be chosen (e.g. plant-based
fermented food products produced by DC1). Data will be collected from previous projects, scientific
literature and relevant open databases (especially for technical data). The analysis of all the collected
data will allow (i) the quantification of the causal relations between the different dimensions of the
studied system and (ii) the identification of barriers and drivers to design the formulation and process
of plant-based fermented food. This analysis will be formalised as a knowledge graph which serve as
data to create a prototype of a serious game which supports the design of plant-based fermented food
products, with a stakeholder approach.
Expected results:
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• Formalised knowledge about plant-based fermented products including consumer, social and
environmental data.
• The development of a prototype of a serious game to support the design of plant-based
fermented food products.
The PhD student will be located at Paderborn University, Germany, for 20 months. The secondment
will be done at INRAE (Joint Research Unit SayFood), Palaiseau, France, under the supervision of Dr.
Caroline Pénicaud for a 16-month period.

1st-degree awarding organisation: University of Paderborn, Germany, https://www.uni-
paderborn.de/en/
2nd-degree awarding organisation: University of Paris-Saclay (UPSaclay),
France, https://www.universite-paris-saclay.fr/en
• Qualification in computer science, applied mathematics, or similar.

• Interest in food sciences, especially in consumer and environmental sciences.
• Interest in serious games.
• Excellent relationship and communication skills.
• Excellent organisational skills.
• Any nationality
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(B2).
Supervisors team
• UPB team: You will work with the Data Science group at Paderborn University. The group focuses
on knowledge representation and machine learning at scale. It is particularly interested in models
with rich semantics, e.g., RDF knowledge graphs. You will be supervised by Prof. Dr. Axel
Ngonga (head of group) and Dr. Mohamed Sherif (head of the knowledge integration and
fusion unit), both knowledge graph specialists.
• INRAE team: You will be based at the SayFood JRU (Paris-Saclay Food and Bioproduct
Engineering Joint Research unit), which aims to contribute to product-process innovation by
integrating upstream production constraints, consumer needs and expectations, and
environmental issues. You will be supervised by Caroline Pénicaud (INRAE research scientist in
food ecodesign), Anne Saint-Eve (Professor at AgroParisTech in sensory and consumer science),
and Lucy Espinosa (INRAE research scientist in sensory engineering).
• The DICE team at Paderborn University is one of the leading research groups on knowledge
graphs worldwide. The group has received over 30 research prizes at top-ranking venues for its
advancements in knowledge research in subfields such as knowledge integration, benchmarking,
link discovery and machine learning.
• The secondment will take place at INRAE and more specifically into the SayFood Joint
Research Unit. INRAE is Europe’s top agricultural research institute and the world’s number two
centre for the agricultural sciences. Its scientists are working towards solutions for society’s major
challenges. Our research topics are the physicial, biochemical and microbiological processes that
govern the food and non-food transformations of bioproducts.
We offer

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Each DC will undergo individual training at individual institutes according to the PCDP
description.
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,
*monthly gross salary.

**family = be married/be in a relationship with equivalent status to a marriage recognised by the
Selection process
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Job description
Title: DC14, PhD fellowship in law, “Legal Aspects of Open Science: FAIROmics as a Case Study”.
Research field: Intellectual Property, Data Law, Open Science, Open Access, Open Data.
Organisation: Université Libre de Bruxelles.

