FAIROmics – PhD fellowship in applied mathematics – Optimal Transportation to improve databases integration

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FAIROmics – PhD fellowship in applied mathematics – Optimal Transportation to improve databases integration

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Job description

Offer Description“FAIRification of multiOmics data to link databases and create knowledge graphs for fermented foods” MSCA-DN-JD Doctoral Network.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.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.Please note that this PhD position will lead to the award of a double diploma after the completion of a stay in each of these organisations: The University of Toulouse III – Paul Sabatier (UT3), France and the University of Bologna (UNIBO), Italy.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 (applied mathematics, statistics, physics, biostatistics, bioinformatics or computer science) interested in biological applications.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.Location and planned secondments: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).

Enrolment in Doctoral degree:1st-degree awarding organisation: University Toulouse III – Paul Sabatier,
2nd-degree awarding organisation: Alma Mater Studiorum Universitá di Bologna,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).Host institutions description: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.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.RequirementsResearch Field Mathematics » Applied mathematics Education Level Master Degree or equivalentResearch Field Physics Education Level Master Degree or equivalentResearch Field Computer science Education Level Master Degree or equivalentResearch Field Biological sciences Education Level Master Degree or equivalentSkills/Qualifications

• 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.
• Networking and good communication skills (writing and presentation skills).
• Willingness to travel abroad for the purpose of research, training and dissemination.

Specific Requirements

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

• 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).

Languages ENGLISH Level GoodResearch Field Computer scienceBiological sciencesPhysicsMathematics » Applied mathematics Years of Research Experience 1 – 4Internal Application form(s) neededFAIROmics_application_form_PDF_8.pdfEnglish(4.33 MB – PDF)Additional InformationBenefitsWe 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.*monthly gross salary.**family = be married/be in a relationship with equivalent status to a marriage recognised by the legislation of the country or region where it was formalised/have dependent children who are being maintained by the researcher.Eligibility criteria

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

• 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).

Selection processThe selection process is based on the merits of providing equal opportunity and will be in agreement with the . * Candidates apply for a position using the online application form found on the FAIROmics website.

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

Website for additional job detailsWork Location(s)Number of offers available 1 Company/Institute University Toulouse III – Paul Sabatier Country France City Toulouse Postal Code 31062 Street 118 route de Narbonne GeofieldNumber of offers available 1 Company/Institute University of Bologna Country Italy City Bologna Postal Code 40127 Street Viale Berti Pichat 6/2 GeofieldNumber of offers available 1 Company/Institute University of Szeged Country Hungary City Szeged Postal Code 6720 Street Dugonics tér 13 GeofieldWhere to apply WebsiteContact CityToulouse WebsiteStreet118 route de Narbonne Postal Code31062STATUS: EXPIRED

Expected salary

Location

Toulouse

Job date

Wed, 27 Mar 2024 23:41:10 GMT

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