Early Stage Researcher (ESR6)  

PhD fellowship in development of kernel approaches for the integration of biological data from heterogeneous sources

Project Title

“E-MUSE Complex microbial ecosystems multiscale modelling: mechanistic and data driven approaches integration” MSCA-ITN-2020 European Training Network

Hosting Organization

Université Paul Sabatier Toulouse III (UT3), established in Route de Narbonne 118, Toulouse Cedex 9 31062, France

Researcher Profiles


Research Field

Biostatisics, data analysis, multi-omics data integration

Application Deadline

31st May 2021 23:59; prolonged till 30.06 2021 23:59 - Europe/Brussels

Envisaged Job Starting Date



3 years

Contract Type

full-time employment (based on COVID-19 evolution and restrictions, possibility to start remotely, once situation allows the presence is required)


€3 783.39 Eur gross salary/month

+ €600 gross mobility allowance/month and €500 gross family allowance/month (if applicable)

Taxation and Social (including Pension) Contribution deductions based on National and company regulations will apply.


A. Investigate non-linear multi-omics data integration with kernel approaches B. Methodological developments to address sparse approaches in kernel-based methods C. Study of ad hoc kernels for time course experiments and compositional data D. Bridge the gap between methodological developments and relevant application in systems biology.

Expected Results

A. Showing how to handle such data and how to interpret the results of recent statistical methods to provide relevant answers to biological questions
B. Deliver a suite of computational tools in easy access through R vignettes and R packages
C. Dissemination via hands-on workshops

Planned Secondments

In total, 2 months will be spent to complete the background of the ESR and its literature review with theoretical aspects of Machine Learning methods; comparison with kernel methods at Szegedi Tudomanyegyetem in Hungary and 1 month at Chr. Hansen A/S in Denmark and 1 month at L'Università ta' Malta in Malta to elaborate a benchmark with real datasets to test and compare methodological developments around kernel methods for data integration.

Enrolment in Doctoral degree


Required Education Level

Master’s degree or engineering degree in statistics, bio-statistics, applied mathematics or bioinformatics no later than September 2021. You should NOT have any kind of PhD degree. Previous research experience (which must be no longer than 4 years) although appreciated, is not mandatory. 

Skills / Qualifications

  • experienced user of the statistical software R, and at least basic kowledge in  one other programming language (python, …)

  • knowledge of the linux environment

  • experiences with real, multivariate data analysis, biological data would be better, `omics’ data even more    

  • interest in biology, biological processes and complexity of living

  • educational background and previous research experience relevant for the chosen position

  • networking and good communications skills (writing and presentation skills)

  • willingness to travel abroad for the purpose of research, training and dissemination

Specific Requirements

For the eligibility please check: Eligibility Criteria

Required Languages

English: B2, good oral and written communication skills in English are compulsory

Supervisors Team

The lead supervisor is Sébastien Déjean, research engineer and expert in statistical data analysis at the Universite Paul Sabatier Toulouse III (UT3) in France. He was awarded his PhD in Applied Statistics in 2002 at Université de Toulouse, France after spending 4 years in a Biometry lab at INRA (French National Institute for Agronomic Research). Since then he has been working at the Toulouse Mathematics Institute (UT3), group Statistics and Optimization. He received his habilitation thesis in 2019. He interacts closely with biologists using high-throughput technologies. He is an expert in statistical data analysis and he contributes to the development of several R packages including mixOmics. He is also deeply committed into teaching, including training statistical/software workshops.


The co-supervisor is Marie-Agnès Dillies – research engineer and head of Bioinformatics and Biostatistics Hub at Institut Pasteur. She was awarded her PhD in Applied Statistics from Université de Technologie de Compiègne (UTC) in 1993 and spent about 10 years applying multivariate data analysis and machine learning methods for diagnostics purposes in an industrial context. She joined Institut Pasteur in 2002 where she specialized in transcriptomic and gene expression data analysis. She is also co-manager of the StatOmique group which gathers more than 60 statisticians from France.

Host Institution Description

The university Toulouse III Paul Sabatier ( is a french university located in Toulouse, the 4th biggest city in France and the 2nd biggest university town. It was named after Paul Sabatier, winner of the Nobel prize in chemistry in 1912. It was established in 1969 on the foundations of the old Toulouse university founded in 1229. The university offers a broad array of programs in the sciences (life science, chemistry, physics, mathematics...), technology, health and sports. It welcomes more than 30 000 students every year.

To successfully complete your application:

1. You need to send an e-mail (subject of the email : ESR6_E-MUSE_2nd Round) to:

Please include your CV (in English) and signed ESR Consent Form (ESR CF)

2. Click candidate on the button below and submit the Microsoft Form in English.

To be eligible please fill in the Microsoft Form

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Only candidates who follow the above instructions will be further considered for the recruitment process.