Country: Belgium.
Address: Campus du Solbosch, Av. F. Roosevelt, 50, 1050 Bruxelles.
a stay in each of these organisations: The Free University of Brussels (ULB), Belgium and the University
of Strasbourg (UNISTRA), France.
Offer description
In brief:
master’s degree in law (with a preference for a focus on European Intellectual Property and Data Laws)
interested in identifying and contributing to the definition of the Open Science legal framework in the
European Union.
FAIROmics project:
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sciences.
Scientific context:
Objectives:
The research project aims at identifying and contributing to the definition of the Open Science legal
framework. According to this project, an appropriate legal environment for Open Science shall ensure
that the principle ‘as open as possible, as closed necessary’ (see, e.g. recital 8, Regulation (EU) 2021/695
establishing Horizon Europe) applies at every stage of the research process.
The research project will be divided into two parts (legal theory and case studies) :
The first part will study the legal aspects (mainly Intellectual Property and Trade Secrets; Personal and
Non-Personal Data; Contract Law) related to:
• Data Access, with a focus on the most recent EU legal instruments, including but not limited to:
Regulation (EU) 2016/679 on the protection of personal data (GDPR); Regulation (EU) 2018/1807
on the free flow of non-personal data; Directive (EU) 2019/1024 on open data; Regulation (EU)
2021/695 establishing Horizon Europe; Regulation (EU) 2022/868 on European Data Governance;
Regulation Proposal on harmonised rules on fair access to and use of data (COM(2022) 68 final)
;
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• Data Analysis, with a focus on the recent Text & Data Mining Exceptions: Art. 3 and 4 Directive
(EU) 2019/790 on Copyright and Related Rights in the Digital Single Market;
• Research Results Exploitation, with a focus on open licensing practices.
The general assumption underlying the first part of the research is that the emerging legal framework
for Data Access and Data Analysis moves apart from the proprietary model and is, therefore, sound for
promoting Open Science. Conversely, it is assumed that the Research Results Exploitation still relies
mainly on a proprietary model, overlooking the potential of open licensing strategies in various fields
(‘more closed than necessary’).
The second part will study the practical implementation of this legal framework (completed with
relevant national law provisions) in relation to case studies selected amongst the Individual Research
Projects carried out in the frame of the FAIROmics Doctoral Network. The case studies will be selected
according to their contribution to each stage of the research (as identified above) in different disciplines.
The general assumption underlying this second part of the research is that the emerging legal
framework does benefit Open Science, but not to the fullest extent envisaged in theory for reasons of
practical hurdles (‘not as open as possible’). The ancillary assumption lies in the preference given by
universities (and their commercial partners) to the proprietary model. If verified, the validity of this
model as to its contribution to Open Science will be tested through counterfactuals based on open
licensing practices.
Expected results:
The expected result is the Ph.D. thesis on the Legal Aspects of Open Science. The thesis will be made
accessible in Open Access.
Ancillary results will comprise scientific papers on selected topics in relation to the main topics, scientific
communication in relation to the topic, dissemination of knowledge as to the main topic within the
network, contribution to the setting up of teaching modules in relation to the topic, to be used in the
network.
The PhD student will mainly be located at ULB, Belgium for 24 months and at the University of
Strasbourg for a 12-month secondment in order to gain expertise in Intellectual Property and Artificial
Intelligence Law.
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1st-degree awarding organisation: Université Libre de Bruxelles, https://www.ulb.be/en/ulb-homepage

2nd-degree awarding organisation: Université de Strasbourg, https://en.unistra.fr/
Required education level:
Candidates should have a background in Intellectual Property, Data Law, Open Science, Open
Access and Open Data.
Applicants must hold a Master's degree or have a university degree equivalent to a European Master's
(5-year duration) at the time when the PhD contract will begin. Supported researchers must be Doctoral
Candidates (DC), i.e., not already in possession of a doctoral degree at the date of the recruitment.
Researchers who have successfully defended their doctoral thesis but who have not yet formally been
awarded the doctoral degree will not be considered eligible. Master's degrees from all countries are
eligible.
Skills and qualifications:
• Legal Expertise in European Intellectual Property and Data Laws: Deep understanding of IP laws,
especially as they pertain to the European Union, is crucial.
• EU data-related regulations: In-depth knowledge of key EU data-related regulations, including
but not limited to the DMA, DSA, GDPR, and the Regulation on the Free Flow of Non-Personal
Data, understanding their implications for data access, privacy, digital markets, and services.
• Open Science Principles: Familiarity with the concepts and practices of Open Science, including
open access, open data, and open methodology, and how they apply within the legal framework
of the EU.
• Regulatory Compliance: Understanding of compliance requirements under various EU data
regulations and the ability to apply these in the context of Open Science, ensuring that research
practices adhere to legal standards.
• Research Skills: Ability to conduct comprehensive legal research, including analysing and
synthesising information from scientific literature, grey literature, and various databases.
• Critical Thinking and Problem-Solving: Ability to identify key legal issues and challenges within
the Open Science framework and propose innovative solutions.
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• Communication Skills: Proficiency in communicating complex legal and scientific concepts clearly
and effectively, both in writing and orally, to a diverse audience, including scientists, legal
professionals, and policymakers.
• Collaboration and Teamwork: Ability to work effectively in an interdisciplinary team and
collaborate with researchers across multiple sites in the EU.
• Interdisciplinary Understanding: Since the project involves innovations in the fields of
biotechnology and microbiology, an interest in these fields would be beneficial to comprehend
the scientific context and its legal implications.
• Any nationality
(B2).
Supervisors team
Université Libre de Bruxelles :
The research will be conducted at JurisLab under the supervision of its Director, Prof. Julien Cabay, who
holds the chair “Intellectual Creations and Innovation Law” in the Faculty of Law at Université Libre de
Bruxelles [ULB].
The JurisLab is a research unit dedicated to the “Law of Creation and Innovation”, with particular
emphasis on Intellectual Property Law, Data Protection, Consumer Law and Unfair Competition Law, as
well as the interaction between these different fields of the law.
Along with other research units, it is a department of the Centre for Private Law (Centre de droit privé)
of the ULB. Engaged in cutting-edge interdisciplinary research, the JurisLab has its offices located in the
FabLab ULB, where it collaborates with academic and scientific members coming from other ULB
Faculties (mainly Civil Engineering, Sciences, and Law).
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Research conducted at JurisLab aims to provide in-depth analysis and propose balanced solutions in
the covered areas. As a matter of policy, all members of JurisLab share a common understanding of the
critical importance of protecting fundamental rights and freedoms in the fields of Creation and
Innovation Law. This is emphasised in the work at JurisLab and is at the very core of some of its
members’ research.
Working languages at JurisLab are French and English.
More information: https://droit-prive.ulb.be/unite/jurislab/ ; https://fablab.ulb.be/
Université de Strasbourg :
The candidate will be integrated into the CEIPI research laboratory under the supervision of Prof. Jean-
Marc Deltorn.
The CEIPI, an international research centre, plays an essential role in the shifting intellectual property
landscape. Its international partnerships enable it to develop common teaching and research programs
and student and academic staff exchanges throughout the world and to guarantee excellent academic
training based on a teaching staff composed of academics and recognised legal professionals of all
backgrounds. A key focus of CEIPI research is addressing the articulation between algorithmic
developments and IP laws. At CEIPI, Jean-Marc Deltorn holds the chair “Dynamics of European norms
& emerging technologies”, which specifically addresses these issues.
The CEIPI also has an important mission of reflection on the evolution of intellectual property law in the
knowledge society through publications, participation in European and international projects, and the
organisation of conferences and symposiums. Each year, CEIPI trains more than 2,500 specialists and
professionals in the intellectual property field. The preparation for the EQE is organised with the
participation of established European patent attorneys and members of the European Patent Office
(EPO).
The working languages at CEIPI are French and English.
More information can be found here: https://www.ceipi.edu/en/
Université Libre de Bruxelles:
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Founded in 1834, Université libre de Bruxelles (http://www.ulb.be) has a long tradition of excellence in
Research with four scientific Nobel Prizes, two Nobel Peace Prizes, one Fields Medal, three Wolf Prizes
and two Marie Curie Excellence Awards. It is one of the largest and best Research Universities in Belgium,
with a student population of 35,000 and almost 2,000 PhD in progress distributed among 22 Doctoral
schools. ULB has considerable experience with European funding programmes, being involved in more
than 310 projects financed by the 7th European Framework Programme (FP7), Horizon 2020 (H2020)
and Horizon Europe (HE), from which 97 MSCA projects. ULB has participated in 36 Marie Skłodowska-
Curie Doctoral Networks.
Université de Strasbourg:
With its 500 years of history, the University of Strasbourg remains a resolutely modern institution. A
pioneer in many fields, our university occupies a position at the forefront of the international scene. The
university hosts 5 Nobel Prizes, 1 Field Medal, 1 Kavli Prize, 4 CNRS Gold Medals, 20 Académie des
Sciences members, 54 members of the Institut Universitaire de France, 62 members of the European
Research Council (ERC). It is ranked as the first university for chemistry in the European Union as well as
the first university in Europe for impact on innovation (16th place globally). The university hosts more
than 60000 enrolled students (including 12000 foreign students), ten doctoral schools and 2300
doctoral students.
We offer

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Selection process
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Job description
Title: DCR, PhD fellowship in Food Microbiology - Omics-driven investigation of unique features of
olive fermentation isolates beneficial for plant fermentation with probiotic properties.
Research field: Food Microbiology, Molecular Microbiology, Analytical Chemistry,
Biotechnology, Biochemistry, Bioinformatics.
Organisation: Department of Food & Nutritional Sciences, University of Reading.

Country: United Kingdom.
Address: Department of Food & Nutritional Sciences, University of Reading, Reading RG6 6AD, UK.
a stay in each of these organisations: the University of Reading (UREAD), UK and the Wageningen
University (WU), Netherlands.
Offer description
In brief:
We are looking for one (1) Doctoral Candidate (DC) to join our project at multiple sites in the EU with a
master’s degree in a relevant discipline (Food Microbiology, Biotechnology, Biology etc.) interested in
the Phenotypic analysis of table olives fermentation and identification of important genetic mechanisms
for fermentation of plant products and health.
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FAIROmics project:
sciences.
Scientific context:
Objectives:
Classical Microbiology techniques (acid resistance, growth properties, antimicrobial activity against
spoilage organisms etc.) will be used to assess the general characteristics of representative olive
fermentation isolates in terms of their usage as starter cultures in food fermentations, not only for olives
but also for other plant-based foods. Additionally, the strains will be assessed for their potential
probiotic properties (bile acid resistance, attachment to Caco-2 cells, antimicrobial activity against
pathogens etc.). Subsequently, based on all data available, the role of target genes of L. plantarum will
be investigated either by deletion or by expression in a heterologous host to study the role of these
genes on the phenotype.
Expected results:
• Physiological, fermentative and probiotic characterisation of representative isolates

of Lactiplantibacillus plantarum from olive fermentations, assessment of their anti-microbial
activity against spoilage organisms.
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• Functional genomics characterisation, identification of the role of GAD system.
• Validation of the ability of these strains to ferment at low salt environments and potential usage
as starters in other plant-based foods.
The secondment schedule will be as follows:
• The first and third secondments will occur at NIZO Food Research, NL, with Marjon Wells-
Bennik at months 15 and 27 for a duration of 4 months each to work on Functional genomics
to identify molecular mechanisms related to plant fermentation & probiotic properties
(construction of mutants and cloning of important genes in L. plantarum).
• The second secondment will take place at the National and Kapodistrian University of Athens,
Greece with Marilena Dasenaki & Vasilis Valdramidis at month 20 for a duration of 4 months
to work on verification of growth/acid production/volatile production of L. plantarum genetically
modified strains.
1st-degree awarding organisation: University of Reading, Reading UK https://www.reading.ac.uk/

2nd-degree awarding organisation: Wageningen University, Wageningen,
Netherlands, https://www.wur.nl/en/wageningen-university.htm
• Applicants should hold or expect to gain a minimum of a 2:1 Bachelor's Degree or equivalent in
subjects such as Food Science, Microbiology, Biomedical Sciences, Genetics, Biochemistry or
relevant disciplines.
• Knowledge of basic Microbiology techniques.
• Knowledge of basic aseptic techniques.
• Knowledge of Molecular techniques is desirable but not necessary.
• Any nationality
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(B2).
Supervisors team
The team of supervisors comprises of:
• Dr. Kimon Andreas Karatzas (M; main supervisor; Department of Food and Nutritional Sciences,
University of Reading, UK) is a Faculty member (Associate Professor in Food Microbiology) at the
Department of Food & Nutritional Sciences, University of Reading. His scientific outputs include
more than 55 articles in high-impact journals (h-index of 26 based on SCOPUS), two international
patents and various chapters in books. In the past, he successfully supervised 10 PhD students
as main PI and 12 as Co-I, and nine postdoctoral researchers and visiting scientists. He has long
experience in microbial physiology of stress and molecular biology and over 22 years of
experience in food fermentations.
• Dr Marjon Wells-Bennik (F; secondary supervisor, during the secondment at NIZO BV) is a
Principal Scientist at NIZO with extensive expertise in food microbiology, including fermentation
and safety of plant-based dairy alternatives. She initiated various consortium projects with
multiple academic and industrial stakeholders, including a recent project on “Microbial
contaminants in plant-based protein ingredients”. Since 2002, she has supervised 8 PhD
students; 2 are ongoing, and 6 obtained their degrees. She has published over 70 research
articles and filed two patents. She can transfer fundamental knowledge to more applied research.
• Dr. Marilena Dasenaki (F) is an Assistant Professor at the Laboratory of Food Chemistry of the
National and Kapodistrian University of Athens. Her research activity focuses on the study of
food metabolomics using cutting-edge mass spectrometric techniques and advanced
chemometric tools. Overall, Dr Dasenaki’s research has been published in 39 peer-reviewed
papers and three book chapters, attracting more than >950 citations, with an h-index of 15, and
her work has been presented at several international scientific conferences.
• Dr. Vasilis Valdramidis (M; secondary supervisor during the secondment at the National and
Kapodistrian University of Athens) is an Associate Prof at the National and Kapodistrian
University of Athens (Department of Chemistry). He holds a Ph.D. degree in Chemical Engineering
from the Catholic University of Leuven, Belgium and a primary degree in Agriculture (Food
Science and Technology) from the Aristotle University of Thessaloniki (Greece). He has about 100
Fermented Multi
food omics
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publications in peer-reviewed Journals and chapters. He supervises/-ed eight post-doctoral
researchers and more than 10 Ph.D.s (as main or co-supervisor) and acted as external examiner
of several PhD Thesis across Europe.
The University of Reading is a public non-profit body. It is one of the leading universities worldwide
and the top university in the UK in the area of Food Sciences (www.reading.ac.uk/food). It currently has
more than 13,000 students, of which 1/3 are postgraduates and 2/3 are undergraduates.
NIZO Food Research is an advanced, independent contract research company. It is a small/medium-

sized company (SME) with over 70 years of experience in dairy and non-dairy science and technology.
NIZO has an annual turnover of around 13 M€. Its 100 employees (80 fte) successfully assist large
multinational food and ingredient companies and start-ups to make better foods and be more
profitable. NIZO applies expertise and competitive technologies to support innovation and cost
reduction for customers.
The National and Kapodistrian University of Athens (NKUA), officially founded on April 14th, 1837,
is the first University not only of Greece but both the Balkan peninsula and the Eastern Mediterranean
region. The main sources of funding of NKUA are European, international and national funds, like for
example, the Partnership Agreement (PA) for the Development Framework, 2014-2020 (European
Structural and Investment FundESIF), Horizon 2020, as well as partnerships with public and private
sector bodies, the provision of services to legal entities and individuals, grants and donations. The Dept
of Chemistry (DoC) will be involved in the project. DoC has expertise, state-of-the-art infrastructure and
facilities available for performing research in the areas of food science, food chemistry, environmental
chemistry and water diagnostics. It also has expertise in the coordination and implementation of
research and development activities, dissemination, and exploitation activities with national mainly
stakeholders, e.g., the Hellenic Food Authority, and private food companies that export all around the
world.
We offer

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Hiring organisation and offer posting contact details

Location and planned secondment:

Enrolment in Doctoral degree:

• Master's degree in microbiology or microbial ecology or related field.

Host institutions description

• A comprehensive, interactive and international training programme covering the broader

*family = be married/be in a relationship with equivalent status to a marriage recognised by the

Hiring organisation and offer posting contact details:

Organisation: NIZO Food Research BV.

Location and planned secondments:

National and Kapodistrian University of Athens, 8 months: metabolomics analyses of metabolites

Enrolment in Doctoral degree:

1st-degree awarding organisation: Wageningen University, Wageningen,

• Master’s degree in Food Microbiology / Molecular Microbiology / Analytical Chemistry /

Within NIZO, comprehensive knowledge is available on fermentation characteristics of starter culture

At the Kapodistrian University of Athens (Department of Chemistry), supervision is provided by

At the University of Reading (UREAD), supervision is provided by Associate Professor Dr Kimon A.

Host institutions description

WUR (https://www.wur.nl/en.htm) is an internationally leading education and research organisation in

• A comprehensive, interactive and international training programme covering the broader

*family = be married/be in a relationship with equivalent status to a marriage recognised by the

Hiring organisation and offer posting contact details:

Organisation: National and Kapodistrian University of Athens.

Location and planned secondments:

Enrolment in Doctoral degree:

• Master's Degree in Food Chemistry, Analytical Chemistry, Biotechnology, Food Microbiology.

Host institutions description

Wageningen University is an internationally leading education and research organisation in life

*family = be married/be in a relationship with equivalent status to a marriage recognised by the

Hiring organisation and offer posting contact details:

Organisation: Vrije Universiteit Amsterdam.

Enrolment in Doctoral degree:

1st-degree awarding organisation: Vrije Universiteit Amsterdam, https://vu.nl/en

• A Master's degree in a relevant field, such as (bio)physics, systems biology, bioinformatics or

The Vrije Universiteit Amsterdam:

The Universita di Bologna:

Host institutions description

• A comprehensive, interactive and international training programme covering the broader

*family = be married/be in a relationship with equivalent status to a marriage recognised by the

Hiring organisation and offer posting contact details:

Organisation: Spanish Council for Scientific Research, IIM-CSIC.

Location and planned secondments:

Enrolment in Doctoral degree:

1st-degree awarding organisation: University of Vigo, https://www.uvigo.gal/en

• Master's Degree in (Applied) Mathematics, Engineering including Computational Engineering,

The Biosystems and Bioprocess Engineering Group at IIM-CSIC (bio2eng.csic.es) focuses on

The vision of BioTeC+ (Chemical & Biochemical Process Technology &

KU Leuven/BioTeC+ runs a state-of-the-art L2 accredited laboratory for experimental predictive

Host institutions description

• A comprehensive, interactive and international training programme covering the broader

*family = be married/be in a relationship with equivalent status to a marriage recognised by the

Hiring organisation and offer posting contact details:

Organisation: CSIC - Insititute for Integrative Systems Biology (I2SysBio).

Location and planned secondment:

Enrolment in Doctoral degree:

1st-degree awarding organisation: Universitat Politècnica de València https://www.upv.es/index-

Host institutions description

AgroParisTech is a school of engineering in the field of life sciences https://www.agroparistech.fr/en,